[gmx-users] no add extra atoms at N and C terms
Dear Users, I would like to avoid gromacs adding the extra atoms (such as hydrogens and hydroxyls) to my N-term and C-terms. Is there any way to do that? my best, Giacomo Bastianelli ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] no add extra atoms at N and C terms
Hi Giacomo, Run pdb2gmx with the -ter flag and select 'none' for both termini. Best, Tsjerk On 11/9/06, Giacomo Bastianelli [EMAIL PROTECTED] wrote: Dear Users, I would like to avoid gromacs adding the extra atoms (such as hydrogens and hydroxyls) to my N-term and C-terms. Is there any way to do that? my best, Giacomo Bastianelli ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. post-doc NMR, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Can I delete Mn^2+ ion from a protein molecule and then run MD?
Dear All, I want to do MD for a protein crystal containing Mn^2+ ion. Because gromacs has not provided the force field for Mn^2+ ion, I want simply delete Mn ion and then run MD.Will thislead any consequences making the MD results unacceptable? If so, what else should I do instead? Zhongqiao Hu Lab E5-04-27 Tel: 65161946(O) Department of Chemical and Biomolecular Engineering National University of Singapore 117576, Singapore ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] no add extra atoms at N and C terms
Tsjerk Wassenaar wrote: Hi Giacomo, Run pdb2gmx with the -ter flag and select 'none' for both termini. Indeed. In general there's a lot of useful information available about the utility programs from using the man pdb2gmx type of commands. The same information is also in the manual. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] question about energy fluctuation
Qiao Baofu wrote: Thanks. but the g_energy -nmol can only give the Bond,Angle data divided by the nmol, for the Proper-Dih. LJ, Coulomb, Potential, Total-Energy, g_energy -nmol 981 gives the same result as without -nmol 981, in which 981 is the number of molecules. I am using Gromacs 3.3.1. If this is reproducible then please submit a bugzilla. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Can I delete Mn^2+ ion from a protein molecule and then run MD?
Hi Zhongqiao Hu, The question is, what is the role of the Mn2+ ion? If it is involved in the structural stability of your protein, I think you should be well able to answer the question 'Will this lead any consequences making the MD results unacceptable?' yourself or find yourself another research field (just kidding). I guess that the Mn2+ ion plays a role in keeping your protein proper. Then the following question is, why Mn2+? Is it the native metal ion or did they use Mn2+ for spectroscopic/electronic properties? In most cases, you can exchange Mn2+ with Ca2+ without a problem. For Ca2+ there are parameters. Wouldn't that do instead of Mn2+? Maybe the protein is also available in a Ca2+ loaded form? I would suggest finding more reading regarding your system and the variations in experiments, and also try finding some papers regarding simulations of Mn2+ containing systems. Hope it helps, Tsjerk On 11/9/06, Hu Zhongqiao [EMAIL PROTECTED] wrote: Dear All, I want to do MD for a protein crystal containing Mn^2+ ion. Because gromacs has not provided the force field for Mn^2+ ion, I want simply delete Mn ion and then run MD. Will this lead any consequences making the MD results unacceptable? If so, what else should I do instead? Zhongqiao Hu Lab E5-04-27 Tel: 65161946(O) Department of Chemical and Biomolecular Engineering National University of Singapore 117576, Singapore ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. post-doc NMR, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Running GROMACS in parallel
