Re: [gmx-users] Creating topology file for TBA cation using OPLS force field
Andrey A. Koverga wrote: Hi all! I'm just a beginner user of Gromacs, that's why my question may seem strange to you. But I hope, that somebody can help me in solving my problem. The point is that I'm trying to perform the analysis of tetrabutylammonium cation solvatation using OPLS force field. Earlier i've modelled tetrametylammonium cation with same force field; the topology *.itp file for TMA was created, using The Dundee PRODRG Server: itp-file was created for some Gromacs force field, and than modified by definition of the UA-groups according to OPLS UA-types. This way is unsuitable for determination of TBA topology, 'couse in this case "all-atom" determination should be performed. So that's why I'm asking your advise what should I do. Thanks a lot! Read how OPLS was parameterized and do something consistent with that. Anything else is random number generation (and even this might be!) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] CNT-protein interaction
Ok, thank you very much. Robert Johnson wrote: Just take the coordinate files for the protein and the nanotube, cat them together and then edit the resulting file. Then you can solvate the composite system using genbox. Bob On 5/10/07, George Abadir <[EMAIL PROTECTED]> wrote: Hi, I have built a topology file for a protein and a topolgy file for a carbon naontube. I am trying to combine them by solvating the protein in water and inserting the CNT molecule using the -ci option with genbox. However, when I view the resulting file, I can only see the protein in water and the CNT is not there. Can anyone help with that?:) Thank you vey much in advance, Regards, George ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] CNT-protein interaction
Just take the coordinate files for the protein and the nanotube, cat them together and then edit the resulting file. Then you can solvate the composite system using genbox. Bob On 5/10/07, George Abadir <[EMAIL PROTECTED]> wrote: Hi, I have built a topology file for a protein and a topolgy file for a carbon naontube. I am trying to combine them by solvating the protein in water and inserting the CNT molecule using the -ci option with genbox. However, when I view the resulting file, I can only see the protein in water and the CNT is not there. Can anyone help with that?:) Thank you vey much in advance, Regards, George ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] CNT-protein interaction
Hi, I have built a topology file for a protein and a topolgy file for a carbon naontube. I am trying to combine them by solvating the protein in water and inserting the CNT molecule using the -ci option with genbox. However, when I view the resulting file, I can only see the protein in water and the CNT is not there. Can anyone help with that?:) Thank you vey much in advance, Regards, George ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Creating topology file for TBA cation using OPLS force field
Hi all! I'm just a beginner user of Gromacs, that's why my question may seem strange to you. But I hope, that somebody can help me in solving my problem. The point is that I'm trying to perform the analysis of tetrabutylammonium cation solvatation using OPLS force field. Earlier i've modelled tetrametylammonium cation with same force field; the topology *.itp file for TMA was created, using The Dundee PRODRG Server: itp-file was created for some Gromacs force field, and than modified by definition of the UA-groups according to OPLS UA-types. This way is unsuitable for determination of TBA topology, 'couse in this case "all-atom" determination should be performed. So that's why I'm asking your advise what should I do. Thanks a lot! ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] error estimates of free energy calculations
Dear GROMACS users, To test my protocol, I have been trying to reproduce some of Berk Hess's hydration free energy results from his 2006 paper (J. Phys. Chem. B 110, 17616-17626, 2006). Although my obtained average free energies are quite comparable, my error estimates are much higher than the errors reported in that paper. I'd like to figure out what's causing this difference in accuracy, because I really need optimal accuracy for my future calculations. I'm using GROMACS 3.3.1, the G53a6 force field and 3.0 nm dodecahedron simulation boxes with ~631 SPC waters. After mimimization and 500 ps of equilibration for each of the 21 equally spaced lambda-values, I simulated 5 ns for the propane, phenylalanine and asparagine analogues. Theoretically, this should give me a significantly better accuracy than the paper's 500 ps production runs (approx. 