[gmx-users] g_hbond segmentation fault
Hi Gmxers, I used the command line, g_hbond -f tst.trr -s tst.tpr -ac test -e 500 -dt 1 and I got the message like, -- Found 1048 different hydrogen bonds in trajectory Found 2292 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 2/10915 Segmentation fault __ Anyone knows what could be the reason for this Segmentation Fault ? A couple of Q's I am also curious, why do we need to swap Acceptors and Acceptors when merging hbonds? Does gromacs suggest that the number of different hydrogen bonds in trajectoryshould be the same as that of different atom-pairs within hydrogen bonding distance? Thanks, Yao -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_hbond segmentation fault
Hi, Could you file a bugzilla and attach the trr and tpr files please? If you do I'll try to sort it out today or at least this week. Erik Yao Yao skrev 2010-09-29 08.22: I tried without -dt or -e, still the same problem exists in either case. Thanks, Yao --- On *Wed, 9/29/10, David van der Spoel /sp...@xray.bmc.uu.se/* wrote: From: David van der Spoel sp...@xray.bmc.uu.se Subject: Re: [gmx-users] g_hbond segmentation fault To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Wednesday, September 29, 2010, 6:11 AM On 2010-09-29 08.02, Yao Yao wrote: Hi Gmxers, I used the command line, g_hbond -f tst.trr -s tst.tpr -ac test -e 500 -dt 1 and I got the message like, try without the -dt 1 -- Found 1048 different hydrogen bonds in trajectory Found 2292 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped 2/10915 *Segmentation fault* __ Anyone knows what could be the reason for this Segmentation Fault ? A couple of Q's I am also curious, why do we need to swap Acceptors and Acceptors when merging hbonds? Does gromacs suggest that the number of different hydrogen bonds in trajectory should be the same as that of different atom-pairs within hydrogen bonding distance? Thanks, Yao -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. sp...@xray.bmc.uu.se /mc/compose?to=sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- gmx-users mailing list gmx-users@gromacs.org /mc/compose?to=gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org /mc/compose?to=gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] 1,4 interactions
Hi all Can someone please get back to me on this. I have generated my own topology file from OPLS parameters by hand with the following format. I am now concerned that I haven't been calculating 1,4 interactions, which I thought were generated by setting gen-pairs = yes. I have read section 5 of the manual several times but am still unclear about this. Cheers Gavin parameter level [defaults] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 3 yes0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) ;Molecular level [moleculetype] ; name nrexcl tertpentane 3 [atoms] ; atomnr type resnr residue namecgnr charge mass [bonds] ; aiaj func b0(nm) kb(kjmol-1 nm-2) [angles] ; aiajak func theta(deg)ktheta(kjmol-1 rad-2) [dihedrals] ;System level [system] [molecules] ; moleculename number -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] 1,4 interactions
Gavin Melaugh wrote: Hi all Can someone please get back to me on this. I have generated my own topology file from OPLS parameters by hand with the following format. I am now concerned that I haven't been calculating 1,4 interactions, which I thought were generated by setting gen-pairs = yes. I have read section 5 of the manual several times but am still unclear about this. You can answer this question by analyzing your .edr file: are there LJ-14 and/or Coul-14 terms? If so, then you're calculating 1-4 interactions. Seems to me that, for OPLS, your approach is fine. It wasn't clear from your earlier posts that you were using OPLS, hence the inability to know if what you were doing was right or not. Different force fields have different underlying mechanics, so the use of [nonbond_params] and/or [pairs]/[pairtypes] is somewhat dependent upon your model. -Justin Cheers Gavin parameter level [defaults] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 3 yes0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) ;Molecular level [moleculetype] ; name nrexcl tertpentane 3 [atoms] ; atomnr type resnr residue namecgnr charge mass [bonds] ; aiaj func b0(nm) kb(kjmol-1 nm-2) [angles] ; aiajak func theta(deg)ktheta(kjmol-1 rad-2) [dihedrals] ;System level [system] [molecules] ; moleculename number -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] g_correlation for version 4.0.7
Dear All, I have been using GROMACS 4.0.7 using the tutorial uploaded by you. I am now trying to analyze my data and have a small request. All the modules related to g_correlation is available only for version 3.3.3.1 which are not accepting the xtc files from version 4.0.7. Are there any related modules of g_correlation for analysis in version 4.0.7? Thanking you for the same Regards Sanchari -- Sanchari Banerjee Research Scholar c/o Prof. M.R.N. Murthy Molecular Biophysics Unit Indian Institute of Science Bangalore - 560 012 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] lipids number
Hi, I am not sure someone asked some similar questions before or not. From Prof. Peter Tieleman's website we can get the 128 lipids pdb file. Are there some trick and easy way to multiply those lipids . I mean, Suppose I need 640 dppc lipids, how can I get those coordinates easily from those dppc128 ones. Thanks and best regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] topolbuild cannot open logfile
Thanks very much for your reply yes i was just being daft and trying to run things from the wrong place therefore wrong permissions! Also i was pointing to the wrong directory for force fields. Things are working now. Thank you once again Andrew --- On Wed, 29/9/10, Bruce D. Ray bruced...@yahoo.com wrote: From: Bruce D. Ray bruced...@yahoo.com Subject: Re: [gmx-users] topolbuild cannot open logfile To: gmx-users@gromacs.org Date: Wednesday, 29 September, 2010, 13:07 On Tue, September 28, 2010 at 7:38 PM, andrew_m_nor...@talk21.com andrew_m_nor...@talk21.com wrote: Hello i am very new to molecular mechanics so please excuse me if my questions are a little naive or stupid. I am trying to minimise a mol2 file with topolbuild1_3 using the following command line arguments from within the topolbuild directory: ./topolbuild -dir /usr/local/gromacs/share/gromacs/top -ff oplsaa -n /Users/bioinformatics/Desktop/zinc_12404782 -purge 0 -move I get the following error: Fatal error. Source code file: topolbuild.c, line: 345 Cannot open log file zinc_12404782.log I realise that i will have to go over the parameters again but i was hoping for some sort of output. Does anyone know if it is a problem with the parameters of the input file shown below or some problem with the way in which topolbuild is called ? I am a little unsure how to point to the oplsaa force fields? The problem with your command is that you do not have write permission in the directory in which topolbuild resides. You need to run the command from the directory in which you want the topology built with a command such as: /path-to-topolbuild-main-directory/src/topolbuild -dir /path-to-topolbuild-main-directory/dat/gromacs -ff oplsaa -n /Users/bioinformatics/Desktop/zinc_12404782 -purge 0 -move Note that the gromacs directory does not contain the topolbuild tables. Please see the examples given in the PROGRAM_TESTING_DONE.txt file in the topolbuild distribution for more information. -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 -Inline Attachment Follows- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] lipids number
#ZHAO LINA# wrote: Hi, I am not sure someone asked some similar questions before or not. From Prof. Peter Tieleman's website we can get the 128 lipids pdb file. Are there some trick and easy way to multiply those lipids . I mean, Suppose I need 640 dppc lipids, how can I get those coordinates easily from those dppc128 ones. You can make integer multiples of a box with genconf -nbox. Otherwise use genbox -cs dppc128.pdb -box (x y z) until you get a system of appropriate size. There was a very similar post yesterday about this same topic. I would suggest you have a look at the information Chris Neale posted about the specifics of box size (genbox caveats) and the need for proper equilibration. -Justin Thanks and best regards, lina -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] lipids number
I have a vague impression about that, seems someone asked similar things before. I will do a try and see. Thanks, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Wednesday, September 29, 2010 9:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] lipids number #ZHAO LINA# wrote: Hi, I am not sure someone asked some similar questions before or not. From Prof. Peter Tieleman's website we can get the 128 lipids pdb file. Are there some trick and easy way to multiply those lipids . I mean, Suppose I need 640 dppc lipids, how can I get those coordinates easily from those dppc128 ones. You can make integer multiples of a box with genconf -nbox. Otherwise use genbox -cs dppc128.pdb -box (x y z) until you get a system of appropriate size. There was a very similar post yesterday about this same topic. I would suggest you have a look at the information Chris Neale posted about the specifics of box size (genbox caveats) and the need for proper equilibration. -Justin Thanks and best regards, lina -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] 1,4 interactions