Hi folks, I'd need an help to run GROMACS in parallel on a cluster with x86_64 architecture, with BioBrew 4.1.2-1 roll (GROMACS is one of the programs included in the package). After launching lamboot (with no problems) on 5 nodes of this machine (with names lilligridgiga,lilligridgiga2/3/4/5), with 2 CPUs each, I'm trying to do the speptide tutorial running the final full MD in parallel. Therefore, I used the grompp -np 10 program (all other settings left as in the tutorial), and after that I made several attempts to launch mdrun. Here a brief resume of all my trials and of error messages received: 1) as indicated in the section Running GROMACS in parallel of the manual: $ mpirun -p lilligridgiga,lilligridgiga2,lilligridgiga3,lilligridgiga4,lilligridgiga5 2 mdrun -v -s full etc (if I understand well, this should mean that mdrun is made on nodes lilligridgigax, 2 processes on each) ERROR MESSAGE: mpirun (locate_aschema): 2: No such file or directory 2) as suggested in a previous post in gmx-user archive: $ mpirun C mdrun -v -s full etc (as in the tutorial) -g flog full.job ERROR MESSAGES: From file flog.log: Fatal error: run input file full.tpr was made for 10 nodes, while mdrun expected it to be for 1 nodes. From file full.job: It seems that [at least] one of the processes that was started with mpirun did not invoke MPI_INIT before quitting (it is possible that more than one process did not invoke MPI_INIT -- mpirun was only notified of the first one, which was on node n0). mpirun can *only* be used with MPI programs (i.e., programs that invoke MPI_INIT and MPI_FINALIZE). You can use the lamexec program to run non-MPI programs over the lambooted nodes. 3) as suggested in another previous post in gmx-user archive: $ mpirun -np 10 mdrun -v -s full etc (as in the tutorial) -g flog1 full1.job ERROR MESSAGE: From file flog1.log :Fatal error: run input file full.tpr was made for 10 nodes, while mdrun expected it to be for 1 nodes. File full1.job was saved in multiple copies as #full1.job.1# and therefore I am not able to see its content 4) as suggested in another previous post in gmx-user archive: $ mpirun -np 10 mdrun -np 10 -v -s full etc (as in the tutorial) -g flog2 full2.job ERROR MESSAGE: same as in 2) 5) Last trial, following error messages: $ lamexec -np 10 -mdrun -np 10 -v -s full etc (as in the tutorial) -g flog3 full3.job ERROR MESSAGE: From flog3.log file: no error messages From file full3.job: Fatal error: run input file full.tpr was made for 10 nodes, while mdrun expected it to be for 1 nodes. I really don't understand why mdrun is not working on 10 processors. As you see I've always checked the gmx-user archive trying to find something that could help me, but I didn't. Could anybody give me a suggestion? To be clear at best, I'm attaching here flog.log file and full.job (transformed in full.txt) file. Many thanks and regards Anna __ Anna Marabotti, Ph.D. Laboratorio di Bioinformatica e Biologia Computazionale Istituto di Scienze dell'Alimentazione, CNR Via Roma 52 A/C 83100 Avellino (Italy) Tel: +39 0825 299651 Fax: +39 0825 299813 Skype: annam1972 E-mail: [EMAIL PROTECTED] Web page: http://bioinformatica.isa.cnr.it/anna.htm If you think you are too small to make a difference, try sleeping with a mosquito flog.log Description: Binary data NNODES=1, MYRANK=0, HOSTNAME=lilligrid.na.iac.cnr.it :-) G R O M A C S (-: Gromacs Runs One Microsecond At Cannonball Speeds :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) mdrun (-: NNODES=1, MYRANK=0, HOSTNAME=lilligrid.na.iac.cnr.it :-) G R O M A C S (-: Gromacs Runs One Microsecond At Cannonball Speeds :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2
Re: [gmx-users] Running GROMACS in parallel
Hi Anna, I suspect that you somehow mixed LAM and MPICH. In the logfile it says that the program is aborted due to a p4_error which is an mpich error message. Probably the included mdrun was not compiled with LAM, so you have to recompile with LAM or use mpich's mpirun. Carsten Anna Marabotti wrote: Hi folks, I'd need an help to run GROMACS in parallel on a cluster with x86_64 architecture, with BioBrew 4.1.2-1 roll (GROMACS is one of the programs included in the package). After launching lamboot (with no problems) on 5 nodes of this machine (with names lilligridgiga,lilligridgiga2/3/4/5), with 2 CPUs each, I'm trying to do the speptide tutorial running the final full MD in parallel. Therefore, I used the grompp -np 10 program (all other settings left as in the tutorial), and after that I made several attempts to launch mdrun. Here a brief resume of all my trials and