[gmx-users] Switch - Shift function electrostatics
Dear Gromacs-users, At the moment I have a question which regards the different electrostatic algorithms mentioned in the Gromacs-manual. I did some simulations and I tried three different electrostatic algorithms: Cut-off, Shift and PME. It is clear to me what Shift and PME means principally, but I ask myself which electrostatic algorithm is used by Cut-off. I know that Cut-off means a twin-range-electrostatics calculation with rlist as the first range and r_coulomb as the second range. Both are calculated within different frequencies. Is that true ? In my .log file it is mentioned that when using Cut-off a default value r_coulombswitch equal to 0 is set. It is the same in the case of r_vdwswitch. Does that mean that I use in this special case a switch function which switches at 0 nm which represents in this case a shift-function that shifts my electrostatic potential in such a way, that it decays to zero at r_coulomb? I think this means that I used a shift-function which is calculated within the twin-range-electrostatics scheme. Is this true? What disadvantages does the twin-range-electrostatics calculation have in comparison to PME? Is it true that PME could stabilize my system artificially? Now another question: Some people who perform molecular-dynamics calculations are stabilizing the dihedral angles in the forcefield to avoid 'unrealistical' fluctuations of their protein. Is this a reasonable way to simulate a protein? Is it also reasonable to heat up a crystal -.pdb structure, determined by x-ray, slowly from 50 K up to 300 K in a couple of steps? Does this have any purpose or is this just a non proven setup of my structure? Thanks for your good advice in advance! Best regards, Emanuel Peter Institute of Phys. and Theor. Chemistry 93053 Regensburg Germany ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Switch - Shift function electrostatics
Emanuel Peter wrote: Dear Gromacs-users, At the moment I have a question which regards the different electrostatic algorithms mentioned in the Gromacs-manual. I did some simulations and I tried three different electrostatic algorithms: Cut-off, Shift and PME. It is clear to me what Shift and PME means principally, but I ask myself which electrostatic algorithm is used by Cut-off. I know that Cut-off means a twin-range-electrostatics calculation with rlist as the first range and r_coulomb as the second range. Both are calculated within different frequencies. Is that true ? In my .log file it is mentioned that when using Cut-off a default value r_coulombswitch equal to 0 is set. It is the same in the case of r_vdwswitch. Does that mean that I use in this special case a switch function which switches at 0 nm which represents in this case a shift-function that shifts my electrostatic potential in such a way, that it decays to zero at r_coulomb? I think this means that I used a shift-function which is calculated within the twin-range-electrostatics scheme. Is this true? What disadvantages does the twin-range-electrostatics calculation have in comparison to PME? Is it true that PME could stabilize my system artificially? No, it is the other way around. Cut-offs are bad. Check: J. Chem. Theor. Comp. 2 pp. 1-11 (2006) Now another question: Some people who perform molecular-dynamics calculations are stabilizing the dihedral angles in the forcefield to avoid 'unrealistical' fluctuations of their protein. Is this a reasonable way to simulate a protein? No, you are changing the force field in that way. I haven't heard of this previously. Is it also reasonable to heat up a crystal -.pdb structure, determined by x-ray, slowly from 50 K up to 300 K in a couple of steps? Does this have any purpose or is this just a non proven setup of my structure? Thanks for your good advice in advance! Best regards, Emanuel Peter Institute of Phys. and Theor. Chemistry 93053 Regensburg Germany ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://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/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/mailing_lists/users.php
[gmx-users] Fes cluster
Hello The protein I am considering is a homodimer with two chains with a Fe4S4 cluster situated at the interface of two chains with connections with both the chains by cystein residues.I have generated the .itp file of the Fe4S4 cluster and .top of the protein with pdb2gmx command.The .top file is like this- -; ; File '1braf.top' was generated ; By user: root (0) ; On host: localhost.localdomain ; At date: Mon Jul 27 13:12:40 2009 ; ; This is your topology file ; I Have a Bad Case Of Purple Diarrhea (Urban Dance Squad) ; ; Include forcefield parameters #include ffoplsaa.itp ; Include chain topologies #include 1braf_A.itp #include 1braf_B.itp ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein_A 1 Protein_B 1 - I want to know how do I include the Fe4S4 .itp file in the topology file of the protein and How do I include the connect information of the protein and FES cluster. Regards Subarna Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8. http://downloads.yahoo.com/in/internetexplorer/___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] diffusion, g_msd and trestart
Dear all, I am trying to calculate diffusion coefficients for a system of (30) glycine molecules in a box with (1000) water. After running: g_msd -f md.xtc -s md.tpr -mol -n molindex.ndx I get a list of diffusion coefficients - one for each glycine molecule. I then calculate the average and the stdev: Average=1.004 Stdev=0.7661 My problem is that the stdev is very great! More than +/- 75% of the average value. Why is that? Also, what is the reason for the trestart=10 default value? Shouldn't it be better to have trestart=1, if my xtc file is saved every 1 ps? Thanks, Soren Enemark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] diffusion, g_msd and trestart
Enemark Soeren wrote: Dear all, I am trying to calculate diffusion coefficients for a system of (30) glycine molecules in a box with (1000) water. After running: g_msd –f md.xtc –s md.tpr –mol –n molindex.ndx I get a list of diffusion coefficients – one for each glycine molecule. I then calculate the average and the stdev: Average=1.004 Stdev=0.7661 My problem is that the stdev is very great! More than +/- 75% of the average value. Why is that? Short simulation most likely. Since these things are big it takes a long time to equilibrate. Also, what is the reason for the trestart=10 default value? Shouldn’t it be better to have trestart=1, if my xtc file is saved every 1 ps? No, because there is correlation in the system. Ideally you would take this time to be longer than the correlation time. You could try to find an estimate of that from the velocity autocorrelation. Thanks, Soren Enemark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://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/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/mailing_lists/users.php
Re: [gmx-users] Switch - Shift function electrostatics
David van der Spoel wrote: Emanuel Peter wrote: Dear Gromacs-users, At the moment I have a question which regards the different electrostatic algorithms mentioned in the Gromacs-manual. I did some simulations and I tried three different electrostatic algorithms: Cut-off, Shift and PME. It is clear to me what Shift and PME means principally, but I ask myself which electrostatic algorithm is used by Cut-off. I know that Cut-off means a twin-range-electrostatics calculation with rlist as the first range and r_coulomb as the second range. Both are calculated within different frequencies. Is that true ? In my .log file it is mentioned that when using Cut-off a default value r_coulombswitch equal to 0 is set. It is the same in the case of r_vdwswitch. Does that mean that I use in this special case a switch function which switches at 0 nm which represents in this case a shift-function that shifts my electrostatic potential in such a way, that it decays to zero at r_coulomb? I think this means that I used a shift-function which is calculated within the twin-range-electrostatics scheme. Is this true? What disadvantages does the twin-range-electrostatics calculation have in comparison to PME? Is it true that PME could stabilize my system artificially? No, it is the other way around. Cut-offs are bad. Check: J. Chem. Theor. Comp. 2 pp. 1-11 (2006) Now another question: Some people who perform molecular-dynamics calculations are stabilizing the dihedral angles in the forcefield to avoid 'unrealistical' fluctuations of their protein. Is this a reasonable way to simulate a protein? No, you are changing the force field in that way. I haven't heard of this previously. I guess you mean CMAP in CHARMM. You can check out the relevant paper, which also includes details about some other force fields. Ran. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] diffusion, g_msd and trestart
