tag:blogger.com,1999:blog-6701417360427959244.comments2024-03-16T12:48:59.660+01:00Molecular Modeling BasicsJan Jensenhttp://www.blogger.com/profile/08595894308946022740noreply@blogger.comBlogger674125tag:blogger.com,1999:blog-6701417360427959244.post-1912921822247100792020-02-25T03:06:40.604+01:002020-02-25T03:06:40.604+01:00Hi, thank you for your blog posts. I am trying to ...Hi, thank you for your blog posts. I am trying to find the the orbital energies for cationic tetrafluoromethane. The problem is that the cationic state is fully dissociative and so I expected to receive this error message that SCF did not converge. I attempted to calculate the energies before optimization: i was able to display the orbitals using Avogadro but they did not come with any corresponding energy values, and the geometry was not correct as I was using the cartesian coordinates for the neutral tetrahedral molecule. I need to optimize my geometry first, or at least stop the optimisation in one instance before the calculation forces the bond to stretch to infinity. Do you have any suggestions to over come this problem? -Many thanks in advance, TiffanyAnonymoushttps://www.blogger.com/profile/13763537409523933649noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-24373902901559784442020-02-20T13:23:04.362+01:002020-02-20T13:23:04.362+01:00Dear Jan,
Could you explain how macmolplt is able...Dear Jan,<br /><br />Could you explain how macmolplt is able to plot electrostatic potential just by using a .log file from geometry optimization (that does not have any info about the potential, i guess)? <br /><br />I have found a $ELPOT group along with the GRID keyword in the gamess manual for the electrostatic potential calculation. After trying it i got ELECTROSTATIC POTENTIAL info point by point in my .log file. <br /><br />Now i am confused what electrostatic potential should i plot: by using a.log file from geometry optimization or by using a .log file from $ELPOT calculation. <br /><br />I would be grateful to you if you could provide an explanation.<br /><br /><br />Anonymoushttps://www.blogger.com/profile/02944476915491493512noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-87093571674868421402020-02-09T20:31:30.205+01:002020-02-09T20:31:30.205+01:00Thanks for your guide. However I faced with a prob...Thanks for your guide. However I faced with a problem. I found SAS of 2,4-pentanedion in PM3 level inside water (with 1.4 angstrom radius) 304.08 (A2) in literature (Orlando Tapia, Solvent Effects and Chemical Reactivity). However, when I open the optimized structure in Jmol, I found 123.81811 (A2) which is very different. What is the Problem?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-62028138846607768622020-01-03T13:49:49.327+01:002020-01-03T13:49:49.327+01:00Prof Prem raj Pushpakaran writes -- 2020 marks the...Prof Prem raj Pushpakaran writes -- 2020 marks the birth centenary year of George Porter who pioneered flash photolysis!!!prof prem raj pushpakaranhttps://www.blogger.com/profile/14561237920972677898noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-34016496256546061702019-12-30T19:01:01.301+01:002019-12-30T19:01:01.301+01:00This blog is really valuable to pass on upgraded e...This blog is really valuable to pass on upgraded enlightening endeavors over web which is genuinely examination. <a href="http://moviemator.net" rel="nofollow">Mac video editing software</a>John kerryhttps://www.blogger.com/profile/04554163357189281558noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-35202761138380640432019-09-19T12:12:21.170+02:002019-09-19T12:12:21.170+02:00Hello.