Gavin Melaugh wrote: Hi Justin Thanks for replying. I have checked the energy file and there are no 1,4 terms, which is what I expected. I should clarify that my parameters are taken from the OPLS ua forcefield but I have relabelled them for my own model, which is not a common molecule. Therefore all the info on the molecule is in .top and obviously the .gro file. i.e. there are no #include statements. Now I take it that the non-bonded LJ are taken from the [atom types] directive? The question is then how and where do I state the 1,4 terms. I always thought that when gen-pairs = yes, then gromacs would generate a list of all the 1,4 interaction types? You don't explicitly state 1-4 terms with OPLS-AA. While you don't need a [pairtypes] directive, you do need a [pairs] directive to dictate the 1-4 interactions. Setting gen-pairs = yes generates the parameters, such that a [pairtypes] directive is unnecessary. -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi all Can someone please get back to me on this. I have generated my own topology file from OPLS parameters by hand with the following format. I am now concerned that I haven't been calculating 1,4 interactions, which I thought were generated by setting gen-pairs = yes. I have read section 5 of the manual several times but am still unclear about this. You can answer this question by analyzing your .edr file: are there LJ-14 and/or Coul-14 terms? If so, then you're calculating 1-4 interactions. Seems to me that, for OPLS, your approach is fine. It wasn't clear from your earlier posts that you were using OPLS, hence the inability to know if what you were doing was right or not. Different force fields have different underlying mechanics, so the use of [nonbond_params] and/or [pairs]/[pairtypes] is somewhat dependent upon your model. -Justin Cheers Gavin parameter level [defaults] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 3 yes0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) ;Molecular level [moleculetype] ; name nrexcl tertpentane 3 [atoms] ; atomnr type resnr residue namecgnr charge mass [bonds] ; aiaj func b0(nm) kb(kjmol-1 nm-2) [angles] ; aiajak func theta(deg)ktheta(kjmol-1 rad-2) [dihedrals] ;System level [system] [molecules] ; moleculename number -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] 1,4 interactions
A few points then, 1) So a [pairs] directive would include all the atom indices of the 1,4 interactions and the coressponding values of sigma and epsilon?, which I would do manually. 2) In the manual it says ''gen-pairs = yes : generate 1,4 interactions which are not present in the pair list from normal LJ parameters using Fudge LJ. Sorry if I am coming across stupid, but that seems different to what you're saying? 3) Also am Icorrect about the normal nb-LJ coming from the [atom types directive] 4) I suppose a very obvious question would be; What is the difference between a [pairtypes] directive and [pairs] directive (bonds, bondtypes etc) Gavin P.S I appreciate you using your time to explain this Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Thanks for replying. I have checked the energy file and there are no 1,4 terms, which is what I expected. I should clarify that my parameters are taken from the OPLS ua forcefield but I have relabelled them for my own model, which is not a common molecule. Therefore all the info on the molecule is in .top and obviously the .gro file. i.e. there are no #include statements. Now I take it that the non-bonded LJ are taken from the [atom types] directive? The question is then how and where do I state the 1,4 terms. I always thought that when gen-pairs = yes, then gromacs would generate a list of all the 1,4 interaction types? You don't explicitly state 1-4 terms with OPLS-AA. While you don't need a [pairtypes] directive, you do need a [pairs] directive to dictate the 1-4 interactions. Setting gen-pairs = yes generates the parameters, such that a [pairtypes] directive is unnecessary. -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi all Can someone please get back to me on this. I have generated my own topology file from OPLS parameters by hand with the following format. I am now concerned that I haven't been calculating 1,4 interactions, which I thought were generated by setting gen-pairs = yes. I have read section 5 of the manual several times but am still unclear about this. You can answer this question by analyzing your .edr file: are there LJ-14 and/or Coul-14 terms? If so, then you're calculating 1-4 interactions. Seems to me that, for OPLS, your approach is fine. It wasn't clear from your earlier posts that you were using OPLS, hence the inability to know if what you were doing was right or not. Different force fields have different underlying mechanics, so the use of [nonbond_params] and/or [pairs]/[pairtypes] is somewhat dependent upon your model. -Justin Cheers Gavin parameter level [defaults] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 3 yes0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) ;Molecular level [moleculetype] ; name nrexcl tertpentane 3 [atoms] ; atomnr type resnr residue namecgnr charge mass [bonds] ; aiaj func b0(nm) kb(kjmol-1 nm-2) [angles] ; aiajak func theta(deg)ktheta(kjmol-1 rad-2) [dihedrals] ;System level [system] [molecules] ; moleculename number -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] 1,4 interactions
Gavin Melaugh wrote: A few points then, 1) So a [pairs] directive would include all the atom indices of the 1,4 interactions and the coressponding values of sigma and epsilon?, which I would do manually. No. A [pairs] directive simply lists the pairs of atoms for which 1,4 interactions should be calculated. No parameters are listed here. Format: atom_i atom_j func_type 2) In the manual it says ''gen-pairs = yes : generate 1,4 interactions which are not present in the pair list from normal LJ parameters using Fudge LJ. Sorry if I am coming across stupid, but that seems different to what you're saying? Not at all. The parameters for a specific interaction are given in a [pairtypes] directive. If these parameters are not present and gen-pairs = yes then they are calculated. If parameters for a specific pair are not present, and gen-pairs = no then grompp generates a fatal error. 3) Also am Icorrect about the normal nb-LJ coming from the [atom types directive] Yes. 4) I suppose a very obvious question would be; What is the difference between a [pairtypes] directive and [pairs] directive (bonds, bondtypes etc) A [*type] directive lists the parameters that should be a applied to whatever interaction type might be found. For instance, a [bondtypes] directive contains default parameters for all the bonds you might find, like C-C. If you then have a [bonds] directive that lists: ; ai aj func 1 21 ...and atoms 1 and 2 are both C, then grompp finds the corresponding parameters in the [bondtypes] directive and applies them to that bond, a process which it carries out for all the rest of the interaction types, including pairs. If you list specific pairs of atoms in a [pairs] directive, then grompp will search for the appropriate parameters listed in a [pairstypes] directive. If none are found, and gen-pairs = yes, grompp generates the appropriate parameters for you. -Justin Gavin P.S I appreciate you using your time to explain this Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Thanks for replying. I have checked the energy file and there are no 1,4 terms, which is what I expected. I should clarify that my parameters are taken from the OPLS ua forcefield but I have relabelled them for my own model, which is not a common molecule. Therefore all the info on the molecule is in .top and obviously the .gro file. i.e. there are no #include statements. Now I take it that the non-bonded LJ are taken from the [atom types] directive? The question is then how and where do I state the 1,4 terms. I always thought that when gen-pairs = yes, then gromacs would generate a list of all the 1,4 interaction types? You don't explicitly state 1-4 terms with OPLS-AA. While you don't need a [pairtypes] directive, you do need a [pairs] directive to dictate the 1-4 interactions. Setting gen-pairs = yes generates the parameters, such that a [pairtypes] directive is unnecessary. -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi all Can someone please get back to me on this. I have generated my own topology file from OPLS parameters by hand with the following format. I am now concerned that I haven't been calculating 1,4 interactions, which I thought were generated by setting gen-pairs = yes. I have read section 5 of the manual several times but am still unclear about this. You can answer this question by analyzing your .edr file: are there LJ-14 and/or Coul-14 terms? If so, then you're calculating 1-4 interactions. Seems to me that, for OPLS, your approach is fine. It wasn't clear from your earlier posts that you were using OPLS, hence the inability to know if what you were doing was right or not. Different force fields have different underlying mechanics, so the use of [nonbond_params] and/or [pairs]/[pairtypes] is somewhat dependent upon your model. -Justin Cheers Gavin parameter level [defaults] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 3 yes0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) ;Molecular level [moleculetype] ; name nrexcl tertpentane 3 [atoms] ; atomnr type resnr residue namecgnr charge mass [bonds] ; aiaj func b0(nm) kb(kjmol-1 nm-2) [angles] ; aiajak func theta(deg)ktheta(kjmol-1 rad-2) [dihedrals] ;System level [system] [molecules] ; moleculename number -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
Re: [gmx-users] 1,4 interactions
Right, I think the penny has finally dropped. On the back of what you said. 1)In my topologies I have always listed say a [bond] directive, with bond indices,function, k, and r0. I could however just list the indices and the function, and then have the corresponding parameters in the [bond types] directive, which save me associating the parameters to each individual bond ? 2) In reponse to what yo said finally If you list specific pairs of atoms in a [pairs] directive, then grompp will search for the appropriate parameters listed in a [pairstypes] directive. If none are found, and gen-pairs = yes, grompp generates the appropriate parameters for you. Are the parameters generated from the [atomtypes] directive? Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: A few points then, 1) So a [pairs] directive would include all the atom indices of the 1,4 interactions and the coressponding values of sigma and epsilon?, which I would do manually. No. A [pairs] directive simply lists the pairs of atoms for which 1,4 interactions should be calculated. No parameters are listed here. Format: atom_i atom_j func_type 2) In the manual it says ''gen-pairs = yes : generate 1,4 interactions which are not present in the pair list from normal LJ parameters using Fudge LJ. Sorry if I am coming across stupid, but that seems different to what you're saying? Not at all. The parameters for a specific interaction are given in a [pairtypes] directive. If these parameters are not present and gen-pairs = yes then they are calculated. If parameters for a specific pair are not present, and gen-pairs = no then grompp generates a fatal error. 