Date: Mon, 27 Jul 2009 11:12:16 +0200 From: sp...@xray.bmc.uu.se To: gmx-users@gromacs.org Subject: Re: [gmx-users] diffusion, g_msd and trestart Enemark Soeren wrote: Dear all, I am trying to calculate diffusion coefficients for a system of (30) glycine molecules in a box with (1000) water. After running: g_msd –f md.xtc –s md.tpr –mol –n molindex.ndx I get a list of diffusion coefficients – one for each glycine molecule. I then calculate the average and the stdev: Average=1.004 Stdev=0.7661 My problem is that the stdev is very great! More than +/- 75% of the average value. Why is that? Short simulation most likely. Since these things are big it takes a long time to equilibrate. Also it depends on what you expect. stdev is not a standard error estimate of the average. It is the spread around the average for all molecules. If all the msd values of the molecules are uncorrelated, which they might or might not be, the error estimate would be stdev/sqrt(30). Berk Also, what is the reason for the trestart=10 default value? Shouldn’t it be better to have trestart=1, if my xtc file is saved every 1 ps? No, because there is correlation in the system. Ideally you would take this time to be longer than the correlation time. You could try to find an estimate of that from the velocity autocorrelation. Thanks, Soren Enemark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. sp...@xray.bmc.uu.se sp...@gromacs.org http://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/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/mailing_lists/users.php _ What can you do with the new Windows Live? Find out http://www.microsoft.com/windows/windowslive/default.aspx___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] diffusion, g_msd and trestart
-Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: Monday, July 27, 2009 5:12 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] diffusion, g_msd and trestart Enemark Soeren wrote: Dear all, I am trying to calculate diffusion coefficients for a system of (30) glycine molecules in a box with (1000) water. After running: g_msd -f md.xtc -s md.tpr -mol -n molindex.ndx I get a list of diffusion coefficients - one for each glycine molecule. I then calculate the average and the stdev: Average=1.004 Stdev=0.7661 My problem is that the stdev is very great! More than +/- 75% of the average value. Why is that? Short simulation most likely. Since these things are big it takes a long time to equilibrate. Also, what is the reason for the trestart=10 default value? Shouldn't it be better to have trestart=1, if my xtc file is saved every 1 ps? No, because there is correlation in the system. Ideally you would take this time to be longer than the correlation time. You could try to find an estimate of that from the velocity autocorrelation. Thanks, Soren Enemark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://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/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Fes cluster
subarna thakur wrote: Hello The protein I am considering is a homodimer with two chains with a Fe4S4 cluster situated at the interface of two chains with connections with both the chains by cystein residues.I have generated the .itp file of the Fe4S4 cluster and .top of the protein with pdb2gmx command.The .top file is like this- -; ; File '1braf.top' was generated ; By user: root (0) ; On host: localhost.localdomain ; At date: Mon Jul 27 13:12:40 2009 ; ; This is your topology file ; I Have a Bad Case Of Purple Diarrhea (Urban Dance Squad) ; ; Include forcefield parameters #include ffoplsaa.itp ; Include chain topologies #include 1braf_A.itp #include 1braf_B.itp ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein_A 1 Protein_B 1 - I want to know how do I include the Fe4S4 .itp file in the topology file of the protein Do you have one? Does your force field have suitable parameters for this moiety? and How do I include the connect information of the protein and FES cluster. You will need to understand parts of chapter 5 of the manual thoroughly. Work on understanding a simple diglycine .top file first. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] diffusion, g_msd and trestart
-Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: Monday, July 27, 2009 5:12 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] diffusion, g_msd and trestart Enemark Soeren wrote: Dear all, I am trying to calculate diffusion coefficients for a system of (30) glycine molecules in a box with (1000) water. After running: g_msd -f md.xtc -s md.tpr -mol -n molindex.ndx I get a list of diffusion coefficients - one for each glycine molecule. I then calculate the average and the stdev: Average=1.004 Stdev=0.7661 My problem is that the stdev is very great! More than +/- 75% of the average value. Why is that? Short simulation most likely. Since these things are big it takes a long time to equilibrate. My simulation is 10ns long with xtc saved every 1 ps. I thought I had enough data!? How long is long time? Also, what is the reason for the trestart=10 default value? Shouldn't it be better to have trestart=1, if my xtc file is saved every 1 ps? No, because there is correlation in the system. Ideally you would take this time to be longer than the correlation time. You could try to find an estimate of that from the velocity autocorrelation. So, I must run velocity autocorrelation to find out when the velocities become uncorrelated, and then use this time as my trestart? Thanks, Soren Thanks, Soren Enemark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://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/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] diffusion, g_msd and trestart
Enemark Soeren wrote: -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of David van der Spoel Sent: Monday, July 27, 2009 5:12 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] diffusion, g_msd and trestart Enemark Soeren wrote: Dear all, I am trying to calculate diffusion coefficients for a system of (30) glycine molecules in a box with (1000) water. After running: g_msd -f md.xtc -s md.tpr -mol -n molindex.ndx I get a list of diffusion coefficients - one for each glycine molecule. I then calculate the average and the stdev: Average=1.004 Stdev=0.7661 My problem is that the stdev is very great! More than +/- 75% of the average value. Why is that? Short simulation most likely. Since these things are big it takes a long time to equilibrate. My simulation is 10ns long with xtc saved every 1 ps. I thought I had enough data!? How long is long time? Also, what is the reason for the trestart=10 default value? Shouldn't it be better to have trestart=1, if my xtc file is saved every 1 ps? No, because there is correlation in the system. Ideally you would take this time to be longer than the correlation time. You could try to find an estimate of that from the velocity autocorrelation. So, I must run velocity autocorrelation to find out when the velocities become uncorrelated, and then use this time as my trestart? . That would be a way (and the VACF also gives you a diffusion constant), you can also check the histogram visually for different run times. It seems that your solution does have a lot of amino acids, which probably means high viscosity and slow diffusion, and hence long time to equilibrate. Looking at the system MSD for all the Gly may also show you when the MSD curve becomes linear, you can use this as well as an estimate for the trestart. Thanks, Soren Thanks, Soren Enemark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.sesp...@gromacs.org http://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/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/mailing_lists/users.php
[gmx-users] GHrace install