Command - sudo /usr/local/gamess/rungms ex...Hello.<br />Command - sudo /usr/local/gamess/rungms exam01.inp<br /><br />LOG - <br />----- GAMESS execution script 'rungms' -----<br />This job is running on host work<br />under operating system Linux at Thu Sep 19 10:09:57 UTC 2019<br />Available scratch disk space (Kbyte units) at beginning of the job is<br />Filesystem 1K-blocks Used Available Use% Mounted on<br />/dev/vda2 15419956 2761756 11989780 19% /<br />GAMESS temporary binary files will be written to /tmp<br />GAMESS supplementary output files will be written to /tmp<br />Copying input file exam01.inp to your run's scratch directory...<br />cp exam01.inp /tmp/exam01.F05<br />unset echo<br />/usr/local/gamess/ddikick.x /usr/local/gamess/gamess.00.x exam01 -ddi 1 1 work -scr /tmp<br /><br /> Distributed Data Interface kickoff program.<br /> Initiating 1 compute processes on 1 nodes to run the following command:<br /> /usr/local/gamess/gamess.00.x exam01<br /><br /> ddikick.x: Timed out while waiting for DDI processes to check in.<br /> ddikick.x: Fatal error detected.<br /> The error is most likely to be in the application, so check for<br /> input errors, disk space, memory needs, application bugs, etc.<br /> ddikick.x will now clean up all processes, and exit...<br /> ddikick.x: Sending kill signal to DDI processes.<br /> ddikick.x: Execution terminated due to error(s).<br />unset echo<br />----- accounting info -----<br />Files used on the master node work were:<br />-rw-r--r-- 1 root root 1163 Sep 19 10:09 /tmp/exam01.F05<br />ls: No match.<br />ls: No match.<br />ls: No match.<br />Thu Sep 19 10:10:58 UTC 2019<br />0.0u 0.0s 1:01.11 0.0% 0+0k 0+8io 0pf+0w<br /><br /><br />Error - <br /> ddikick.x: Timed out while waiting for DDI processes to check in.<br /> ddikick.x: Fatal error detected.<br /> The error is most likely to be in the application, so check for<br /> input errors, disk space, memory needs, application bugs, etc.<br /> ddikick.x will now clean up all processes, and exit...<br /> ddikick.x: Sending kill signal to DDI processes.<br /> ddikick.x: Execution terminated due to error(s).<br />unset echo<br /><br />HOW CAN I FIX IT?Anonymoushttps://www.blogger.com/profile/11303770337597872931noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-56636602754517830132019-08-07T23:17:48.497+02:002019-08-07T23:17:48.497+02:00Thank you for a wonderful and useful blog. Am I co...Thank you for a wonderful and useful blog. Am I correct that the command should be:<br /><br />isosurface cutoff 0.002 "density.cube.gz" color range -0.05 0.05 "potential.cube.gz"<br /><br />or am I missing something (it could well be, I'm not very experience with jmol, but this way I could make it work)esbennoreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-55408289635017578932019-04-12T04:24:18.083+02:002019-04-12T04:24:18.083+02:00Hello sir, I am trying to calculate TS energy of O...Hello sir, I am trying to calculate TS energy of OH- + CH3Cl using your method. First I have not been able to get a negative frequency after several trials. Second, I don't know how you got the data about $HESS that you copied into your ts.inp file below the $DATA. Thanks in anticipationAnonymoushttps://www.blogger.com/profile/09698737997575237892noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-41730698644822588672019-03-29T15:36:34.651+01:002019-03-29T15:36:34.651+01:00Hi I need your help
When I run a job for optimisat...Hi I need your help<br />When I run a job for optimisation I have error:<br />Restart file not find..<br />Anonymoushttps://www.blogger.com/profile/12809914614694714482noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-21361404687917933032013-04-26T11:04:05.436+02:002013-04-26T11:04:05.436+02:00Thanks for your work, I think actually this will h...Thanks for your work, I think actually this will help me to understand, like some basic knowledge from biology, physics chemistry insight.<br /><br />On the other hand, this animation is very positive to examine and understanding to the biochemist's methods. Anonymoushttps://www.blogger.com/profile/13116870661277064373noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-91296837603697419432013-04-25T10:40:17.779+02:002013-04-25T10:40:17.779+02:00Rob
Please post the input and output somewhere (e...Rob<br /><br />Please post the input and output somewhere (e.g. dropbox or Google Docs) and provide a link here. This way everyone benefits from the discussion<br /><br />I'm pretty busy at the moment so the GAMESS Google discussion group would also be good idea.<br /><br />https://groups.google.com/forum/?fromgroups#!forum/gamessJan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-63438764924337259452013-04-21T21:20:16.036+02:002013-04-21T21:20:16.036+02:00Hello Jan,
I am currently running a geometry calcu...Hello Jan,<br />I am currently running a geometry calculation for a MnCp(CO)2 -> MnCp(CO)3 freezing string method. I am using a custom basis set, actually the same custom basis you recommended, but am getting non-convergence. Do you have any advice for fsm methods? Can I email you?<br /><br />Robboblodiablohttps://www.blogger.com/profile/05939574320376553390noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-54604143994486208672013-04-02T15:23:00.453+02:002013-04-02T15:23:00.453+02:00you have right,
thank you!you have right, <br />thank you!Anonymoushttps://www.blogger.com/profile/10966593518005514130noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-45333199035523375852013-04-01T20:22:32.471+02:002013-04-01T20:22:32.471+02:00Hi Jan. The input constructed using macmolplt work...Hi Jan. The input constructed using macmolplt worked very well. Problem solved! Thank you very much.Anonymoushttps://www.blogger.com/profile/17165807886600952663noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-55304611098990414862013-03-29T21:44:05.443+01:002013-03-29T21:44:05.443+01:00Ok Jan. I will try to rewrite the input. If any so...Ok Jan. I will try to rewrite the input. If any solution comes up, I will post it here later. Thank you for helping!Anonymoushttps://www.blogger.com/profile/17165807886600952663noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-40443906716190554232013-03-29T17:31:55.529+01:002013-03-29T17:31:55.529+01:00What's your question again? It looks like you...What's your question again? It looks like you just ran out of steps. Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-37529228136935162772013-03-29T10:47:53.311+01:002013-03-29T10:47:53.311+01:00Yes, you have right!