3) Also am Icorrect about the normal nb-LJ coming from the [atom types directive] Yes. 4) I suppose a very obvious question would be; What is the difference between a [pairtypes] directive and [pairs] directive (bonds, bondtypes etc) A [*type] directive lists the parameters that should be a applied to whatever interaction type might be found. For instance, a [bondtypes] directive contains default parameters for all the bonds you might find, like C-C. If you then have a [bonds] directive that lists: ; ai aj func 1 21 ...and atoms 1 and 2 are both C, then grompp finds the corresponding parameters in the [bondtypes] directive and applies them to that bond, a process which it carries out for all the rest of the interaction types, including pairs. If you list specific pairs of atoms in a [pairs] directive, then grompp will search for the appropriate parameters listed in a [pairstypes] directive. If none are found, and gen-pairs = yes, grompp generates the appropriate parameters for you. -Justin Gavin P.S I appreciate you using your time to explain this Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Thanks for replying. I have checked the energy file and there are no 1,4 terms, which is what I expected. I should clarify that my parameters are taken from the OPLS ua forcefield but I have relabelled them for my own model, which is not a common molecule. Therefore all the info on the molecule is in .top and obviously the .gro file. i.e. there are no #include statements. Now I take it that the non-bonded LJ are taken from the [atom types] directive? The question is then how and where do I state the 1,4 terms. I always thought that when gen-pairs = yes, then gromacs would generate a list of all the 1,4 interaction types? You don't explicitly state 1-4 terms with OPLS-AA. While you don't need a [pairtypes] directive, you do need a [pairs] directive to dictate the 1-4 interactions. Setting gen-pairs = yes generates the parameters, such that a [pairtypes] directive is unnecessary. -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi all Can someone please get back to me on this. I have generated my own topology file from OPLS parameters by hand with the following format. I am now concerned that I haven't been calculating 1,4 interactions, which I thought were generated by setting gen-pairs = yes. I have read section 5 of the manual several times but am still unclear about this. You can answer this question by analyzing your .edr file: are there LJ-14 and/or Coul-14 terms? If so, then you're calculating 1-4 interactions. Seems to me that, for OPLS, your approach is fine. It wasn't clear from your earlier posts that you were using OPLS, hence the inability to know if what you were doing was right or not. Different force fields have different underlying mechanics, so the use of [nonbond_params] and/or [pairs]/[pairtypes] is somewhat dependent upon your model. -Justin Cheers Gavin parameter level [defaults] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 3 yes0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) ;Molecular level
Re: [gmx-users] 1,4 interactions
Gavin Melaugh wrote: Right, I think the penny has finally dropped. On the back of what you said. 1)In my topologies I have always listed say a [bond] directive, with bond indices,function, k, and r0. I could however just list the indices and the function, and then have the corresponding parameters in the [bond types] directive, which save me associating the parameters to each individual bond ? Yes. 2) In reponse to what yo said finally If you list specific pairs of atoms in a [pairs] directive, then grompp will search for the appropriate parameters listed in a [pairstypes] directive. If none are found, and gen-pairs = yes, grompp generates the appropriate parameters for you. Are the parameters generated from the [atomtypes] directive? Yes, in conjunction with FudgeLJ and FudgeQQ. -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: A few points then, 1) So a [pairs] directive would include all the atom indices of the 1,4 interactions and the coressponding values of sigma and epsilon?, which I would do manually. No. A [pairs] directive simply lists the pairs of atoms for which 1,4 interactions should be calculated. No parameters are listed here. Format: atom_i atom_j func_type 2) In the manual it says ''gen-pairs = yes : generate 1,4 interactions which are not present in the pair list from normal LJ parameters using Fudge LJ. Sorry if I am coming across stupid, but that seems different to what you're saying? Not at all. The parameters for a specific interaction are given in a [pairtypes] directive. If these parameters are not present and gen-pairs = yes then they are calculated. If parameters for a specific pair are not present, and gen-pairs = no then grompp generates a fatal error. 3) Also am Icorrect about the normal nb-LJ coming from the [atom types directive] Yes. 4) I suppose a very obvious question would be; What is the difference between a [pairtypes] directive and [pairs] directive (bonds, bondtypes etc) A [*type] directive lists the parameters that should be a applied to whatever interaction type might be found. For instance, a [bondtypes] directive contains default parameters for all the bonds you might find, like C-C. If you then have a [bonds] directive that lists: ; ai aj func 1 21 ...and atoms 1 and 2 are both C, then grompp finds the corresponding parameters in the [bondtypes] directive and applies them to that bond, a process which it carries out for all the rest of the interaction types, including pairs. If you list specific pairs of atoms in a [pairs] directive, then grompp will search for the appropriate parameters listed in a [pairstypes] directive. If none are found, and gen-pairs = yes, grompp generates the appropriate parameters for you. -Justin Gavin P.S I appreciate you using your time to explain this Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Thanks for replying. I have checked the energy file and there are no 1,4 terms, which is what I expected. I should clarify that my parameters are taken from the OPLS ua forcefield but I have relabelled them for my own model, which is not a common molecule. Therefore all the info on the molecule is in .top and obviously the .gro file. i.e. there are no #include statements. Now I take it that the non-bonded LJ are taken from the [atom types] directive? The question is then how and where do I state the 1,4 terms. I always thought that when gen-pairs = yes, then gromacs would generate a list of all the 1,4 interaction types? You don't explicitly state 1-4 terms with OPLS-AA. While you don't need a [pairtypes] directive, you do need a [pairs] directive to dictate the 1-4 interactions. Setting gen-pairs = yes generates the parameters, such that a [pairtypes] directive is unnecessary. -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi all Can someone please get back to me on this. I have generated my own topology file from OPLS parameters by hand with the following format. I am now concerned that I haven't been calculating 1,4 interactions, which I thought were generated by setting gen-pairs = yes. I have read section 5 of the manual several times but am still unclear about this. You can answer this question by analyzing your .edr file: are there LJ-14 and/or Coul-14 terms? If so, then you're calculating 1-4 interactions. Seems to me that, for OPLS, your approach is fine. It wasn't clear from your earlier posts that you were using OPLS, hence the inability to know if what you were doing was right or not. Different force fields have different underlying mechanics, so the use of [nonbond_params] and/or [pairs]/[pairtypes] is somewhat dependent upon your model. -Justin Cheers Gavin parameter level [defaults] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 3 yes0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) ;Molecular
Re: [gmx-users] 1,4 interactions
Hi Justin I just wanted to say a big thanks for your time and patience Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Right, I think the penny has finally dropped. On the back of what you said. 1)In my topologies I have always listed say a [bond] directive, with bond indices,function, k, and r0. I could however just list the indices and the function, and then have the corresponding parameters in the [bond types] directive, which save me associating the parameters to each individual bond ? Yes. 2) In reponse to what yo said finally If you list specific pairs of atoms in a [pairs] directive, then grompp will search for the appropriate parameters listed in a [pairstypes] directive. If none are found, and gen-pairs = yes, grompp generates the appropriate parameters for you. Are the parameters generated from the [atomtypes] directive? Yes, in conjunction with FudgeLJ and FudgeQQ. -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: A few points then, 1) So a [pairs] directive would include all the atom indices of the 1,4 interactions and the coressponding values of sigma and epsilon?, which I would do manually. No. A [pairs] directive simply lists the pairs of atoms for which 1,4 interactions should be calculated. No parameters are listed here. Format: atom_i atom_j func_type 2) In the manual it says ''gen-pairs = yes : generate 1,4 interactions which are not present in the pair list from normal LJ parameters using Fudge LJ. Sorry if I am coming across stupid, but that seems different to what you're saying? Not at all. The parameters for a specific interaction are given in a [pairtypes] directive. If these parameters are not present and gen-pairs = yes then they are calculated. If parameters for a specific pair are not present, and gen-pairs = no then grompp generates a fatal error. 