hi alli'm facing alot of trouble in installing grace in my redhat machine. its always complaining about Motiff API. ive installed Lesstiff but even afetr that grace is not getting installed...i can't make out how to install it? is there any problem in the path? should i've to set path before grace install. i've gone through several pages about grace installation but with no effect.ac anyone pls tell me how to install Grace in Fedora of Redhat? thanking you all Shamik See the Web#39;s breaking stories, chosen by people like you. Check out Yahoo! Buzz. http://in.buzz.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] GHrace install
On Mon, 2009-07-27 at 16:48 +0530, Samik Bhattacharya wrote: hi alli'm facing alot of trouble in installing grace in my redhat machine. its always complaining about Motiff API.. ive installed Lesstiff but even afetr that grace is not getting installedi can't make out how to install it? is there any problem in the path? should i've to set path before grace install. i've gone through several pages about grace installation but with no effect.ac anyone pls tell me how to install Grace in Fedora of Redhat? You should avoid compiling software yourself, because that beats the whole idea of having a) a distribution that has ready-to-use software and b) a package management system that makes upgrades possible. In Fedora # yum -y install grace In RHEL, first enable the Fedora EPEL repository with # rpm -Uvh \ http://download.fedora.redhat.com/pub/epel/5/i386/epel-release-5-3.noarch.rpm and then install grace with # yum -y install grace Then you can run grace with $ xmgrace -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi -- ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] About exclusion of non-bonded interaction for pairs of energy groups
I see in the .top file generated by pdb2gmx: [ pairs ] ; aiaj functc0c1c2c3 The [ pairs ] directive accepts these four parameters c0, c1, c2 and c3. Do c2 and c3 parametrize electrostatic interactions? And what do they stand for respectively? Thanks! 2009/7/27 Mark Abraham mark.abra...@anu.edu.au Lee Soin wrote: My problem is actually as follows: Please describe in as full detail as reasonable the first time :-) I have three groups of atoms: A, B and C. Now I want to keep full interaction between A-B and A-C, but only retain the repulsive part of VDW interaction between B-C. I'm using the OPLS force field. It seems to me that the parameters for OPLS in the .itp files are specified for each atom, so is there any way to treat the interaction pairwise? Yes, use [ pairs ] directives to overrride the atomtype-based lookup. That will be tedious if there are many such atoms. Read parts of chapter 5. Probably, no force field was parameterized to reproduce whatever it is you're trying to observe. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- SUN Li Department of Physics Nanjing University, China ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] GHrace install
If you are using a vanilla RedHat system, the yum method will work. However, if you are using a prepackaged clustering environment (like ROCKS) you may break it. All you nee to know to install grace is the location of the headers and libraries for Lesstiff. You then supply them to grace as a part of the ./configure command and things should go smoothly. It's unfortunate the person who wrote and maintains grace is unwilling to provide this information to the people that want to use grace. However, you can't stop people from being jerks. That's why I'd prefer gromacs use a different plotting package like gnuplot. Jim -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Samik Bhattacharya Sent: Monday, July 27, 2009 7:19 AM To: Gromacs Subject: [gmx-users] GHrace install hi alli'm facing alot of trouble in installing grace in my redhat machine. its always complaining about Motiff API.. ive installed Lesstiff but even afetr that grace is not getting installedi can't make out how to install it? is there any problem in the path? should i've to set path before grace install. i've gone through several pages about grace installation but with no effect.ac anyone pls tell me how to install Grace in Fedora of Redhat? thanking you all Shamik Looking for local information? Find it on Yahoo! Local http://in.rd.yahoo.com/tagline_local_1/*http://in.local.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] POSITION-RESTRAIN
Dear gmxusers. I want to restrain the lipids in my system which contains protein,lipid and water. I make the restraint itp file by genpr then I added it in toplogy file. After doing grompp to make tpr file I get the following message: Fatal error: [ file posre_entirelipid1.itp, line 56 ]: Atom index (53) in position_restraints out of bounds (1-52) I found the similar error in the mailing list and they suggested probably the place of restraint itp file which was included in topology file is wrong. However, I tried several positions for restraint itp but I think it is not the solution. Do you have any other suggestion about this problem?? 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/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/mailing_lists/users.php
Re: [gmx-users] POSITION-RESTRAIN
Morteza Khabiri wrote: Dear gmxusers. I want to restrain the lipids in my system which contains protein,lipid and water. I make the restraint itp file by genpr then I added it in toplogy file. After doing grompp to make tpr file I get the following message: Fatal error: [ file posre_entirelipid1.itp, line 56 ]: Atom index (53) in position_restraints out of bounds (1-52) I found the similar error in the mailing list and they suggested probably the place of restraint itp file which was included in topology file is wrong. However, I tried several positions for restraint itp but I think it is not the solution. Do you have any other suggestion about this problem?? You're using a [ position_restraints ] directive that requires at least 53 atoms in a position where only 52 are defined. There are various explanations, including #including in the wrong place, or #including a wrong file. Look carefully at a correct example. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] GHrace install
jimkress_58 wrote: If you are using a vanilla RedHat system, the yum method will work. However, if you are using a prepackaged clustering environment (like ROCKS) you may break it. All you nee to know to install grace is the location of the headers and libraries for Lesstiff. You then supply them to grace as a part of the ./configure command and things should go smoothly. It's unfortunate the person who wrote and maintains grace is unwilling to provide this information to the people that want to use grace. However, you can't stop people from being jerks. That's why I'd prefer gromacs use a different plotting package like gnuplot. Agreed, although it is straightforward to use gnuplot anyway. See http://oldwiki.gromacs.org/index.php/Graphing_Data Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] About exclusion of non-bonded interaction for pairs of energy groups
Lee Soin wrote: I see in the .top file generated by pdb2gmx: [ pairs ] ; aiaj functc0c1c2c3 The [ pairs ] directive accepts these four parameters c0, c1, c2 and c3. Do c2 and c3 parametrize electrostatic interactions? And what do they stand for respectively? Thanks! No, they're two pairs of VDW parameters, one pair each for two possible states for a free-energy calculation. The tables in chapter 5 imply this, but it is not at all obvious to a newcomer. Yes, use [ pairs ] directives to overrride the atomtype-based lookup. That will be tedious if there are many such atoms. Read parts of chapter 5. You should still do this. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] About exclusion of non-bonded interaction for pairs of energy groups
So there is no place to specify electrostatic interactions for pair interactions? 2009/7/27 Mark Abraham mark.abra...@anu.edu.au Lee Soin wrote: I see in the .top file generated by pdb2gmx: [ pairs ] ; aiaj functc0c1c2c3 The [ pairs ] directive accepts these four parameters c0, c1, c2 and c3. Do c2 and c3 parametrize electrostatic interactions? And what do they stand for respectively? Thanks! No, they're two pairs of VDW parameters, one pair each for two possible states for a free-energy calculation. The tables in chapter 5 imply this, but it is not at all obvious to a newcomer. Yes, use [ pairs ] directives to overrride the atomtype-based lookup. That will be tedious if there are many such atoms. Read parts of chapter 5. You should still do this. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- SUN Li Department of Physics Nanjing University, China ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] doubt - how to fix all atoms ?