Meantime, I changed structur...Yes, you have right! <br />Meantime, I changed structure geometry (I built it again) but I have error again. I attach the file: <br />http://figshare.com/download/file/1000152/1<br /><br />I think I must rebuild the structure again.<br /><br />Thank you in advance, <br />M.Anonymoushttps://www.blogger.com/profile/10966593518005514130noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-31230510652536569052013-03-29T08:45:31.613+01:002013-03-29T08:45:31.613+01:00I'm not sure what the problem is, but it is no...I'm not sure what the problem is, but it is not just with the MEMORY keyword. MAXIT and UNITS are also ignored. The remaining keywords are defaults, so it's unknown whether they are read correctly. <br /><br />The $basis group is definitely read correctly. The input looks OK but GAMESS is not interpreting the text correctly. My best guess is a keyboard issue. Try copying commands from input files that work, or generate the files using MacMolPlt of Avogadro. <br /><br />You may also want to post the question to the Google GAMESS group to see if anyone else has better ideasJan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-29301446600089772982013-03-27T21:34:51.542+01:002013-03-27T21:34:51.542+01:00Here is the link.
https://www.dropbox.com/s/knedc...Here is the link.<br /><br />https://www.dropbox.com/s/knedchtjxizipgf/estrutura.log<br /><br />Sorry for not sending it sooner. Thanks a lot for the help!Anonymoushttps://www.blogger.com/profile/17165807886600952663noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-51205265442419553862013-03-27T13:09:18.604+01:002013-03-27T13:09:18.604+01:00You can simply paste the link to the file of folde...You can simply paste the link to the file of folder here in the comments section. I'd like for everyone to have access to the file.Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-82514193650428974722013-03-27T13:02:12.565+01:002013-03-27T13:02:12.565+01:00Hi Jan. Can I email that to you? Or even create a ...Hi Jan. Can I email that to you? Or even create a dropbox shared folder, but I need to know you email account.<br /><br />Thanks a lot!Anonymoushttps://www.blogger.com/profile/17165807886600952663noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-55457759054213127662013-03-27T07:26:04.713+01:002013-03-27T07:26:04.713+01:00I would need to see the log file (dropbox, google ...I would need to see the log file (dropbox, google docs, github, patebin, ...)<br /><br />Glad to hear you find the blog useful.Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-19661767071111023242013-03-26T23:22:26.128+01:002013-03-26T23:22:26.128+01:00Hi Jan. First of all, very usefull blog!
I am havi...Hi Jan. First of all, very usefull blog!<br />I am having the 'not enough memory' error in my calculations, and changed the mwords to 125 as you suggested. Of course 2 mwords would be enough as gammes told me, but just in case. The thing is, even with this modification, gamess still recognize only 1 mword. I have tried even the memory keyword, and the same result came up. Can you give me a little help with this?<br />Thank you very much Jan, keep up with the good work! Greetings from Brazil!Anonymoushttps://www.blogger.com/profile/17165807886600952663noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-10913298491413904812013-03-26T18:00:22.398+01:002013-03-26T18:00:22.398+01:00The aim of this blog is to help everyone in an ope...The aim of this blog is to help everyone in an open way so please share the file somehow (figshare, google docs, pastebin, github, ....)Jan Jensenhttps://www.blogger.com/profile/08595894308946022740noreply@blogger.comtag:blogger.com,1999:blog-6701417360427959244.post-89717252544152429522013-03-26T15:48:50.541+01:002013-03-26T15:48:50.541+01:00could I send you an e'mail? it is easier to at...could I send you an e'mail? it is easier to attach file.Anonymoushttps://www.blogger.com/profile/10966593518005514130noreply@blogger.com