3) Also am Icorrect about the normal nb-LJ coming from the [atom types directive] Yes. 4) I suppose a very obvious question would be; What is the difference between a [pairtypes] directive and [pairs] directive (bonds, bondtypes etc) A [*type] directive lists the parameters that should be a applied to whatever interaction type might be found. For instance, a [bondtypes] directive contains default parameters for all the bonds you might find, like C-C. If you then have a [bonds] directive that lists: ; ai aj func 1 21 ...and atoms 1 and 2 are both C, then grompp finds the corresponding parameters in the [bondtypes] directive and applies them to that bond, a process which it carries out for all the rest of the interaction types, including pairs. If you list specific pairs of atoms in a [pairs] directive, then grompp will search for the appropriate parameters listed in a [pairstypes] directive. If none are found, and gen-pairs = yes, grompp generates the appropriate parameters for you. -Justin Gavin P.S I appreciate you using your time to explain this Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Thanks for replying. I have checked the energy file and there are no 1,4 terms, which is what I expected. I should clarify that my parameters are taken from the OPLS ua forcefield but I have relabelled them for my own model, which is not a common molecule. Therefore all the info on the molecule is in .top and obviously the .gro file. i.e. there are no #include statements. Now I take it that the non-bonded LJ are taken from the [atom types] directive? The question is then how and where do I state the 1,4 terms. I always thought that when gen-pairs = yes, then gromacs would generate a list of all the 1,4 interaction types? You don't explicitly state 1-4 terms with OPLS-AA. While you don't need a [pairtypes] directive, you do need a [pairs] directive to dictate the 1-4 interactions. Setting gen-pairs = yes generates the parameters, such that a [pairtypes] directive is unnecessary. -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi all Can someone please get back to me on this. I have generated my own topology file from OPLS parameters by hand with the following format. I am now concerned that I haven't been calculating 1,4 interactions, which I thought were generated by setting gen-pairs = yes. I have read section 5 of the manual several times but am still unclear about this. You can answer this question by analyzing your .edr file: are there LJ-14 and/or Coul-14 terms? If so, then you're calculating 1-4 interactions. Seems to me that, for OPLS, your approach is fine. It wasn't clear from your earlier posts that you were using OPLS, hence the inability to know if what you were doing was right or not. Different force fields have different underlying mechanics, so the use of [nonbond_params] and/or [pairs]/[pairtypes] is somewhat dependent upon your model. -Justin Cheers Gavin parameter level [defaults] ; nbfunccomb-rule gen-pairs
Re: [gmx-users] 1,4 interactions
Gavin Melaugh wrote: Hi Justin I just wanted to say a big thanks for your time and patience No problem. This exchange has made me realize that what's in the manual, while complete, lacks a bit of clarity. I'm going to make some updates to the documentation for a future release. Hopefully this will clarify some issues. -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Right, I think the penny has finally dropped. On the back of what you said. 1)In my topologies I have always listed say a [bond] directive, with bond indices,function, k, and r0. I could however just list the indices and the function, and then have the corresponding parameters in the [bond types] directive, which save me associating the parameters to each individual bond ? Yes. 2) In reponse to what yo said finally If you list specific pairs of atoms in a [pairs] directive, then grompp will search for the appropriate parameters listed in a [pairstypes] directive. If none are found, and gen-pairs = yes, grompp generates the appropriate parameters for you. Are the parameters generated from the [atomtypes] directive? Yes, in conjunction with FudgeLJ and FudgeQQ. -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: A few points then, 1) So a [pairs] directive would include all the atom indices of the 1,4 interactions and the coressponding values of sigma and epsilon?, which I would do manually. No. A [pairs] directive simply lists the pairs of atoms for which 1,4 interactions should be calculated. No parameters are listed here. Format: atom_i atom_j func_type 2) In the manual it says ''gen-pairs = yes : generate 1,4 interactions which are not present in the pair list from normal LJ parameters using Fudge LJ. Sorry if I am coming across stupid, but that seems different to what you're saying? Not at all. The parameters for a specific interaction are given in a [pairtypes] directive. If these parameters are not present and gen-pairs = yes then they are calculated. If parameters for a specific pair are not present, and gen-pairs = no then grompp generates a fatal error. 3) Also am Icorrect about the normal nb-LJ coming from the [atom types directive] Yes. 4) I suppose a very obvious question would be; What is the difference between a [pairtypes] directive and [pairs] directive (bonds, bondtypes etc) A [*type] directive lists the parameters that should be a applied to whatever interaction type might be found. For instance, a [bondtypes] directive contains default parameters for all the bonds you might find, like C-C. If you then have a [bonds] directive that lists: ; ai aj func 1 21 ...and atoms 1 and 2 are both C, then grompp finds the corresponding parameters in the [bondtypes] directive and applies them to that bond, a process which it carries out for all the rest of the interaction types, including pairs. If you list specific pairs of atoms in a [pairs] directive, then grompp will search for the appropriate parameters listed in a [pairstypes] directive. If none are found, and gen-pairs = yes, grompp generates the appropriate parameters for you. -Justin Gavin P.S I appreciate you using your time to explain this Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Thanks for replying. I have checked the energy file and there are no 1,4 terms, which is what I expected. I should clarify that my parameters are taken from the OPLS ua forcefield but I have relabelled them for my own model, which is not a common molecule. Therefore all the info on the molecule is in .top and obviously the .gro file. i.e. there are no #include statements. Now I take it that the non-bonded LJ are taken from the [atom types] directive? The question is then how and where do I state the 1,4 terms. I always thought that when gen-pairs = yes, then gromacs would generate a list of all the 1,4 interaction types? You don't explicitly state 1-4 terms with OPLS-AA. While you don't need a [pairtypes] directive, you do need a [pairs] directive to dictate the 1-4 interactions. Setting gen-pairs = yes generates the parameters, such that a [pairtypes] directive is unnecessary. -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi all Can someone please get back to me on this. I have generated my own topology file from OPLS parameters by hand with the following format. I am now concerned that I haven't been calculating 1,4 interactions, which I thought were generated by setting gen-pairs = yes. I have read section 5 of the manual several times but am still unclear about this. You can answer this question by analyzing your .edr file: are there LJ-14 and/or Coul-14 terms? If so, then you're calculating 1-4 interactions. Seems to me that, for OPLS, your approach is fine. It wasn't clear from your earlier posts that you were using OPLS, hence the inability to know if what you were doing was right or not. Different force fields have different underlying mechanics, so the use
[gmx-users] g_clustsize not recognize the -mol option and ignore the index file
Hello everybody, I'm using g_clustsize to analyze clusters formed in my solution. However I noticed that not would get consistent results using the complete trajectory (containing both solvent and solute). To see the aggregation, using g_clustsize, I had to convert my trajectory to a file containing only the solute molecules. That's because -mol option considered all the molecules in the box (ignoring the index file) and as a result I always got a single cluster with all the solvent+solute molecules. Is there a more efficient way to do this? Is this a bug in the program? I've been reading all information on this tool from the gmx-list and I could see some difficulties in dealing with it the way it is. Bests eef ___ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 http://fileti.ufabc.edu.br -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] rlist and rlistlong in gmx451
Dear Gromacs Users and Developers, I am testing gromacs-4.5.1 with different running parameters, in particular switching potentials and rlistlong. I have a question about this NOTEs given by grompp when rlist=rvdw=rcoulomb (I thought that was rlonglist that should be longer than rvdw and rcoulomb): NOTE 1 [file qua.mdp]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rcoulomb. NOTE 2 [file qua.mdp]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw. I am using: rlist= 1.2 rlistlong= 1.5 coulombtype = pme-switch rcoulomb-switch = 1.0 rcoulomb = 1.2 vdw-type = switch rvdw-switch = 1.0 rvdw = 1.2 If rlist should be larger than rvdw what's the use of rlonglist? Thanks, Carlo -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] 1,4 interactions
Justin One last question.What is the point of the [nonbond_params] directive if all your LJ parameters are already specified in [atomtypes]?, also [pairs_nb]. Surely it is not necessary to list all nb pairs? Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin I just wanted to say a big thanks for your time and patience No problem. This exchange has made me realize that what's in the manual, while complete, lacks a bit of clarity. I'm going to make some updates to the documentation for a future release. Hopefully this will clarify some issues. -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Right, I think the penny has finally dropped. On the back of what you said. 1)In my topologies I have always listed say a [bond] directive, with bond indices,function, k, and r0. I could however just list the indices and the function, and then have the corresponding parameters in the [bond types] directive, which save me associating the parameters to each individual bond ? Yes. 2) In reponse to what yo said finally If you list specific pairs of atoms in a [pairs] directive, then grompp will search for the appropriate parameters listed in a [pairstypes] directive. If none are found, and gen-pairs = yes, grompp generates the appropriate parameters for you. Are the parameters generated from the [atomtypes] directive? Yes, in conjunction with FudgeLJ and FudgeQQ. -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: A few points then, 1) So a [pairs] directive would include all the atom indices of the 1,4 interactions and the coressponding values of sigma and epsilon?, which I would do manually. No. A [pairs] directive simply lists the pairs of atoms for which 1,4 interactions should be calculated. No parameters are listed here. Format: atom_i atom_j func_type 2) In the manual it says ''gen-pairs = yes : generate 1,4 interactions which are not present in the pair list from normal LJ parameters using Fudge LJ. Sorry if I am coming across stupid, but that seems different to what you're saying? Not at all. The parameters for a specific interaction are given in a [pairtypes] directive. If these parameters are not present and gen-pairs = yes then they are calculated. If parameters for a specific pair are not present, and gen-pairs = no then grompp generates a fatal error. 