1/sqrt(10) times better). Below the .mdp file I used for te production run of the solvated system: === .mdp file === ; RUN CONTROL PARAMETERS integrator = sd dt = 0.002 nsteps = 250 comm_mode= none ; OUTPUT CONTROL OPTIONS nstxout = 5 nstvout = 5 nstfout = 5 nstlog = 5 nstxtcout= 100 ; NEIGHBORSEARCHING PARAMETERS nstlist = 5 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = pme rvdw = 1.4 ; OPTIONS FOR WEAK COUPLING ALGORITHMS tc_grps = system tau_t= 1.0 ref_t= 298.15 pcoupl = berendsen tau_p= 0.5 compressibility = 4.5e-5 ref_p= 1.01325 ; OPTIONS FOR BONDS constraints = all-bonds ; FREE ENERGY CONTROL STUFF free_energy = yes init_lambda = 0.00 sc_alpha = 0.6 sc_power = 1.0 sc_sigma = 0.28 === end of .mdp file === For the in vacuo simulations a similar protocol was used, but without pbc and cutoffs. The error estimates of the in vacuo run were negligibly small compared to those of the solvated system. To the best of my knowledge, the only real difference in parameters is the pressure coupling. The paper uses stochastic pressure coupling which is not available in standard GROMACS 3.3.1. But I doubt that that should make this much of a difference. My results in kJ/mol: Val: 8.0 +/- 0.3 Phe: -1.9 +/- 0.6 Asn: -47.0 +/- 0.6 When I limt my calculation to the first 500 ps of my production runs, to be able to compare them directly to the paper's results, it unsurprisingly gets even worse (paper's results in parentheses): Val: -7.7 +/- 1.0 (7.8 +/- 0.2) Phe: -1.7 +/- 2.0 (-2.0 +/- 0.3) Asn: -47.1 +/- 1.7 (-43.1 +/- 0.3) My averages and error estimates for each lamda value were calculated with the -ee option of g_analyze (a block average fitting procedure, similar to the paper). The average free energies and total error estimates for each lambda-value were integrated with g_analyze - integrate -xydy. My accuracy is also significantly worse than the ones reported in A. Villa, J Comput Chem 23, 548-553, 2002 and J. Maccallum, J Comput Chem 24, 1930-1935, 2003. And it doesn't even come near to the extraordinary accuracy reported by Michael Shirts in his papers (who btw also uses 5 ns runs). I read the recent discussion on this list about error estimation of free energie calulations (starting with http://www.gromacs.org/pipermail/gmx-users/2007-May/027237.html). But since I'm trying to reproduce Berk's results, also using the same error estimation procedure, I don't think that discussion gives a good explanation for my deviations. Does somebody have a clue why my error estimates consistently are approx. 6 times worse? Am I doing something totally wrong here, either during simulation or during analysis? Should my error estimates be divided by some number that I'm not aware of? I know this is a rather detailed question, but I really hope someone can help me with this. Many thanks in advance, Jeroen ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Parameterizing a force field (Mark Abraham)
Thank you both for the response! I looked at the -j option in mdrun, but it looks like that has about as much documentation as ffscan (i.e. none at all). I also fruitlessly checked the mailing list archives for the past year and a half; there are some questions about ffscan, but none of which contained instructions on how to run it. The next step is to look inside the gromacs source code, but there are a lot of different files and I'm not sure as to which pieces of source code describe how the input files are parsed. If you could tell me which files to look at, I would appreciate it a lot. Thanks again! Specifically: 1) What piece of code do I look at to see how mdrun parses the wham.gct file (turned on by the -j switch)? 2) Which file describes how ffscan parses its inputs? Also: If ffscan performs a grid scan, is it really able to fit 100+ parameters in a reasonable period of time (couple of hours)? Would a numerical optimization procedure for the parameters be a possible improvement over this? - Lee-Ping ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Regarding conversion of C6/C12 parameters to sigma/epsilon