Please I need to fix all atoms of a proetin and I need to calculte the initital enregy without to exceute septs of dynsmics. How can i do this ? Thanks best regrads luis Scott 2009/7/27 gmx-users-requ...@gromacs.org Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. GHrace install (Samik Bhattacharya) 2. Re: GHrace install (Jussi Lehtola) 3. Re: About exclusion of non-bonded interaction for pairs of energy groups (Lee Soin) 4. RE: GHrace install (jimkress_58) 5. POSITION-RESTRAIN (Morteza Khabiri) 6. Re: POSITION-RESTRAIN (Mark Abraham) 7. Re: GHrace install (Mark Abraham) 8. Re: About exclusion of non-bonded interaction for pairs of energy groups (Mark Abraham) -- Message: 1 Date: Mon, 27 Jul 2009 16:48:57 +0530 (IST) From: Samik Bhattacharya samikb...@yahoo.co.in Subject: [gmx-users] GHrace install To: Gromacs gmx-users@gromacs.org Message-ID: 224940.85000...@web95411.mail.in2.yahoo.com Content-Type: text/plain; charset=iso-8859-1 hi alli'm facing alot of trouble in installing grace in my redhat machine. its always complaining about Motiff API. ive installed Lesstiff but even afetr that grace is not getting installed...i can't make out how to install it? is there any problem in the path? should i've to set path before grace install. i've gone through several pages about grace installation but with no effect.ac anyone pls tell me how to install Grace in Fedora of Redhat? thanking you all Shamik See the Web#39;s breaking stories, chosen by people like you. Check out Yahoo! Buzz. http://in.buzz.yahoo.com/ -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20090727/a13124cb/attachment-0001.html -- Message: 2 Date: Mon, 27 Jul 2009 14:28:31 +0300 From: Jussi Lehtola jussi.leht...@helsinki.fi Subject: Re: [gmx-users] GHrace install To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 1248694111.5152.2.ca...@hawking.theorphys.helsinki.fi Content-Type: text/plain On Mon, 2009-07-27 at 16:48 +0530, Samik Bhattacharya wrote: hi alli'm facing alot of trouble in installing grace in my redhat machine. its always complaining about Motiff API.. ive installed Lesstiff but even afetr that grace is not getting installedi can't make out how to install it? is there any problem in the path? should i've to set path before grace install. i've gone through several pages about grace installation but with no effect.ac anyone pls tell me how to install Grace in Fedora of Redhat? You should avoid compiling software yourself, because that beats the whole idea of having a) a distribution that has ready-to-use software and b) a package management system that makes upgrades possible. In Fedora # yum -y install grace In RHEL, first enable the Fedora EPEL repository with # rpm -Uvh \ http://download.fedora.redhat.com/pub/epel/5/i386/epel-release-5-3.noarch.rpm and then install grace with # yum -y install grace Then you can run grace with $ xmgrace -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi -- -- Message: 3 Date: Mon, 27 Jul 2009 21:56:08 +0800 From: Lee Soin nomad...@gmail.com Subject: Re: [gmx-users] About exclusion of non-bonded interaction for pairs of energy groups To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: e2838e4e0907270656n4be59b34w4488a610fefd4...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 I see in the .top file generated by pdb2gmx: [ pairs ] ; aiaj functc0c1c2c3 The [ pairs ] directive accepts these four parameters c0, c1, c2 and c3. Do c2 and c3 parametrize electrostatic interactions? And what do they stand for respectively? Thanks! 2009/7/27 Mark Abraham mark.abra...@anu.edu.au Lee Soin wrote: My problem is actually as follows: Please describe in as full detail as reasonable the first time :-) I have
[gmx-users] Huge acceleration needed to reproduce results!
Hello users, I am trying to reproduce a calculation that I carried out in DL_POLY. It is to calculate the transport diffusion coefficient for CH4 in a frozen mesoporous silica. In DL_POLY I used an external force of 0.1 kJ mol-1 A-1. (0.1 KJ per mole per angstrom). This equates to 10 dl_poly internal units which I add in this way at each timestep; Fsum = Fsum + Fex In Gromacs, I want to apply the same force as I used in DL_POLY so I calculated the required acceleration using F=ma. Where I took the mass to be the mass of one molecule of methane (16 a.m.u). The final value for acceleration that I came up with (which corresponds to a force of 0.1kj mol-1 A-1 on each molecule) was 0.0625 nm ps-2. The first hiccup was when I used this value, the MSD was negative (though linear in the negative region of the graph). I assumed that this had something to do with the orientation of the unit cell and tried applying 0.0 0.0 -0.0625. The plot then looked much better. The problem is when I calculate the Mean displacement of the CH4 molecules. (I do this using a slightly altered version of the g_msd code). The Mean displacement from gromacs is very different to that which I calculate using DL_POLY, Gromacs gives 95.0, dl_poly 21347.0. The MSD however (where I don?t add an acceleration are similar) so the problem lies with the force I am adding. To test that it wasn?t some bug in my code to calculate the Mean displacement, I also looked at how the acceleration/force altered the MSD in DL_POLY and gromacs. In DL_POLY, adding an external force of 0.1kj mol-1 A-1 would change the MSD of methane by 3 orders of magnitude compared to a run with no force added. My equivalent acceleration of -0.0625 in gromacs, in comparison, barely changes the MSD from that of a run with no acceleration added. In fact it takes an acceleration of -200 in the z direction to cause such a difference in the Ds coefficients between runs with and without acceleration. Does anyone have any idea what is going on here? An acceleration of 200 ps nm-2 surely is not reasonable is it?. It seems very large compared to the example in the manual of 0.1. This would then imply that my back of the envelope calculation for relating force and acceleration is wrong. Am I missing something? I?m quite sure that the force I am adding in DL_POLY is equivalent to 0.1 kJ mol-1 A-1 so why are my methane molecules moving so much less in gromacs in response to the equivalent acceleration? Also I noticed that although in the .mdp file I specify: ; Non-equilibrium MD stuff acc-grps = CH4 accelerate = 0.0 0.0 -200.00 In the md.log file I get the following output acc:0 0-154.549 0 0 45.4514 Can someone clarify what this means? Any advice/comments appreciated -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] OPLS-AA: LJ problem? Atoms overlapping...