of error messages received: 1) as indicated in the section Running GROMACS in parallel of the manual: $ mpirun -p lilligridgiga,lilligridgiga2,lilligridgiga3,lilligridgiga4,lilligridgiga5 2 mdrun -v -s full etc (if I understand well, this should mean that mdrun is made on nodes lilligridgigax, 2 processes on each) ERROR MESSAGE: mpirun (locate_aschema): 2: No such file or directory 2) as suggested in a previous post in gmx-user archive: $ mpirun C mdrun -v -s full etc (as in the tutorial) -g flog full.job ERROR MESSAGES: From file flog.log: Fatal error: run input file full.tpr was made for 10 nodes, while mdrun expected it to be for 1 nodes. From file full.job: It seems that [at least] one of the processes that was started with mpirun did not invoke MPI_INIT before quitting (it is possible that more than one process did not invoke MPI_INIT -- mpirun was only notified of the first one, which was on node n0). mpirun can *only* be used with MPI programs (i.e., programs that invoke MPI_INIT and MPI_FINALIZE). You can use the lamexec program to run non-MPI programs over the lambooted nodes. 3) as suggested in another previous post in gmx-user archive: $ mpirun -np 10 mdrun -v -s full etc (as in the tutorial) -g flog1 full1.job ERROR MESSAGE: From file flog1.log :Fatal error: run input file full.tpr was made for 10 nodes, while mdrun expected it to be for 1 nodes. File full1.job was saved in multiple copies as #full1.job.1# and therefore I am not able to see its content 4) as suggested in another previous post in gmx-user archive: $ mpirun -np 10 mdrun -np 10 -v -s full etc (as in the tutorial) -g flog2 full2.job ERROR MESSAGE: same as in 2) 5) Last trial, following error messages: $ lamexec -np 10 -mdrun -np 10 -v -s full etc (as in the tutorial) -g flog3 full3.job ERROR MESSAGE: From flog3.log file: no error messages From file full3.job: Fatal error: run input file full.tpr was made for 10 nodes, while mdrun expected it to be for 1 nodes. I really don't understand why mdrun is not working on 10 processors. As you see I've always checked the gmx-user archive trying to find something that could help me, but I didn't. Could anybody give me a suggestion? To be clear at best, I'm attaching here flog.log file and full.job (transformed in full.txt) file. Many thanks and regards Anna __ Anna Marabotti, Ph.D. Laboratorio di Bioinformatica e Biologia Computazionale Istituto di Scienze dell'Alimentazione, CNR Via Roma 52 A/C 83100 Avellino (Italy) Tel: +39 0825 299651 Fax: +39 0825 299813 Skype: annam1972 E-mail: [EMAIL PROTECTED] Web page: http://bioinformatica.isa.cnr.it/anna.htm If you think you are too small to make a difference, try sleeping with a mosquito Halting program mdrun gcq#302: The Candlelight Was Just Right (Beastie Boys) [0] MPI Abort by user Aborting program ! [0] Aborting program! p4_error: latest msg from perror: No such file or directory p0_5520: p4_error: : -1 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Department Am Fassberg 11 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/research/dep/grubmueller/ http://www.gwdg.de/~ckutzne ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Creation of an index file with seperate lipid leaflets
Hi, I've written a python script that does what you want. I cleaned the script (make_2leaflets_index) and put it on my web page at the following URL: http://condor.ebgm.jussieu.fr/~fuchs/download/index.html Hope it helps. Ciao, Patrick Jay Mashl a écrit : Wasted work would be bad ;) Rather than headgroup orientation, maybe try looking at atom distributions along the bilayer normal direction. Neutron scattering experiments show that for atom groups far from the bilayer midplane, the corresponding z-coordinates form two distinct distributions. So one way could be the following. Pick a headgroup atom and obtain its z-coordinate. Have make_ndx accept this value as input. Search the system by looping over lipids and ask whether that atom type has a z-coordinate within some amount around the input value. From this you know the membership of the leaflets. A more automatic way would be to have the program first discern the distribution and then