I assume that you are talking about the [ nonbons_params ] section from lipid.itp. To answer this question requires an understanding of what information is contained in the [ nonbond_params ] section (A) generally, and (B) in lipid.itp The answer to (A) is in the manual and the mailing list For the answer to (B) look at the lipid.itp file. First there is a section that describes lipid-lipid parameters. Feel free to convert them and include them if you want but you can take care of that simply by using the default comb-rule 3 from oplsaa. To check that out for yourself check some of the combinations in that section vs the rule for comb-rule 3. Next there is a section that begins with the comment ";; paramaters for lipid-GROMOS interactions". You obviously don't want any of those from the lipid-GROMOS section if you are using oplsaa (in fact it would be a disaster to include them.) Next there is a section that begins with the comment ";; lipid-SPC/SPCE interactions". This section is treated similarly. Therefore the simple answer is: Ignore them. I have seen your (many) posts of this question but I have been too busy to reply until now. Chris. --- original message --- I have one doubt regarding conversion of C6/C12 parameters to sigma /epsilon. I added atomtypes, pairtypes and dihedraltypes from lipid.itp to ffoplsaanb.itp---after changing C6/C12 paramters to sigma/epsilon as given in mailing list (http://www.gromacs.org/pipermail/gmx-users/2006-May/021416.html ). My questions are (1) Is it also required to do conversion of C6/C12 parameters of “nonbond_params“to sigma/epsilon and adding these parameters from lipid.itp to ffoplsaanb.itp. (2) If it is not required to convert” nonbond_params” parameters, is it required to call these parameters without conversion. Any suggestion is appreciated, thank you in advance. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] R: grompp atomtype problem
Dear John, you are right, that's what happened! I set up the protein with the Gromos96 ff as I use to do, but I followed the tutorial for the ligand, and so I used the gromacs forcefield. I will use the prodrg_beta site to obtain Gromos96 itp files. Many thanks for your help and best regards Anna -Messaggio originale- Da: John E. Kerrigan [mailto:[EMAIL PROTECTED] Inviato: giovedì 10 maggio 2007 16.41 A: [EMAIL PROTECTED]; gmx-users@gromacs.org Oggetto: grompp atomtype problem Hi Anna, Your input files did not come through. However, it might be possible you are using two different forcefields unintentionally? In the tutorial, we use the gromacs forcefield (ffgmx or pdb2gmx -ff gmx). Perhaps you have used a different forcefield? The prodrg site creates ffgmx itp files. The prodrg beta site creates Gromos96 itp files. It's easy to mix these up because the output is so similar. John > Hi all, > > I'm trying to simulate the MD of a protein with a ligand. Since it is the > first time, I followed exactly (at least, I think so!) suggestions from > "GROMACS tutorial for drug-enzyme complex" by J. Kerrigan. I started from > the PDB coordinates of the complex, I extracted the coordinates of the > ligand and created a .itp file for the ligand using the PRODRG server. Then > I submitted the protein alone to pdb2gmx, and then I manually edited the > .pdb and the .top files in order to re-introduce the coordinates of the > ligand into the protein. Therefore, I opened the .pdb file of the protein > created by pdb2gmx, and pasted the coordinates of the ligand obtained by > PRODRG (changing the n. of residue to continue numbering), and I edited the > .top file by adding #include "lig.itp" in the ff statement, LIG in the [ > molecules ] section etc. Then I created the box with editconf, solvated it > with genbox and started grompp before neutralizing the -5 charge of the > protein with genion. > The grompp output gave me a fatal error: > > Source code file: toputil.c, line 61 > FATAL ERROR: ATOMTYPE 'CH3' NOT FOUND ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] grompp atomtype problem
This may be the case. However if not, I suggest you use the PRODRG beta server (top right hand corner on the main page) to produce output files for a more appropriate forcefield. I have generated and used files successfully using the beta server in the ff43a1. Cheers Mitch John E. Kerrigan wrote: Hi Anna, Your input files did not come through. However, it might be possible you are using two different forcefields unintentionally? In the tutorial, we use the gromacs forcefield (ffgmx or pdb2gmx -ff gmx). Perhaps you have used a different forcefield? The prodrg site creates ffgmx itp files. The prodrg beta site creates Gromos96 itp files. It's easy to mix these up because the output is so similar. John Hi all, I'm trying to simulate the MD of a protein with a ligand. Since it is the first time, I followed exactly (at least, I think so!) suggestions from "GROMACS tutorial for drug-enzyme complex" by J. Kerrigan. I started from the PDB coordinates of the complex, I