Hello, I'm using ffoplsaa with a new atom type (Ag) that I've included in the .atp file, LJ parameters I've specified in the nb file. My system topology I've written by hand in an itp file. The problem is that after any kind of run the molecule penetrates the metal surface! This shouldn't be happening. I had been using g45a3 quite successfully for the same system and everything was working fine. Do I need to do something different/special with oplsaa? What am I missing? Advice appreciated, Chris Rowan ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] LINCS warnings with timestep of 5 fs (but not 4 fs)
Hello, I am recently experimenting with a 5 fs timestep using virtual hydrogens and LINCS. I am getting sporadic LINCS warnings, although the system appears stable and does not blow up during the 100ns in which I get such warnings. If I reduce the timestep to 4 fs from 5 fs (and increase nstlist to 5 from 4), then I do not get any such LINCS warnings. It occurs to me that in a larger timestep there could be a larger rotation and that this warning may be entirely benign. I am not sure about that, however, and would welcome any advice here, especially on the way that the 30 deg threshold for a warning message is derived. Thank you, Chris. Here is a snippit from my stderr output during a run: ... Step 1387503, time 6937.51 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000156, max 0.001672 (between atoms 17832 and 17831) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 17832 17831 30.90.0946 0.0947 0.0945 Step 1387503, time 6937.51 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000139, max 0.001582 (between atoms 17832 and 17828) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 17832 17831 31.10.0946 0.0946 0.0945 Step 3601434, time 18007.2 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.35, max 0.000308 (between atoms 18168 and 18165) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 18168 18167 30.10.0945 0.0945 0.0945 Step 4391822, time 21959.1 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000121, max 0.002041 (between atoms 14190 and 14189) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 14190 14189 30.50.0945 0.0947 0.0945 Step 4796357, time 23981.8 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000128, max 0.001443 (between atoms 15532 and 15531) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 15532 15531 31.50.0945 0.0946 0.0945 Step 4796357, time 23981.8 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000111, max 0.001185 (between atoms 15532 and 15531) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 15532 15531 31.80.0945 0.0946 0.0945 Step 4796358, time 23981.8 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000221, max 0.002694 (between atoms 15532 and 15531) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 15532 15531 34.00.0946 0.0948 0.0945 ... With a .mdp file that looks like this: integrator = sd nsteps = 2000 tinit = 0 dt = 0.005 comm_mode = linear nstcomm = 4 comm_grps = System nstxout = 2000 nstvout = 2000 nstfout = 2000 nstlog = 0 nstlist = 4 nstenergy = 2 nstxtcout = 2 ns_type = grid pbc = xyz coulombtype = PME rcoulomb= 0.9 fourierspacing = 0.12 pme_order = 4 vdwtype = cut-off rvdw_switch = 0 rvdw= 1.4 rlist = 0.9 DispCorr= no Pcoupl = Berendsen pcoupltype = semiisotropic compressibility = 4.5e-5 4.5e-5 ref_p = 1. 1. tau_p = 4.04.0 tcoupl = Berendsen tc_grps = System tau_t = 1.0 ref_t = 310. ld-seed = -1 annealing = no gen_vel = yes unconstrained-start = no gen_temp= 310. gen_seed= -1 constraints = all-bonds constraint_algorithm= lincs lincs-iter = 1 lincs-order = 6 ;;;EOF ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Huge acceleration needed to reproduce results!
Gromacs uses nm as the unit of distance. Did you account for that? If so, please add some .mdp file snippits and any other relevant files so that we can see directly what you are doing. Chris. --- original message --- Hello users, I am trying to reproduce a calculation that I carried out in DL_POLY. It is to calculate the transport diffusion coefficient for CH4 in a frozen mesoporous silica. In DL_POLY I used an external force of 0.1 kJ mol-1 A-1. (0.1 KJ per mole per angstrom). This equates to 10 dl_poly internal units which I add in this way at each timestep; Fsum = Fsum + Fex In Gromacs, I want to apply the same force as I used in DL_POLY so I calculated the required acceleration using F=ma. Where I took the mass to be the mass of one molecule of methane (16 a.m.u). The final value for acceleration that I came up with (which corresponds to a force of 0.1kj mol-1 A-1 on each molecule) was 0.0625 nm ps-2. The first hiccup was when I used this value, the MSD was negative (though linear in the negative region of the graph). I assumed that this had something to do with the orientation of the unit cell and tried applying 0.0 0.0 -0.0625. The plot then looked much better. The problem is when I calculate the Mean displacement of the CH4 molecules. (I do this using a slightly altered version of the g_msd code). The Mean displacement from gromacs is very different to that which I calculate using DL_POLY, Gromacs gives 95.0, dl_poly 21347.0. The MSD however (where I don?t add an acceleration are similar) so the problem lies with the force I am adding. To test that it wasn?t some bug in my code to calculate the Mean displacement, I also looked at how the acceleration/force altered the MSD in DL_POLY and gromacs. In DL_POLY, adding an external force of 0.1kj mol-1 A-1 would change the MSD of methane by 3 orders of magnitude compared to a run with no force added. My equivalent acceleration of -0.0625 in gromacs, in comparison, barely changes the MSD from that of a run with no acceleration added. In fact it takes an acceleration of -200 in the z direction to cause such a difference in the Ds coefficients between runs with and without acceleration. Does anyone have any idea what is going on here? An acceleration of 200 ps nm-2 surely is not reasonable is it?. It seems very large compared to the example in the manual of 0.1. This would then imply that my back of the envelope calculation for relating force and acceleration is wrong. Am I missing something? I?m quite sure that the force I am adding in DL_POLY is equivalent to 0.1 kJ mol-1 A-1 so why are my methane molecules moving so much less in gromacs in response to the equivalent acceleration? Also I noticed that although in the .mdp file I specify: ; Non-equilibrium MD stuff acc-grps = CH4 accelerate = 0.0 0.0 -200.00 In the md.log file I get the following output acc:0 0-154.549 0 0 45.4514 Can someone clarify what this means? Any advice/comments appreciated -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] OPLS-AA: LJ problem? Atoms overlapping...
Sounds like your topology/forcefield is incorrect or incomplete. Does your log file from mdrun or the stderr/stdout from grompp/mdrun indicate that you don't have any LJ parameters for some atom types? Try a gmxdump on your .tpr file and inspect the LJ parameters by hand. Are there any zero's where you should have numbers? Perhaps you mixed up some atom types (e.g. with capitilization) or you simply didn't add the necessary values. Chris. -- original message -- Hello, I'm using ffoplsaa with a new atom type (Ag) that I've included in the .atp file, LJ parameters I've specified in the nb file. My system topology I've written by hand in an itp file. The problem is that after any kind of run the molecule penetrates the metal surface! This shouldn't be happening. I had been using g45a3 quite successfully for the same system and everything was working fine. Do I need to do something different/special with oplsaa? What am I missing? Advice appreciated, Chris Rowan ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: OPLS-AA: LJ problem? Atoms overlapping...