reread the system to decide the leaflet membership. Jay On Wed, 8 Nov 2006, Alan Dodd wrote: Wouldn't shuffle/sort undo all the good work? I did wonder if I should have labelled the lipids in different leaflets as different molecule types, or different chains, but it's a bit late now... --- Jay Mashl [EMAIL PROTECTED] wrote: On Wed, 8 Nov 2006, Alan Dodd wrote: Has anyone already created a way to generate an index file with the atoms from the two leaflets of a bilayer listed seperately? I can't believe it hasn't already been done, but can't find a direct description of a solution. I'm attempting a modification to make_ndx, (or perhaps something considerably less ambitious, judging by the way it's going so far) to permit lipid selection based on headgroup orientation, though I'd quite like to save myself the effort. Incidentally, splitres and splitat seem to be the wrong way around, unless I'm misunderstanding them - they do the opposite of what they say. From the gromacs 3.3.1 source download I did on April of this year. Reordering the lipids into leaflets in your starting coordinate file might be a good idea. If you anticipate lipid exchange between leaflets, then a more general tool like what you suggest would be helpful. Jay ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php Sponsored Link Mortgage rates near 39yr lows. $420k for $1,399/mo. Calculate new payment! http://www.LowerMyBills.com/lre ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 E-mail : [EMAIL PROTECTED] Web Site: http://www.ebgm.jussieu.fr/~fuchs ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] question about energy fluctuation
I did again two group of tests, as follows. But I don't know how to submit a bugzilla.Test 1.g_energy -f md3.edrEnergy Average RMSD Fluct. Drift Tot-Drift ---Bond 1370.47 64.952 64.8116 0.0295732 14.7866Angle 3541.69 99.9164 99.9059 0.0100593 5.02964LJ-(SR) -3601.66 151.232 131.574 -0.516572 -258.287Coulomb-(SR) -10883 143.406 134.139 -0.351347 -175.674Potential -30962.9 304.081 265.607 -1.0257 -512.85Total-Energy -22436.1 287.863 245.635 -1.03989 -519.945g_energy -nmol 115 -f md3.edrEnergy Average RMSD Fluct. Drift Tot-Drift ---Bond 11.9171 0.5648 0 0.0295732 14.7866Angle 30.7973 0.868838 0 0.0100593 5.02964LJ-(SR) -3601.66 151.232 131.574 -0.516572 -258.287Coulomb-(SR) -10883 143.406 134.139 -0.351347 -175.674Potential -269.242 2.64418 0 -1.0257 -512.85Total-Energy -22436.1 287.863 245.635 -1.03989 -519.945Test 2.g_energy -f md3.edrEnergy Average RMSD Fluct. Drift Tot-Drift---Bond 27255.4 288.517 287.731 0.147486 73.7433Angle 30206.8 299.196 299.151 -0.0361126 -18.0563LJ-(SR) -27021.1 1153.88 1015.89 -3.7911 -1895.55Coulomb-(SR) -116585 1327.11 1120.39 -4.92805 -2464.03Potential -271448 2889.94 2444.54 -10.6792 -5339.61Total-Energy -183054 2912.13 2478.91 -10.588 -5293.99g_energy -nmol 981 -f md3.edrEnergy Average RMSD Fluct. Drift Tot-Drift---Bond 27.7833 0.294105 0 0.147486 73.7433Angle 30.7919 0.304991 0 -0.0361126 -18.0563LJ-(SR) -27021.1 1153.88 1015.89 -3.7911 -1895.55Coulomb-(SR) -116585 1327.11 1120.39 -4.92805 -2464.03Potential -276.705 2.94591 0 -10.6792 -5339.61Total-Energy -183054 2912.13 2478.91 -10.588 -5293.99 2006/11/9, David van der Spoel [EMAIL PROTECTED]: Qiao Baofu wrote: Thanks. but the g_energy -nmol can only give the Bond,Angle data divided by the nmol, for the Proper-Dih. LJ, Coulomb, Potential, Total-Energy, g_energy -nmol 981 gives the same result as without -nmol 981, in which 981 is the number of molecules. I am using Gromacs 3.3.1.If this is reproducible then please submit a bugzilla. --David.David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Swedenphone:46 18 471 4205fax: 46 18 511 755[EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Sincerely yours,**Baofu Qiao, PhDFrankfurt Institute for Advanced StudiesMax-von-Laue-Str. 160438 Frankfurt am Main, Germany TEL:+49-69-7984-7529 ** ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] (dH/dl) calculation
Dear David and Mauricio,
I am also confused about the details of dgdl (or dHdl) calculation in GROMACS. For example, if the lambda is fixed at certain value, how did the program determine dHdl?