3) Also am Icorrect about the normal nb-LJ coming from the [atom types directive] Yes. 4) I suppose a very obvious question would be; What is the difference between a [pairtypes] directive and [pairs] directive (bonds, bondtypes etc) A [*type] directive lists the parameters that should be a applied to whatever interaction type might be found. For instance, a [bondtypes] directive contains default parameters for all the bonds you might find, like C-C. If you then have a [bonds] directive that lists: ; ai aj func 1 21 ...and atoms 1 and 2 are both C, then grompp finds the corresponding parameters in the [bondtypes] directive and applies them to that bond, a process which it carries out for all the rest of the interaction types, including pairs. If you list specific pairs of atoms in a [pairs] directive, then grompp will search for the appropriate parameters listed in a [pairstypes] directive. If none are found, and gen-pairs = yes, grompp generates the appropriate parameters for you. -Justin Gavin P.S I appreciate you using your time to explain this Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Thanks for replying. I have checked the energy file and there are no 1,4 terms, which is what I expected. I should clarify that my parameters are taken from the OPLS ua forcefield but I have relabelled them for my own model, which is not a common molecule. Therefore all the info on the molecule is in .top and obviously the .gro file. i.e. there are no #include statements. Now I take it that the non-bonded LJ are taken from the [atom types] directive? The question is then how and where do I state the 1,4 terms. I always thought that when gen-pairs = yes, then gromacs would generate a list of all the 1,4 interaction types? You don't explicitly state 1-4 terms with OPLS-AA. While you don't need a [pairtypes] directive, you do need a [pairs] directive to dictate the 1-4 interactions. Setting gen-pairs = yes generates the parameters, such that a [pairtypes] directive is unnecessary. -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi all Can someone please get back to me on this. I have generated my own topology file from OPLS parameters by hand with the following format. I am now concerned that I haven't been calculating 1,4 interactions, which I thought were generated by setting gen-pairs = yes. I have read section 5 of the manual several times but am still unclear about this. You can answer this question by analyzing your .edr file: are there
Re: [gmx-users] rlist and rlistlong in gmx451
Carlo Camilloni wrote: Dear Gromacs Users and Developers, I am testing gromacs-4.5.1 with different running parameters, in particular switching potentials and rlistlong. I have a question about this NOTEs given by grompp when rlist=rvdw=rcoulomb (I thought that was rlonglist that should be longer than rvdw and rcoulomb): NOTE 1 [file qua.mdp]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rcoulomb. NOTE 2 [file qua.mdp]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw. I am using: rlist= 1.2 rlistlong= 1.5 coulombtype = pme-switch rcoulomb-switch = 1.0 rcoulomb = 1.2 vdw-type = switch rvdw-switch = 1.0 rvdw = 1.2 If rlist should be larger than rvdw what's the use of rlonglist? The value of rlistlong is only relevant when using twin-range cutoffs (per the manual), which you are not (rlist=rcoulomb=rvdw). Note that this equality leads to bad energy conservation, as grompp is warning you. Increase rlist properly and you should have no problem. -Justin Thanks, Carlo -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] 1,4 interactions
Gavin Melaugh wrote: Justin One last question.What is the point of the [nonbond_params] directive if all your LJ parameters are already specified in [atomtypes]?, also You can define non-standard parameters here. Otherwise, the normal combination rules are used. It seems like, at least in the cases of the Gromos force fields, some of the values provided are the normal values that would be calculated by the combination rules, so I don't see the point. Maybe it's a relic of previous versions where the section was necessary. Just a guess. [pairs_nb]. Never heard of this directive. I see it in the manual, but I can't find it in any of the actual force field files. Surely it is not necessary to list all nb pairs? No. If an interaction is based solely on the normal combination rules for a force field, those combination rules are applied, as stated in section 5.3.3 (after equation 5.2). -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin I just wanted to say a big thanks for your time and patience No problem. This exchange has made me realize that what's in the manual, while complete, lacks a bit of clarity. I'm going to make some updates to the documentation for a future release. Hopefully this will clarify some issues. -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Right, I think the penny has finally dropped. On the back of what you said. 1)In my topologies I have always listed say a [bond] directive, with bond indices,function, k, and r0. I could however just list the indices and the function, and then have the corresponding parameters in the [bond types] directive, which save me associating the parameters to each individual bond ? Yes. 2) In reponse to what yo said finally If you list specific pairs of atoms in a [pairs] directive, then grompp will search for the appropriate parameters listed in a [pairstypes] directive. If none are found, and gen-pairs = yes, grompp generates the appropriate parameters for you. Are the parameters generated from the [atomtypes] directive? Yes, in conjunction with FudgeLJ and FudgeQQ. -Justin Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: A few points then, 1) So a [pairs] directive would include all the atom indices of the 1,4 interactions and the coressponding values of sigma and epsilon?, which I would do manually. No. A [pairs] directive simply lists the pairs of atoms for which 1,4 interactions should be calculated. No parameters are listed here. Format: atom_i atom_j func_type 2) In the manual it says ''gen-pairs = yes : generate 1,4 interactions which are not present in the pair list from normal LJ parameters using Fudge LJ. Sorry if I am coming across stupid, but that seems different to what you're saying? Not at all. The parameters for a specific interaction are given in a [pairtypes] directive. If these parameters are not present and gen-pairs = yes then they are calculated. If parameters for a specific pair are not present, and gen-pairs = no then grompp generates a fatal error. 3) Also am Icorrect about the normal nb-LJ coming from the [atom types directive] Yes. 4) I suppose a very obvious question would be; What is the difference between a [pairtypes] directive and [pairs] directive (bonds, bondtypes etc) A [*type] directive lists the parameters that should be a applied to whatever interaction type might be found. For instance, a [bondtypes] directive contains default parameters for all the bonds you might find, like C-C. If you then have a [bonds] directive that lists: ; ai aj func 1 21 ...and atoms 1 and 2 are both C, then grompp finds the corresponding parameters in the [bondtypes] directive and applies them to that bond, a process which it carries out for all the rest of the interaction types, including pairs. If you list specific pairs of atoms in a [pairs] directive, then grompp will search for the appropriate parameters listed in a [pairstypes] directive. If none are found, and gen-pairs = yes, grompp generates the appropriate parameters for you. -Justin Gavin P.S I appreciate you using your time to explain this Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Thanks for replying. I have checked the energy file and there are no 1,4 terms, which is what I expected. I should clarify that my parameters are taken from the OPLS ua forcefield but I have relabelled them for my own model, which is not a common molecule. Therefore all the info on the molecule is in .top and obviously the .gro file. i.e. there are no #include statements. Now I take it that the non-bonded LJ are taken from the [atom types] directive? The question is then how and where do I state the 1,4 terms. I always thought that when gen-pairs = yes, then gromacs would generate a list of all the 1,4 interaction types? You don't explicitly state 1-4 terms with OPLS-AA. While you don't need a [pairtypes] directive, you do need a [pairs] directive
[gmx-users] Pull Code for Secondary Stability
Does anyone know if the pull code can be used to determine structure stability? If I wanted to generate a stress-strain plot of an alpha-helix, would the pull simulation give me the data such as the force vs displacement? Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] viscosity calculation
Hello, I used g_energy f *.edr vis *.xvg s *.tpr to calculate the viscosity of my system which is water. Two files are generate: *.xvg and the enecorr.xvg. Now, what should I do to calculate the viscosity of my system with these two files? Sorry for such naïve question. Regards, Payman -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] viscosity calculation
Payman Pirzadeh wrote: Hello, I used g_energy –f *.edr –vis *.xvg –s *.tpr to calculate the viscosity of my system which is water. Two files are generate: *.xvg and the enecorr.xvg. Now, what should I do to calculate the viscosity of my system with these two files? Sorry for such naïve question. Plot the output .xvg; you will find it should contain two quantities: bulk and shear viscosity. -Justin Regards, Payman -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] viscosity calculation
Well, two questions: 1. My bulk values are fluctuating around 60 (I assume cP). But it looks like very weird to me since experimental value for water viscosity is 0.854 cP. My system is at 265K with 4202 molecules. Is sth strange going on? Or I am missing some unit conversions in the plot. 2. For calculation of protein diffusion constant, should we use the bulk or shear viscosity of the solvent (water)? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: September 29, 2010 12:28 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] viscosity calculation Payman Pirzadeh wrote: Hello, I used g_energy f *.edr vis *.xvg s *.tpr to calculate the viscosity of my system which is water. Two files are generate: *.xvg and the enecorr.xvg. Now, what should I do to calculate the viscosity of my system with these two files? Sorry for such naïve question. Plot the output .xvg; you will find it should contain two quantities: bulk and shear viscosity. -Justin Regards, Payman -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Steered molecular dynamics and Parinello-Rahman and bond constraints.