Hi Chris, I've done a gmxdump and there aren't any zeros for any of the LJ values. No capital letter problems either. Chris Rowan Mon, 27 Jul 2009 12:30:54 -0700 Sounds like your topology/forcefield is incorrect or incomplete. Does your log file from mdrun or the stderr/stdout from grompp/mdrun indicate that you don't have any LJ parameters for some atom types? Try a gmxdump on your .tpr file and inspect the LJ parameters by hand. Are there any zero's where you should have numbers? Perhaps you mixed up some atom types (e.g. with capitilization) or you simply didn't add the necessary values. Chris. -- original message -- Hello, I'm using ffoplsaa with a new atom type (Ag) that I've included in the .atp file, LJ parameters I've specified in the nb file. My system topology I've written by hand in an itp file. The problem is that after any kind of run the molecule penetrates the metal surface! This shouldn't be happening. I had been using g45a3 quite successfully for the same system and everything was working fine. Do I need to do something different/special with oplsaa? What am I missing? Advice appreciated, Chris Rowan ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: OPLS-AA: LJ problem? Atoms overlapping...
what's your minimum atomic distance achieved between Ag and your other molecule (g_mindist)? If it's 0.09 nm then you definitely do have some error in your setup. For proof of that, generate a new system that is identical to yours but this time use only standard OPLS atom-types and see the problem likely disapear. If not, then the penetration is just because it goes between atoms and in this case, while you may not have an error per se, you should check your parameters and possibly your assumptions about what should be happening. Also, it's very difficult to offer advice when you describe a problem without showing some of the important files directly. Can you paste the changes to your .itp files and the ffopsaa.itp main file that you are using? Hi Chris, -- original message -- I've done a gmxdump and there aren't any zeros for any of the LJ values. No capital letter problems either. Chris Rowan Mon, 27 Jul 2009 12:30:54 -0700 Sounds like your topology/forcefield is incorrect or incomplete. Does your log file from mdrun or the stderr/stdout from grompp/mdrun indicate that you don't have any LJ parameters for some atom types? Try a gmxdump on your .tpr file and inspect the LJ parameters by hand. Are there any zero's where you should have numbers? Perhaps you mixed up some atom types (e.g. with capitilization) or you simply didn't add the necessary values. Chris. -- original message -- Hello, I'm using ffoplsaa with a new atom type (Ag) that I've included in the .atp file, LJ parameters I've specified in the nb file. My system topology I've written by hand in an itp file. The problem is that after any kind of run the molecule penetrates the metal surface! This shouldn't be happening. I had been using g45a3 quite successfully for the same system and everything was working fine. Do I need to do something different/special with oplsaa? What am I missing? ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: OPLS-AA: LJ problem? Atoms overlapping...
Here are some more details: My cg minimized structure has a distance of 0.3 Angstroms between Ag and another atom of another molecule. Changing all my Ag to hydrogens and running a cg still gives a distance of 0.3 Angstroms. I could also add that each Ag belongs to its own charge group, so they should be felt. I've tried starting with a different geometry as well with similar results. Files were modified as follows: ffoplsaa.atp I added Silver as: AG107.87 ffoplsaanb.itp I've added: AG AG 47 107.8700 0.000 A2.80455e-01 1.73304e-01 Chris Rowan ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Segmentation Fault (Address not mapped)
Hi Justin, With regard to your comment about using other force fields for my simulation of graphene surrounded by ammonia gas, are referring to the force fields for both graphene and ammonia or only to the force field for graphene? I reviewed my selection of the force field parameters for graphene and see that I selected the parameters from the paper by Cornell et al. since a paper on deformation of carbon nanotubes (A structural mechanics approach for the analysis of carbon nanotubes by Chunyu Li, Tsu-Wei Chou in International Journal of Solids and Structures 40 (2003) 2487–2499) used parameters from the paper by Cornell et al. Is this sufficient to justify the use of these parameters? I also thought that graphene and ammonia would be considered organic since they are comprised of carbon, nitrogen, and hydrogen, which are all common elements found in organic matter. With regard to the parameters for ammonia, is it acceptable to use the parameters from the paper by Cornell et al. or do I need to find papers specifically related to ammonia gas molecular dynamics simulations? With regard to dihedral selection, I looked at the .top file and see that the function type is listed as 3 in the dihedrals section, which I believe indicates that my simulation is using a Ryckaert-Bellemans function. It appears to me that if I am using the OPLS force field that the Ryckaert-Bellemans dihedral type is automatically selected. I do see in the ffoplsaabon.itp file that there is an improper dihedral definition which think I could potentially use in my simulation improper_Z_CA_X_Y, but how do I cause my simulation to use this definition? Do I need to add the following line to my .top file? #define improper_Z_CA_X_Y Further, I thought that I could simply modify the appropriate lines of the ffoplsaanb.itp and ffoplsaabon.itp to enter in the parameters found in the paper by Cornell et al. so that they will be used in my simulation. Am I correct in my assumption? Thanks again for your help. Darrell Date: Fri, 17 Jul 2009 22:11:07 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Segmentation Fault (Address not mapped) To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4a612f3b.7060...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed darre...@ece.ubc.ca wrote: Hi Justin, I am using the ffoplsaabon.itp parameters for: bonds (CA-CA, CA-CT, CA-HA, CT-HC, H-N3) angles (CA-CA-CA, CA-CA-HA, CA-CT-HC, H-N3-H) dihedrals (X-CA-CA-X, X-CA-CT-X) I am using the ffolpsaanb.itp VdW parameters for H N3 And I am using the VdW parameters found in the paper A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules for CA, HA, CT, HC doing the conversion from Angstroms (paper units) to nm (ffoplsaanb.itp units) for sigma and from kcal/mol (paper units) to kJ/mol (ffoplsaanb.itp units) for epsilon. The converted parameters for sigma were different by only +/-2% to +/-8% from the values in ffoplsaanb.itp, but the converted parameters for epsilon were different by +/-23% to +/-66% from the values in ffoplsaanb.itp. Is this a valid paper to use for selection of parameters? If memory serves, that paper is the derivation by Cornell, et al. for the AMBER94 parameter set, so no, you are not going to find those same parameters in ffoplsaanb.itp. Furthermore, the title of the paper indicates that the parameters are for proteins, nucleic acids, and organic molecules. Has anyone else in the literature used these parameters for graphene lattices? I would suggest using a force field that others have used for such solid materials, like nanotubes or other graphene surfaces. Otherwise, you will have to somehow demonstrate that a force field designed for use with condensed phase biomolecules is applicable to your gas-phase graphene lattice. The graphene lattice is only vibrating slightly and looks like a bunch of travelling waves. I believe I am using proper dihedrals and not improper dihedrals in my model. It would seem. Consider if impropers might be necessary to keep your planar groups planar. That's what they are there for. Since the graphene structure will be connected to electrodes at both ends and will be mounted above a substrate, I assume the atoms in the structure are not completely free and thus I need to model them being restricted in their movement. Maybe position restraints are more appropriate than freezing to model such a situation. I do not see anything in the trajectory that provides clues as to what might be causing the segmentation fault. Then it will be very difficult to get any more remote help ;) If you consistently get the crash between step 20,000 and 30,000, then perhaps split your simulation into shorter sections, and during the time when you expect the crash to occur, set nstxtcout = (some small value, like 1 or 10) to obtain the most
[gmx-users] Fwd: fixed 3.3.3?