My initial understanding was kind of similiar to that of Mauricio that dHdl equals the difference in total potential energy between two time frame (snapshots). However, this seems does not make sense when lambda is fixed. Could you give more details about the calculation of the derivative dHdl at each snapshot? Thank you.
Best regards,
Lei Zhou
On 11/6/06, David Mobley [EMAIL PROTECTED] wrote:
Mauricio,I'm somewhat confused by your question and notation. However, I thinkthe basic answer is something like this: In molecular dynamics, you
know the Hamiltonian from which you are sampling; call it H(x,p, l),where x denotes all of the positions, p the momentums, and l lambda.This, of course, is closely linked to the potential energy. Anyway, at
any snapshot, you can simply take the derivative dH(x,p,l)/dl, and youhave dH/dl at that snapshot. This is usually straightforward since youknow the dependence of all of the terms in your Hamiltonian on lambda,
so you actually have the functional form for dH/dl as well -- so itjust involves taking the appropriate combination of positions,momentums, etc. This is of course all handled internally by the code.dH/dl, then, is just the time-average of dH/dl, which can be
evaluated every step by the code.I am not sure if that's helpful at all, as I'm not entirely sure whatproblem you're having. After all, whenever you do TI calculations inGROMACS, the code gives you back dG/dl (or dH/dl, or dA/dl) for every
snapshot in an xvg output file. Are you just confused about how thecode gets this (I think I just answered that above), or are you tryingto figure out how to use it? If you're confused about how to use it,
try to ask a question that relates to the specific issue you'reconfused about.Best wishes,David MobleyUCSFOn 11/5/06, Mauricio Sica [EMAIL PROTECTED]
wrote: Dear experts I am doing FEP (thermodynamic integration method) simulations. I have a questions about dH/dl calculation in GROMACS. Take in mind equation 3.77 from the GROMACS
3.3 manual. There, dA/dl is calculated as dA/dl = SS{ (dH/dl) exp()dp dq } / SS{ exp()dp dq = dA/dlNVT;l } where SS are doble integrals (sorry for the notation).
My question is: how is (dH/dl) (in the middel-term of the equation) calculated? My idea is that the difference V(L=1)-V(L=0) is calculated for every time step (irrespective of the lambda value of the simulation) and dG/dl is
the time average of that difference. dG/dl = V(L=1)(i)-V(L=0)(i)/1 Is this correct? Thanks ___
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Re: [gmx-users] (dH/dl) calculation
Lei,
I am also confused about the details of dgdl (or dHdl) calculation in
GROMACS. For example, if the lambda is fixed at certain value, how did the
program determine dHdl?
See below.
My initial understanding was kind of similiar to that of Mauricio that dHdl
equals the difference in total potential energy between two time frame
(snapshots).
That's never even approximately true unless you are changing lambda as
a function of time, and even then, it is not really true, as dH/dl
isn't evaluated using that approach, and it also contains an extra
factor of 1/dl relative to the difference in total potential energy,
plus there are dynamics going on...
However, this seems does not make sense when lambda is fixed.
Could you give more details about the calculation of the derivative dHdl at
each snapshot? Thank you.
Try reading the manual, for example, equation 4.116 and 4.120 in the
Gromacs 3.3 manual. If you read that, and my previous e-mail, where I
talked about taking the derivative, and you're still confused, write
back and try to be more specific about the nature of your confusion.
You're talking about evaluating dH/dl using a finite-difference
scheme, which is not how it's done -- it's done analytically, since
H(x,p,l) is known.
Take this example: Suppose f(l)=sin(l), and you want to know df/dl.