Hi GMX-users, I am beginning to use the steered molecular dynamics method to perform a potential of mean field calculation. In your experience, does it matter what kind of a thermostat and pressure coupling is used? Does Nose-Hoover and Parinello-Rahman perform better than Berendsen for this purpose? Does it even matter? Also with regards to the constraints on the bonds using the all-bonds option, Does it matter? I worry that applying constraints on the molecule being pulled will prevent it from sampling the configurational space effectively and thus giving false results on the PMF and binding energies. Maybe I am completely off the mark here. Thanks in advance. Regards Rama -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] viscosity calculation
On 2010-09-29 20.52, Payman Pirzadeh wrote: Well, two questions: 1. My bulk values are fluctuating around 60 (I assume cP). But it looks like very weird to me since experimental value for water viscosity is 0.854 cP. My system is at 265K with 4202 molecules. Is sth strange going on? Or I am missing some unit conversions in the plot. Is the experimental value 0.854 at that temperature? Could be the the unit is different in the output too. Doesn't it say in the xvg file? 2. For calculation of protein diffusion constant, should we use the bulk or shear viscosity of the solvent (water)? Why not use g_msd? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: September 29, 2010 12:28 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] viscosity calculation Payman Pirzadeh wrote: Hello, I used g_energy –f *.edr –vis *.xvg –s *.tpr to calculate the viscosity of my system which is water. Two files are generate: *.xvg and the enecorr.xvg. Now, what should I do to calculate the viscosity of my system with these two files? Sorry for such naïve question. Plot the output .xvg; you will find it should contain two quantities: bulk and shear viscosity. -Justin Regards, Payman -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Steered molecular dynamics and Parinello-Rahman and bond constraints.
quantrum75 wrote: Hi GMX-users, I am beginning to use the steered molecular dynamics method to perform a potential of mean field calculation. In your experience, does it matter what kind of a thermostat and pressure coupling is used? Does Nose-Hoover and Parinello-Rahman perform better than Berendsen for this purpose? Does it even matter? That depends on how rigorously correct you want your ensemble to be. Berendsen coupling does not generate temperatures/pressures that correspond to any known statistical mechanical ensemble. This issue has been discussed dozens of times across this list. Check the archives (and the literature) for details. Also with regards to the constraints on the bonds using the all-bonds option, Does it matter? I worry that applying constraints on the molecule being pulled will prevent it from sampling the configurational space effectively and thus giving false results on the PMF and binding energies. Maybe I am completely off the mark here. See the manual, section 6.3, where this very topic is discussed. -Justin Thanks in advance. Regards Rama -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] viscosity calculation
265 K is -8C, so ice, not liquid water. That would be more viscous than you might expect. Waren Gallin On 2010-09-29, at 12:52 PM, Payman Pirzadeh wrote: Well, two questions: 1. My bulk values are fluctuating around 60 (I assume cP). But it looks like very weird to me since experimental value for water viscosity is 0.854 cP. My system is at 265K with 4202 molecules. Is sth strange going on? Or I am missing some unit conversions in the plot. 2. For calculation of protein diffusion constant, should we use the bulk or shear viscosity of the solvent (water)? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: September 29, 2010 12:28 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] viscosity calculation Payman Pirzadeh wrote: Hello, I used g_energy –f *.edr –vis *.xvg –s *.tpr to calculate the viscosity of my system which is water. Two files are generate: *.xvg and the enecorr.xvg. Now, what should I do to calculate the viscosity of my system with these two files? Sorry for such naïve question. Plot the output .xvg; you will find it should contain two quantities: bulk and shear viscosity. -Justin Regards, Payman -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] viscosity calculation
Apparently, in the file the unit in the file is cP. It might be the case that I plotted the wrong column. I think I should get the third column. Regarding the diffusion, I read in papers about rotational diffusion of the proteins which could be calculated having the viscosity of the liquid and hydrodynamic volume of the protein. So, volume could be calculated with radius of gyration + 0.3nm of hydration shell and viscosity is given by g_energy. So, a rotational diffusion constant could be theoretically calculated. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: September 29, 2010 1:03 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] viscosity calculation On 2010-09-29 20.52, Payman Pirzadeh wrote: Well, two questions: 1. My bulk values are fluctuating around 60 (I assume cP). But it looks like very weird to me since experimental value for water viscosity is 0.854 cP. My system is at 265K with 4202 molecules. Is sth strange going on? Or I am missing some unit conversions in the plot. Is the experimental value 0.854 at that temperature? Could be the the unit is different in the output too. Doesn't it say in the xvg file? 2. For calculation of protein diffusion constant, should we use the bulk or shear viscosity of the solvent (water)? Why not use g_msd? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: September 29, 2010 12:28 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] viscosity calculation Payman Pirzadeh wrote: Hello, I used g_energy f *.edr vis *.xvg s *.tpr to calculate the viscosity of my system which is water. Two files are generate: *.xvg and the enecorr.xvg. Now, what should I do to calculate the viscosity of my system with these two files? Sorry for such naïve question. Plot the output .xvg; you will find it should contain two quantities: bulk and shear viscosity. -Justin Regards, Payman -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: Problem with pressure coupling
Hi again, I have made available a testcase that reproduces the problem here: http://marge.uochb.cas.cz/~marsalek/tmp/test-volume-drift.tar.bz2 To see the problem, use grompp from GMX 4.5.1 and run the resulting tpr. Then extract the volume: echo Volume | g_energy -f ener.edr -o volume and observe the drift. I would be very grateful if someone could help me confirm the behavior. I have found one more thing indicative of this being a bug in 4.5.1. If I use grompp from 4.0.7 and then run the tpr using 4.5.1 it runs fine, just as it runs in 4.0.7. The tpr produced by grompp from 4.5.1 has the drift in box volume when run in 4.5.1. Of course, it will not run in 4.0.7, so there is no way of testing that. Thanks for any help on this, Ondrej On Thu, Sep 23, 2010 at 15:16, Ondrej Marsalek ondrej.marsa...@gmail.com wrote: Dear all, running a box of neat water with the below mdp file in GROMACS 4.5.1 results in a fast linear increase of the volume of the box, the water getting torn into clusters. The same simulation in 4.0.7 (with nstcalcenergy removed, of course) runs just fine, with the box volume stable and fluctuating. In 4.5.1 the problem can be fixed by setting nstlist = 1. I assume this would also be the case for other positive numbers. The same behavior can be seen for the Parrinello-Rahman barostat. I can of course provide full testcases ready to run, if needed. This looks like a bug to me. Can anyone help me resolve this? Thanks, Ondrej ; RUN CONTROL PARAMETERS integrator = md tinit = 0 dt = 0.002 nsteps = 5000 comm-mode = Linear nstcomm = 10 ; OUTPUT CONTROL OPTIONS nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 100 nstcalcenergy = 10 nstenergy = 100 nstxtcout = 100 xtc-precision = 1000 ; NEIGHBORSEARCHING PARAMETERS nstlist = -1 ns_type = grid pbc = xyz periodic_molecules = no rlist = 1.3 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = PME-Switch rcoulomb-switch = 0.6 rcoulomb = 0.8 vdw-type = Shift rvdw-switch = 0.6 rvdw = 0.8 DispCorr = EnerPres fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 3d optimize_fft = yes ; OPTIONS FOR WEAK COUPLING ALGORITHMS Tcoupl = v-rescale tc-grps = system tau_t = 0.5 ref_t = 300 Pcoupl = berendsen Pcoupltype = isotropic tau_p = 1 compressibility = 4.5e-5 ref_p = 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = no ; OPTIONS FOR BONDS constraints = none -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Problem with pressure coupling