All, Is there any chance of getting an official patch released for 3.3.3 that fixes the mdrun bug I have pointed out in the past, or perhaps an official, super-minor point release? I can provide the patch -- I'd just like it posted somewhere official. The reason for this is that I'm trying to get some supercomputing folks to install the software system-wide, and they are reluctant to do it for my own custom code but I can probably get them to do it if it's an official patch. I realize the developers are probably less than enthusiastic about doing anything further with 3.3.x. But I've got some free energy projects going in my own group and with some others that use tools that work only with 3.3.x, not 4.0.x. Additionally, we are reluctant to switch to 4.0.x without doing a lot of testing of the free energy components (which is yet another reason why we need a patched 3.3.x to compare to), given the number of times we were burned by free energy bugs in 3.3.x. Thanks for your help. David Mobley, Ph.D. Assistant Professor of Chemistry University of New Orleans New Orleans, LA 70148 dlmob...@uno.edu Office 504-280-6445 Fax 504-280-6860 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Segmentation Fault (Address not mapped)
Darrell Koskinen wrote: Hi Justin, With regard to your comment about using other force fields for my simulation of graphene surrounded by ammonia gas, are referring to the force fields for both graphene and ammonia or only to the force field for graphene? The force field should be one in the same. The parameters should be suitably derived using the same scheme as the original work. I reviewed my selection of the force field parameters for graphene and see that I selected the parameters from the paper by Cornell et al. since a paper on deformation of carbon nanotubes (A structural mechanics approach for the analysis of carbon nanotubes by Chunyu Li, Tsu-Wei Chou in International Journal of Solids and Structures 40 (2003) 2487–2499) used parameters from the paper by Cornell et al. Is this sufficient to justify the use of these parameters? I also thought that graphene and ammonia would be considered organic since they are comprised of carbon, nitrogen, and hydrogen, which are all common elements found in organic matter. If you feel that precedent is sufficient, then I guess go ahead. But realize that the paper by Cornell et al. refers to parameters suitable for simulations of proteins and nucleic acids, as well as a few organic functional groups. Parameterization was based on peptide backbone geometry, as well as other parameters, likely none of which involved graphene and gaseous ammonia (they were doing liquid simulations). With regard to the parameters for ammonia, is it acceptable to use the parameters from the paper by Cornell et al. or do I need to find papers specifically related to ammonia gas molecular dynamics simulations? I would seriously consider finding parameters (if they exist) that have been derived for use with gas-phase simulations. With regard to dihedral selection, I looked at the .top file and see that the function type is listed as 3 in the dihedrals section, which I believe indicates that my simulation is using a Ryckaert-Bellemans function. It appears to me that if I am using the OPLS force field that the Ryckaert-Bellemans dihedral type is automatically selected. I do see in the ffoplsaabon.itp file that there is an improper dihedral definition which think I could potentially use in my simulation improper_Z_CA_X_Y, but how do I cause my simulation to use this definition? Do I need to add the following line to my .top file? #define improper_Z_CA_X_Y No, you would have to use a special dihedrals section, that specifies the four atoms involved (function type 1), followed by the specification of that particular improper (improper_Z_CA_X_Y). See the manual for more details, and/or generate a topology for a protein with pdb2gmx with OPLS-AA and see how they're defined. Further, I thought that I could simply modify the appropriate lines of the ffoplsaanb.itp and ffoplsaabon.itp to enter in the parameters found in the paper by Cornell et al. so that they will be used in my simulation. Am I correct in my assumption? Modifying ffoplsaa files to parameters that are not OPLS-AA is probably a bad choice. If you're dead-set on using these parameters, download the ffamber ports and use the ffamber94 force field, not some Frankensteined-OPLS. Besides, all of the parameters in the Cornell paper are in kcal/mol/A^2, which will require conversion to Gromacs standard units. If you've printed them directly in your previous attempts, I can guarantee you you're not getting the values you think you are. -Justin Thanks again for your help. Darrell Date: Fri, 17 Jul 2009 22:11:07 -0400 From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Segmentation Fault (Address not mapped) To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4a612f3b.7060...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed darre...@ece.ubc.ca wrote: Hi Justin, I am using the ffoplsaabon.itp parameters for: bonds (CA-CA, CA-CT, CA-HA, CT-HC, H-N3) angles (CA-CA-CA, CA-CA-HA, CA-CT-HC, H-N3-H) dihedrals (X-CA-CA-X, X-CA-CT-X) I am using the ffolpsaanb.itp VdW parameters for H N3 And I am using the VdW parameters found in the paper A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules for CA, HA, CT, HC doing the conversion from Angstroms (paper units) to nm (ffoplsaanb.itp units) for sigma and from kcal/mol (paper units) to kJ/mol (ffoplsaanb.itp units) for epsilon. The converted parameters for sigma were different by only +/-2% to +/-8% from the values in ffoplsaanb.itp, but the converted parameters for epsilon were different by +/-23% to +/-66% from the values in ffoplsaanb.itp. Is this a valid paper to use for selection of parameters? If memory serves, that paper is the derivation by Cornell, et al. for the AMBER94 parameter set, so no, you are not going to find those same parameters in
[gmx-users] Re: NH3 / graphene
Darrell; If memory serves, there was a paper in the late '80s of a simulation of monolayer NH3/graphite by William Steele. It reproduced the lattice dimensions of our experiments, but seemed to over-estimate the corrugation in the binding energy relative to our diffraction experiments. Hope this helps, Paul Rowntree Dept. of Chemistry, University of Guelph Darrell Koskinen wrote: Hi Justin, With regard to your comment about using other force fields for my simulation of graphene surrounded by ammonia gas, are referring to the force fields for both graphene and ammonia or only to the force field for graphene? The force field should be one in the same. The parameters should be suitably derived using the same scheme as the original work. I reviewed my selection of the force field parameters for graphene and see that I selected the parameters from the paper by Cornell et al. since a paper on deformation of carbon nanotubes (A structural mechanics approach for the analysis of carbon nanotubes by Chunyu Li, Tsu-Wei Chou in International Journal of Solids and Structures 40 (2003) 2487�2499) used parameters from the paper by Cornell et al. Is this sufficient to justify the use of these parameters? I also thought that graphene and ammonia would be considered organic since they are comprised of carbon, nitrogen, and hydrogen, which are all common elements found in organic matter. If you feel that precedent is sufficient, then I guess go ahead. But realize that the paper by Cornell et al. refers to parameters suitable for simulations of proteins and nucleic acids, as well as a few organic functional groups. Parameterization was based on peptide backbone geometry, as well as other parameters, likely none of which involved graphene and gaseous ammonia (they were doing liquid simulations). With regard to the parameters for ammonia, is it acceptable to use the parameters from the paper by Cornell et al. or do I need to find papers specifically related to ammonia gas molecular dynamics simulations? I would seriously consider finding parameters (if they exist) that have been derived for use with gas-phase simulations. With regard to dihedral selection, I looked at the .top file and see that the function type is listed as 3 in the dihedrals section, which I believe indicates that my simulation is using a Ryckaert-Bellemans function. It appears to me that if I am using the OPLS force field that the Ryckaert-Bellemans dihedral type is automatically selected. I do see in the ffoplsaabon.itp file that there is an improper dihedral definition which think I could potentially use in my simulation improper_Z_CA_X_Y, but how do I cause my simulation to use this definition? Do I need to add the following line to my .top file? #define improper_Z_CA_X_Y No, you would have to use a special dihedrals section, that specifies the four atoms involved (function type 1), followed by the specification of that particular improper (improper_Z_CA_X_Y). See the manual for more details, and/or generate a topology for a protein with pdb2gmx with OPLS-AA and see how they're defined. Further, I thought that I could simply modify the appropriate lines of the ffoplsaanb.itp and ffoplsaabon.itp to enter in the parameters found in the paper by Cornell et al. so that they will be used in my simulation. Am I correct in my assumption? Modifying ffoplsaa files to parameters that are not OPLS-AA is probably a bad choice. If you're dead-set on using these parameters, download the ffamber ports and use the ffamber94 force field, not some Frankensteined-OPLS. Besides, all of the parameters in the Cornell paper are in kcal/mol/A^2, which will require conversion to Gromacs standard units. If you've printed them directly in your previous attempts, I can guarantee you you're not getting the values you think you are. -Justin Thanks again for your help. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Re: OPLS-AA: LJ problem? Atoms overlapping...