You ask, how do we evaluate this while keeping l fixed? Simple: Take
the derivative of sin(l) with respect to l. You could *also* do it
with a finite difference scheme (f(l+dl)-f(l))/dl or some such), but
there's no reason to do that, since the derivative approach is
simpler.
Isn't this clear from the manual? As much as I think the manual is
unclear sometimes, this isn't one of those times...
David
Best regards,
Lei Zhou
On 11/6/06, David Mobley [EMAIL PROTECTED] wrote:
Mauricio,
I'm somewhat confused by your question and notation. However, I think
the basic answer is something like this: In molecular dynamics, you
know the Hamiltonian from which you are sampling; call it H(x,p, l),
where x denotes all of the positions, p the momentums, and l lambda.
This, of course, is closely linked to the potential energy. Anyway, at
any snapshot, you can simply take the derivative dH(x,p,l)/dl, and you
have dH/dl at that snapshot. This is usually straightforward since you
know the dependence of all of the terms in your Hamiltonian on lambda,
so you actually have the functional form for dH/dl as well -- so it
just involves taking the appropriate combination of positions,
momentums, etc. This is of course all handled internally by the code.
dH/dl, then, is just the time-average of dH/dl, which can be
evaluated every step by the code.
I am not sure if that's helpful at all, as I'm not entirely sure what
problem you're having. After all, whenever you do TI calculations in
GROMACS, the code gives you back dG/dl (or dH/dl, or dA/dl) for every
snapshot in an xvg output file. Are you just confused about how the
code gets this (I think I just answered that above), or are you trying
to figure out how to use it? If you're confused about how to use it,
try to ask a question that relates to the specific issue you're
confused about.
Best wishes,
David Mobley
UCSF
On 11/5/06, Mauricio Sica [EMAIL PROTECTED] wrote:
Dear experts
I am doing FEP (thermodynamic integration method) simulations.
I have a questions about dH/dl calculation in GROMACS.
Take in mind equation 3.77 from the GROMACS 3.3 manual.
There, dA/dl is calculated as
dA/dl = SS{ (dH/dl) exp()dp dq } / SS{ exp()dp dq = dA/dlNVT;l }
where SS are doble integrals (sorry for the notation).
My question is: how is (dH/dl) (in the middel-term of the equation)
calculated?
My idea is that the difference V(L=1)-V(L=0) is calculated for every
time
step (irrespective of the lambda value of the simulation) and dG/dl is
the time average of that difference.
dG/dl = V(L=1)(i)-V(L=0)(i)/1
Is this correct?
Thanks
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[gmx-users] pdb2gmx with force field option
As my first Gromacs simulation I am trying to simulate a protein with K+ ion. When I use pdb2gmx with GROMACS96 43a2, it complains about the K+ ion and does not generate the topology file.When I remove the K+ ion, I get a topology file, but I need the K+ for the simulation. Can I add the K+ ions at the end of the .gro files and proceed? 1. How can I run pdb2gmx and tell it to look for the force filed information for K in a different file? I tried -ff but got unclear message?2. When I searched in the share/top directrory I found that each force field name with several extensions:.itp, .dhb and .atp. I only have a K.itp file, is that enough?3. To insert the protein into a lipid I used genbox command: genbox -cp protein.pdb -cs lipid.pdbThe protein sinks deep into the lipid and I need to shift the protein back up? What is the best to do it without overlapping with the solvent molecules? 4. What is a better way of doing step 3? ThanksMohamed OsmanProfessor of Electrical EngineeringWashington State University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] question about energy fluctuation
I did again two group of tests, as follows. But I don't know how to submit a bugzilla. http://www.gromacs.org/external/bugzilla.html ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] invalid order of directive moleule type