On 2010-09-29 21.15, Ondrej Marsalek wrote: Hi again, I have made available a testcase that reproduces the problem here: http://marge.uochb.cas.cz/~marsalek/tmp/test-volume-drift.tar.bz2 To see the problem, use grompp from GMX 4.5.1 and run the resulting tpr. Then extract the volume: echo Volume | g_energy -f ener.edr -o volume and observe the drift. I would be very grateful if someone could help me confirm the behavior. I have found one more thing indicative of this being a bug in 4.5.1. If I use grompp from 4.0.7 and then run the tpr using 4.5.1 it runs fine, just as it runs in 4.0.7. The tpr produced by grompp from 4.5.1 has the drift in box volume when run in 4.5.1. Of course, it will not run in 4.0.7, so there is no way of testing that. Thanks for any help on this, Ondrej I have confirmed this as a bug. In 4.0.5 (which I had handy) the density is constant Density (SI) 999.5543.823773.80651 0.06283451.25694 In 4.5.1 with 4.0.5 tpr file it is as you say: Density995.2771.34.32625 -1.24517 (kg/m^3) In 4.5.1 with 4.5.1 tpr file I get Density709.919 66137.824 -467.285 (kg/m^3) Now the differences in the tpr files are revealing: [anfinsen:test-volume-drift] % gmxcheck -s1 topol405.tpr -s2 topol.tpr snip Note: tpx file_version 58, software version 73 Reading file topol.tpr, VERSION 4.5.1-%ci-21e8a32 (single precision) comparing inputrec inputrec-nstcalcenergy (1 - 10) inputrec-rgbradii (2.00e+00 - 1.00e+00) inputrec-sa_surface_tension (2.092000e+00 - 2.050160e+00) inputrec-sc_sigma_min (0.00e+00 - 3.00e-01) inputrec-nstdhdl (1 - 10) inputrec-separate_dhdl_file (0 - 10) snip After setting nstcalcenergy = 1 I get Density996.8941.23.850831.86718 (kg/m^3) In other words the bug can be circumvented by setting this variable to 1. I will file a bugzilla. On Thu, Sep 23, 2010 at 15:16, Ondrej Marsalek ondrej.marsa...@gmail.com wrote: Dear all, running a box of neat water with the below mdp file in GROMACS 4.5.1 results in a fast linear increase of the volume of the box, the water getting torn into clusters. The same simulation in 4.0.7 (with nstcalcenergy removed, of course) runs just fine, with the box volume stable and fluctuating. In 4.5.1 the problem can be fixed by setting nstlist = 1. I assume this would also be the case for other positive numbers. The same behavior can be seen for the Parrinello-Rahman barostat. I can of course provide full testcases ready to run, if needed. This looks like a bug to me. Can anyone help me resolve this? Thanks, Ondrej ; RUN CONTROL PARAMETERS integrator = md tinit= 0 dt = 0.002 nsteps = 5000 comm-mode= Linear nstcomm = 10 ; OUTPUT CONTROL OPTIONS nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 100 nstcalcenergy= 10 nstenergy= 100 nstxtcout= 100 xtc-precision= 1000 ; NEIGHBORSEARCHING PARAMETERS nstlist = -1 ns_type = grid pbc = xyz periodic_molecules = no rlist= 1.3 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = PME-Switch rcoulomb-switch = 0.6 rcoulomb = 0.8 vdw-type = Shift rvdw-switch = 0.6 rvdw = 0.8 DispCorr = EnerPres fourierspacing = 0.12 pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d optimize_fft = yes ; OPTIONS FOR WEAK COUPLING ALGORITHMS Tcoupl = v-rescale tc-grps = system tau_t= 0.5 ref_t= 300 Pcoupl = berendsen Pcoupltype = isotropic tau_p= 1 compressibility = 4.5e-5 ref_p= 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = no ; OPTIONS FOR BONDS constraints = none -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] viscosity calculation_2
Adding to my previous comments, It looks like that the third column is the appropriate one to plot. However, I tried to use g_energy -b 0 -e 2 to take the whole trajectory (2 ps) rather than half of the frames. But, still g_energy take half of the frames. This has caused improper convergence in viscosity values. If I take only the last 3000 ps (out of 1ps), I will get a viscosity of 0.920 with a large rmsd. Is there a bug in g_energy switches? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: September 29, 2010 1:03 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] viscosity calculation On 2010-09-29 20.52, Payman Pirzadeh wrote: Well, two questions: 1. My bulk values are fluctuating around 60 (I assume cP). But it looks like very weird to me since experimental value for water viscosity is 0.854 cP. My system is at 265K with 4202 molecules. Is sth strange going on? Or I am missing some unit conversions in the plot. Is the experimental value 0.854 at that temperature? Could be the the unit is different in the output too. Doesn't it say in the xvg file? 2. For calculation of protein diffusion constant, should we use the bulk or shear viscosity of the solvent (water)? Why not use g_msd? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: September 29, 2010 12:28 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] viscosity calculation Payman Pirzadeh wrote: Hello, I used g_energy f *.edr vis *.xvg s *.tpr to calculate the viscosity of my system which is water. Two files are generate: *.xvg and the enecorr.xvg. Now, what should I do to calculate the viscosity of my system with these two files? Sorry for such naïve question. Plot the output .xvg; you will find it should contain two quantities: bulk and shear viscosity. -Justin Regards, Payman -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] viscosity calculation_2
On 2010-09-29 22.00, Payman Pirzadeh wrote: Adding to my previous comments, It looks like that the third column is the appropriate one to plot. However, I tried to use g_energy -b 0 -e 2 to take the whole trajectory (2 ps) rather than half of the frames. But, still g_energy take half of the frames. This has caused improper convergence in viscosity values. If I take only the last 3000 ps (out of 1ps), I will get a viscosity of 0.920 with a large rmsd. Is there a bug in g_energy switches? I think this is because it use an autocorrelation function of the pressure. By default it uses an FFT to compute it. The ACF at 2 ps has very poor statistics (1 data point) and can therefore ruin the viscosity. Therefore ACFs by default are plotted to half the traj. There is a flag to get a longer (noisier) ACF. g_energy -h might tell you which one. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: September 29, 2010 1:03 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] viscosity calculation On 2010-09-29 20.52, Payman Pirzadeh wrote: Well, two questions: 1. My bulk values are fluctuating around 60 (I assume cP). But it looks like very weird to me since experimental value for water viscosity is 0.854 cP. My system is at 265K with 4202 molecules. Is sth strange going on? Or I am missing some unit conversions in the plot. Is the experimental value 0.854 at that temperature? Could be the the unit is different in the output too. Doesn't it say in the xvg file? 2. For calculation of protein diffusion constant, should we use the bulk or shear viscosity of the solvent (water)? Why not use g_msd? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: September 29, 2010 12:28 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] viscosity calculation Payman Pirzadeh wrote: Hello, I used g_energy –f *.edr –vis *.xvg –s *.tpr to calculate the viscosity of my system which is water. Two files are generate: *.xvg and the enecorr.xvg. Now, what should I do to calculate the viscosity of my system with these two files? Sorry for such naïve question. Plot the output .xvg; you will find it should contain two quantities: bulk and shear viscosity. -Justin Regards, Payman -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Problem with pressure coupling
On Wed, Sep 29, 2010 at 21:56, David van der Spoel sp...@xray.bmc.uu.se wrote: Now the differences in the tpr files are revealing: [anfinsen:test-volume-drift] % gmxcheck -s1 topol405.tpr -s2 topol.tpr snip Note: tpx file_version 58, software version 73 Reading file topol.tpr, VERSION 4.5.1-%ci-21e8a32 (single precision) comparing inputrec inputrec-nstcalcenergy (1 - 10) inputrec-rgbradii (2.00e+00 - 1.00e+00) inputrec-sa_surface_tension (2.092000e+00 - 2.050160e+00) inputrec-sc_sigma_min (0.00e+00 - 3.00e-01) inputrec-nstdhdl (1 - 10) inputrec-separate_dhdl_file (0 - 10) snip After setting nstcalcenergy = 1 I get Density 996.894 1.2 3.85083 1.86718 (kg/m^3) In other words the bug can be circumvented by setting this variable to 1. I will file a bugzilla. Thank you. The suggested workaround does indeed avoid the bug. For the simulations that I need at the moment, having nstcalcenergy = 1 is not a problem, as no extreme parallelization is needed. I would also like to point out that, as I said before, setting nstlist 0 also works around the bug. Perhaps it will be useful in debugging. Ondrej -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] viscosity calculation_2