What hydrogen did you use? Without substantially more cut and paste on your end I am in the dark and can't help very much. On the side, I'll mention that your sigma, and especially your epsilon, looks very low here. I'm no gold expert though, and I am just pointing that out even though that is not likely to be the source of your problem. AG AG 47 107.8700 0.000 A2.80455e-01 1.73304e-01 I believe that I also asked for your ffoplsaa.itp file. Is your comb-rule set correctly? Are you sure that you are getting the ffoplsaanb.itp inclusion that you intend? For example, I use ... [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 3 yes 0.5 0.5 #include /home/cneale/gromacs/oplspope.top/ffoplsaanb.itp #include /home/cneale/gromacs/oplspope.top/ffoplsaabon.itp ... in my modified ffoplsaa.itp where the directories are hard coded to ensure that I get what I expect (rather than some unmodified ffoplsaanb.itp from $GMXLIB) I can't think of anything else. You need to send a lot more data to this list. I am currently working under the assumption that you have made a mistake somewhere, and thus also assume that one of your descriptive statements is either misleading or incorrect -- hence the need for seeing the actual files (on list please). If, on the other hand, you are sure that you have done everything correctly then I can't help. Good luck, Chris -- original message -- Here are some more details: My cg minimized structure has a distance of 0.3 Angstroms between Ag and another atom of another molecule. Changing all my Ag to hydrogens and running a cg still gives a distance of 0.3 Angstroms. I could also add that each Ag belongs to its own charge group, so they should be felt. I've tried starting with a different geometry as well with similar results. Files were modified as follows: ffoplsaa.atp I added Silver as: AG107.87 ffoplsaanb.itp I've added: AG AG 47 107.8700 0.000 A2.80455e-01 1.73304e-01 Chris Rowan ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] POSITION-RESTRAIN
--- On Mon, 27/7/09, Morteza Khabiri khab...@greentech.cz wrote: From: Morteza Khabiri khab...@greentech.cz Subject: [gmx-users] POSITION-RESTRAIN To: gmx-users@gromacs.org Date: Monday, 27 July, 2009, 7:35 PM Dear gmxusers. I want to restrain the lipids in my system which contains protein,lipid and water. I make the restraint itp file by genpr then I added it in toplogy file. After doing grompp to make tpr file I get the following message: Fatal error: [ file posre_entirelipid1.itp, line 56 ]: Atom index (53) in position_restraints out of bounds (1-52) I found the similar error in the mailing list and they suggested probably the place of restraint itp file which was included in topology file is wrong. However, I tried several positions for restraint itp but I think it is not the solution. Do you have any other suggestion about this problem?? Thanks hi, Mark is right.the position restrain.itp file should be included in your topology file in the proper place otherwise the problem would continue. place the .itp file after the section ; Include Position restraint file #ifdef POSRES #include posre.itp #endif best wishes Shamik ___ 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/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/mailing_lists/users.php Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] POSITION-RESTRAIN
Sounds to me like you have a 52 atom lipid and have a posre.itp file with more than 52 atoms (or referencing atom numbers greater than 52). What one usually does is has a somelipid.itp file that, upon some .mdp define, includes a someposre.itp file that looks like this: [ position_restraints ] ; atom type fx fy fz 8 1 1000 1000 1000 where for a 52 atom lipid I assume that you are using Berger lipids and atom 8 is the Phosphorous. On the other hand, if you have a .itp file that specifies N-lipids, then you would need lots of [ position_restraints ]. Caution: this is not the best way to go as you will need to modify many files every time you set up a new bilayer. As an analogy, look at the way that the SOL (tip4p in this case) posre is applied in a generic .top out of pdb2gmx: #include tip4p.itp #ifdef POSRES_SOL ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif where it is a per-molecule atomic index definition such that atom 1 is applied to each solvent molecule. If you are still unclear, I strongly suspect that there is a gmx manual description of all of this, and suggest that you read the manual in search of it. If you can't find one then probably you should complain back to this list about the absence of a section that should definitely be there. Chris. -- original message -- From: Morteza Khabiri khabiri at greentech.cz Subject: [gmx-users] POSITION-RESTRAIN To: gmx-users at gromacs.org Date: Monday, 27 July, 2009, 7:35 PM Dear gmxusers. I want to restrain the lipids in my system which contains protein,lipid and water. I make the restraint itp file by genpr then I added it in toplogy file. After doing grompp to make tpr file I get the following message: Fatal error: [ file posre_entirelipid1.itp, line 56 ]: Atom index (53) in position_restraints out of bounds (1-52) I found the similar error in the mailing list and they suggested probably the place of restraint itp file which was included in topology file is wrong. However, I tried several positions for restraint itp but I think it is not the solution. Do you have any other suggestion about this problem?? Thanks hi, Mark is right.the position restrain.itp file should be included in your topology file in the proper place otherwise the problem would continue. place the .itp file after the section ; Include Position restraint file #ifdef POSRES #include posre.itp #endif best wishes Shamik ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] About exclusion of non-bonded interaction for pairs of energy groups
Lee Soin wrote: So there is no place to specify electrostatic interactions for pair interactions? No. The charges are specified in the [ atoms ] directive. Read the example in chapter 5. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] doubt - how to fix all atoms ?
Luis Paulo wrote: Please I need to fix all atoms of a proetin and I need to calculte the initital enregy without to exceute septs of dynsmics. How can i do this ? Please start a fresh email when posting, lest search engines be confused by the contents of some other discussion. You can do a zero-step energy minimization to calculate an energy. Fixing atoms would be irrelevant for that, and is a topic properly read about in the manual. Be aware that constraints, restraints and freeze groups are all distinct topics. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