extracted the coordinates of the ligand and created a .itp file for the ligand using the PRODRG server. Then I submitted the protein alone to pdb2gmx, and then I manually edited the .pdb and the .top files in order to re-introduce the coordinates of the ligand into the protein. Therefore, I opened the .pdb file of the protein created by pdb2gmx, and pasted the coordinates of the ligand obtained by PRODRG (changing the n. of residue to continue numbering), and I edited the .top file by adding #include "lig.itp" in the ff statement, LIG in the [ molecules ] section etc. Then I created the box with editconf, solvated it with genbox and started grompp before neutralizing the -5 charge of the protein with genion. The grompp output gave me a fatal error: Source code file: toputil.c, line 61 FATAL ERROR: ATOMTYPE 'CH3' NOT FOUND ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] EM steep Total Energy
Dear Sir, You are absolutely right. The same question was made on 11th of April. I was searching the emailing list with steep mainly as keyword, which did't bring me in the answer in question. I'm realy sorry for the repetition of the question. Thank you very much for your immediate answer. Yours Sincerely, Nikos --- Berk Hess <[EMAIL PROTECTED]> schrieb: > > > > >From: Claus Valka <[EMAIL PROTECTED]> > >Reply-To: Discussion list for GROMACS users > > >To: gmx-users@gromacs.org > >Subject: [gmx-users] EM steep Total Energy > >Date: Thu, 10 May 2007 13:56:34 +0200 (CEST) > > > >Dear GROMACS Developers, > > > >I have noticed that while doing Steep Energy > >Minimization, the Total Energy in the log file is > >zero. > >The potential energy is calculated as it should. In > >Conjugate Gradient or MD the total energy is > >calculated correctly. > >Is this a bug or a feature? > >I suppose that, under these circumstances, the > total > >energy in steep energy minimization equals the > >potential energy. > > > >Yours Sincerely, > >Nikos > > The same question was asked a month ago. > I would say it is neither a bug nor a feature. > Since there is no kinetic energy, there is nothing > to sum into a total. > But to avoid questions like this I have added the > total energy, > identical to the potential energy, for the next > release. > > Berk. > > _ > Play online games with your friends with Messenger > http://www.join.msn.com/messenger/overview > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.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 > [EMAIL PROTECTED] > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > __ Yahoo! Clever: Sie haben Fragen? Yahoo! Nutzer antworten Ihnen. www.yahoo.de/clever ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] grompp atomtype problem
Hi Anna, Your input files did not come through. However, it might be possible you are using two different forcefields unintentionally? In the tutorial, we use the gromacs forcefield (ffgmx or pdb2gmx -ff gmx). Perhaps you have used a different forcefield? The prodrg site creates ffgmx itp files. The prodrg beta site creates Gromos96 itp files. It's easy to mix these up because the output is so similar. John > Hi all, > > I'm trying to simulate the MD of a protein with a ligand. Since it is the > first time, I followed exactly (at least, I think so!) suggestions from > "GROMACS tutorial for drug-enzyme complex" by J. Kerrigan. I started from > the PDB coordinates of the complex, I extracted the coordinates of the > ligand and created a .itp file for the ligand using the PRODRG server. Then > I submitted the protein alone to pdb2gmx, and then I manually edited the > .pdb and the .top files in order to re-introduce the coordinates of the > ligand into the protein. Therefore, I opened the .pdb file of the protein > created by pdb2gmx, and pasted the coordinates of the ligand obtained by > PRODRG (changing the n. of residue to continue numbering), and I edited the > .top file by adding #include "lig.itp" in the ff statement, LIG in the [ > molecules ] section etc. Then I created the box with editconf, solvated it > with genbox and started grompp before neutralizing the -5 charge of the > protein with genion. > The grompp output gave me a fatal error: > > Source code file: toputil.c, line 61 > FATAL ERROR: ATOMTYPE 'CH3' NOT FOUND begin:vcard fn:John Kerrigan n:Kerrigan;John org:UMDNJ;IST/AST adr:;;675 Hoes Lane, SB-11;Piscataway;NJ;08854;USA email;internet:[EMAIL PROTECTED] tel;work:(732) 235-4473 tel;fax:(732) 235-5252 url:http://www2.umdnj.edu/~kerrigje version:2.1 end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Where to start ? Gmx Newb !!