Thanks for the tips. I just realized that there two other outputs two the g_energy -vis: evisco.xvg and eviscoi.xvg These files contain 5 columns among which the first one looks to be time. But what are the other 4? What are their differences? Regards, Paymon -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: September 29, 2010 2:07 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] viscosity calculation_2 On 2010-09-29 22.00, Payman Pirzadeh wrote: Adding to my previous comments, It looks like that the third column is the appropriate one to plot. However, I tried to use g_energy -b 0 -e 2 to take the whole trajectory (2 ps) rather than half of the frames. But, still g_energy take half of the frames. This has caused improper convergence in viscosity values. If I take only the last 3000 ps (out of 1ps), I will get a viscosity of 0.920 with a large rmsd. Is there a bug in g_energy switches? I think this is because it use an autocorrelation function of the pressure. By default it uses an FFT to compute it. The ACF at 2 ps has very poor statistics (1 data point) and can therefore ruin the viscosity. Therefore ACFs by default are plotted to half the traj. There is a flag to get a longer (noisier) ACF. g_energy -h might tell you which one. Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: September 29, 2010 1:03 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] viscosity calculation On 2010-09-29 20.52, Payman Pirzadeh wrote: Well, two questions: 1. My bulk values are fluctuating around 60 (I assume cP). But it looks like very weird to me since experimental value for water viscosity is 0.854 cP. My system is at 265K with 4202 molecules. Is sth strange going on? Or I am missing some unit conversions in the plot. Is the experimental value 0.854 at that temperature? Could be the the unit is different in the output too. Doesn't it say in the xvg file? 2. For calculation of protein diffusion constant, should we use the bulk or shear viscosity of the solvent (water)? Why not use g_msd? Payman -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: September 29, 2010 12:28 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] viscosity calculation Payman Pirzadeh wrote: Hello, I used g_energy f *.edr vis *.xvg s *.tpr to calculate the viscosity of my system which is water. Two files are generate: *.xvg and the enecorr.xvg. Now, what should I do to calculate the viscosity of my system with these two files? Sorry for such naïve question. Plot the output .xvg; you will find it should contain two quantities: bulk and shear viscosity. -Justin Regards, Payman -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] distance restrained D simulations
Hi! I am trying to perform distance restrained MD simulations of a protein with Gromacs4.0.5. I have a bunch of FRET distances ranging from 10Angs to 40 angs that I am incorporating simular to NOE distance restraints in NMR. When I use one processor for the simulations its all fine, but, when I use multiple processors I get a bunch of errors lets me start with the NOTE found below. Well do not want to increase the cut-off distance but want the program to use multiple processors. How can I overcome this problem? I would appreciate your input Thanks JJ NOTE: atoms involved in distance restraints should be within the longest cut-off distance, if this is not the case mdrun generates a fatal error, in that case use particle decomposition (mdrun option -pd) WARNING: Can not write distance restraint data to energy file with domain decomposition Loaded with Money --- Program mdrun_mpi, VERSION 4.0.5 Source code file: ../../../src/mdlib/domdec.c, line: 5873 Fatal error: There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 8.89355 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition --- What Kind Of Guru are You, Anyway ? (F. Zappa) Error on node 0, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 0 out of 4 gcq#21: What Kind Of Guru are You, Anyway ? (F. Zappa) -- mpirun has exited due to process rank 2 with PID 28700 on node compute-3-73.local exiting without calling finalize. This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). - MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] distance restrained D simulations
jayant james wrote: Hi! I am trying to perform distance restrained MD simulations of a protein with Gromacs4.0.5. I have a bunch of FRET distances ranging from 10Angs to 40 angs that I am incorporating simular to NOE distance restraints in NMR. When I use one processor for the simulations its all fine, but, when I use multiple processors I get a bunch of errors lets me start with the NOTE found below. Well do not want to increase the cut-off distance but want the program to use multiple processors. How can I overcome this problem? I would appreciate your input As the note tells you, use particle decomposition. Long distance restraints can't be split over domain decomposition cells. -Justin Thanks JJ NOTE: atoms involved in distance restraints should be within the longest cut-off distance, if this is not the case mdrun generates a fatal error, in that case use particle decomposition (mdrun option -pd) WARNING: Can not write distance restraint data to energy file with domain decomposition Loaded with Money --- Program mdrun_mpi, VERSION 4.0.5 Source code file: ../../../src/mdlib/domdec.c, line: 5873 Fatal error: There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 8.89355 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition --- What Kind Of Guru are You, Anyway ? (F. Zappa) Error on node 0, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 0 out of 4 gcq#21: What Kind Of Guru are You, Anyway ? (F. Zappa) -- mpirun has exited due to process rank 2 with PID 28700 on node compute-3-73.local exiting without calling finalize. This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). - MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp http://www.chick.com/reading/tracts/0096/0096_01.asp) -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] distance restrained D simulations
What is happening is that you've got bonds too long and the dd can not manage to cut things in 4 subsystems ... try particle decomposition but you might end up with the same problem :(( On Sep 29, 2010, at 5:35 PM, jayant james wrote: Hi! I am trying to perform distance restrained MD simulations of a protein with Gromacs4.0.5. I have a bunch of FRET distances ranging from 10Angs to 40 angs that I am incorporating simular to NOE distance restraints in NMR. When I use one processor for the simulations its all fine, but, when I use multiple processors I get a bunch of errors lets me start with the NOTE found below. Well do not want to increase the cut-off distance but want the program to use multiple processors. How can I overcome this problem? I would appreciate your input Thanks JJ NOTE: atoms involved in distance restraints should be within the longest cut-off distance, if this is not the case mdrun generates a fatal error, in that case use particle decomposition (mdrun option - pd) WARNING: Can not write distance restraint data to energy file with domain decomposition Loaded with Money --- Program mdrun_mpi, VERSION 4.0.5 Source code file: ../../../src/mdlib/domdec.c, line: 5873 Fatal error: There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 8.89355 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition --- What Kind Of Guru are You, Anyway ? (F. Zappa) Error on node 0, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 0 out of 4 gcq#21: What Kind Of Guru are You, Anyway ? (F. Zappa) -- mpirun has exited due to process rank 2 with PID 28700 on node compute-3-73.local exiting without calling finalize. This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). - MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] distance restrained D simulations
Yes you are right particle decomposition does not work too! On Thu, Sep 30, 2010 at 12:19 AM, XAvier Periole x.peri...@rug.nl wrote: What is happening is that you've got bonds too long and the dd can not manage to cut things in 4 subsystems ... try particle decomposition but you might end up with the same problem :(( On Sep 29, 2010, at 5:35 PM, jayant james wrote: Hi! I am trying to perform distance restrained MD simulations of a protein with Gromacs4.0.5. I have a bunch of FRET distances ranging from 10Angs to 40 angs that I am incorporating simular to NOE distance restraints in NMR. When I use one processor for the simulations its all fine, but, when I use multiple processors I get a bunch of errors lets me start with the NOTE found below. Well do not want to increase the cut-off distance but want the program to use multiple processors. How can I overcome this problem? I would appreciate your input Thanks JJ NOTE: atoms involved in distance restraints should be within the longest cut-off distance, if this is not the case mdrun generates a fatal error, in that case use particle decomposition (mdrun option -pd) WARNING: Can not write distance restraint data to energy file with domain decomposition Loaded with Money --- Program mdrun_mpi, VERSION 4.0.5 Source code file: ../../../src/mdlib/domdec.c, line: 5873 Fatal error: There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 8.89355 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition --- What Kind Of Guru are You, Anyway ? (F. Zappa) Error on node 0, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 0 out of 4 gcq#21: What Kind Of Guru are You, Anyway ? (F. Zappa) -- mpirun has exited due to process rank 2 with PID 28700 on node compute-3-73.local exiting without calling finalize. This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). - MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode -1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] viscosity calculation_2
Sorry, haven't looked at these files before so this might not be the case, but doesn't the top of the .xvg file explain what each column is? Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9909 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