Thanks for the valueable suggessions, but sir i am actually want to use this program for small molecules. I have taken single FAD molecule as u suggested modified the atom type as described in ffgmx.rtp, program results top and gro files using pdb2gmx, but while running grompp i am getting the error: Back Off! I just backed up mdout.mdp to ./#mdout.mdp.10# checking input for internal consistency... calling /usr/bin/cpp... processing topology... Generated 1284 of the 1485 non-bonded parameter combinations WARNING 1 [file fad.top, line 128]: No default Bond types, using zeroes WARNING 2 [file fad.top, line 139]: No default Bond types, using zeroes WARNING 3 [file fad.top, line 141]: No default Bond types, using zeroes WARNING 4 [file fad.top, line 328]: No default Angle types, using zeroes WARNING 5 [file fad.top, line 329]: No default Angle types, using zeroes WARNING 6 [file fad.top, line 334]: No default Proper Dih. types, using zeroes WARNING 7 [file fad.top, line 336]: No default Proper Dih. types, using zeroes WARNING 8 [file fad.top, line 338]: No default Proper Dih. types, using zeroes WARNING 9 [file fad.top, line 341]: No default Proper Dih. types, using zeroes WARNING 10 [file fad.top, line 343]: No default Proper Dih. types, using zeroes Cleaning up temporary file gromppLLm3l8 --- Program grompp, VERSION 3.3.1 Source code file: fatal.c, line: 416 Fatal error: Too many warnings, grompp terminated --- I Need Love, Not Games (Iggy Pop Kate Pierson) Those errors mean exactly what they say, you have no definition (in the forcefield that you have used) for those bonds, angle and proper dihedral types. Moreover , suppose if we want to use this program (grompp) for say, a molecule which has no entry in any .rtp file provided with Gromacs and we grompp doesn't use the .rtp files, that is for pdb2gmx. use the PRODRG server, then how to deal with the error invalid molecular directive type. Amazing what you can find by searching the emailing list ;) http://www.gromacs.org/external/search.html http://www.gromacs.org/pipermail/gmx-users/2006-November/024540.html http://www.gromacs.org/pipermail/gmx-users/2003-December/008346.html Might be an idea to have a read through the manual as well, particularly the chapters on topologies. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Running GROMACS in parallel
Hi folks, I'd need an help to run GROMACS in parallel on a cluster with x86_64 architecture, with BioBrew 4.1.2-1 roll (GROMACS is one of the programs included in the package). After launching lamboot (with no problems) on 5 nodes of this machine (with names lilligridgiga,lilligridgiga2/3/4/5), with 2 CPUs each, I'm trying to do the speptide tutorial running the final full MD in parallel. Therefore, I used the grompp -np 10 program (all other settings left as in the tutorial), and after that I made several attempts to launch mdrun. Here a brief resume of all my trials and of error messages received: I'd suggest walking before running. Get gromacs working on one machine with two cpus, and then maybe two machines with one cpu each before you go and throw all this extra complexity around. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pdb2gmx with force field option
As my first Gromacs simulation I am trying to simulate a protein with K+ ion. When I use pdb2gmx with GROMACS96 43a2, it complains about the K+ ion and does not generate the topology file. When I remove the K+ ion, I get a topology file, but I need the K+ for the simulation. Can I add the K+ ions at the end of the .gro files and proceed? No that won't work. You need to choose a force field that has been parameterized to include your protein and your ion. I don't know if this one has. 1. How can I run pdb2gmx and tell it to look for the force filed information for K in a different file? I tried -ff but got unclear message? You can use the #include mechanism in your .top if you have an .itp file for potassium. 2. When I searched in the share/top directrory I found that each force field name with several extensions:.itp, .dhb and .atp. I only have a K.itpfile, is that enough? Yes, if it's complete. Have a read of chapter five of the manual. 3. To insert the protein into a lipid I used genbox command: genbox -cp protein.pdb -cs lipid.pdb The protein sinks deep into the lipid and I need to shift the protein back up? What is the best to do it without overlapping with the solvent molecules? Start with MD on a simple system while you work out how things work. First just your protein. Then with the ion. Then worry about the lipid. 4. What is a better way of doing step 3? I don't know. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RESP fitting using MOPAC
Hi gmxions, I have found many article for calculating partial charges for a ligand using RESP (restricted electro static fitting) within active site using gaussian. But I do not have gaussion, So Is it done also by MOPAC? And if it is so kindly refer me the protocol to do that. With thanks! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - Access all of your messages and folders wherever you are ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