You appear to have found this mailing list fine. I would suggest the gromacs manual on the gromacs website. This provides an introduction to MD topics and theory. This manual also provides references for literature of both historical and general importance in the field. There are plenty of tutorials also available. Search tools are your friend. Cheers Mitch I BioKid wrote: Dear all, I am new to the field of simulation and dynamics. I am an undergraduate student with background in physics , biology and computer science. Planning to work on Biomolecular Dynamics and simulation for my thesis work. Can you please recommend me some starting point (reading material, ppts, webs )to scale up my knowledge about the field Thanks, S Khadar ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with grompp and atomtype
Anna Marabotti a écrit : Hi all, I'm trying to simulate the MD of a protein with a ligand. Since it is the first time, I followed exactly (at least, I think so!) suggestions from "GROMACS tutorial for drug-enzyme complex" by J. Kerrigan. I started from the PDB coordinates of the complex, I extracted the coordinates of the ligand and created a .itp file for the ligand using the PRODRG server. Then I submitted the protein alone to pdb2gmx, and then I manually edited the .pdb and the .top files in order to re-introduce the coordinates of the ligand into the protein. Therefore, I opened the .pdb file of the protein created by pdb2gmx, and pasted the coordinates of the ligand obtained by PRODRG (changing the n. of residue to continue numbering), and I edited the .top file by adding #include "lig.itp" in the ff statement, LIG in the [ molecules ] section etc. Then I created the box with editconf, solvated it with genbox and started grompp before neutralizing the -5 charge of the protein with genion. The grompp output gave me a fatal error: Source code file: toputil.c, line 61 FATAL ERROR: ATOMTYPE 'CH3' NOT FOUND There is nothing wrong in you procedure. For the moment, proDRG outputs atom types for the deprecated gromacs force field (ffgmx). You need to alter these atom types in order to get the proper ones (i.e. the ones coming from the force field you're using). In a first *rough* approach, you can compare the atom types presents in share/gromacs/top/ffgmx.atp (the one you have from proDRG) to share/gromacs/top/ffG45a3.atp (for the force filed G45a3 for instance) Please pay great attention to atom types since changing the atom does not provide a straight-forward conversion from the old FF to the new one. Atom types are not everything, you'll need to check bonds, angles, dihedrals, and overall, if your ligand is correctly described with these modifications on the itp file. I'll add a section on the wiki when it's up to be more explicit (kinda sort of updating the tutorial). Note there is a proDRG beta 2.5 mentionning gromacs 96.1 but for now i have no idea about the forcefield used, its validation state, and my question to Dr. van Aalten about this beta server version has not been answered yet (if someone on the list has an explanation, i'm opened to explanations). Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] EM steep Total Energy
From: Claus Valka <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: [gmx-users] EM steep Total Energy Date: Thu, 10 May 2007 13:56:34 +0200 (CEST) Dear GROMACS Developers, I have noticed that while doing Steep Energy Minimization, the Total Energy in the log file is zero. The potential energy is calculated as it should. In Conjugate Gradient or MD the total energy is calculated correctly. Is this a bug or a feature? I suppose that, under these circumstances, the total energy in steep energy minimization equals the potential energy. Yours Sincerely, Nikos The same question was asked a month ago. I would say it is neither a bug nor a feature. Since there is no kinetic energy, there is nothing to sum into a total. But to avoid questions like this I have added the total energy, identical to the potential energy, for the next release. Berk. _ Play online games with your friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Where to start ? Gmx Newb !!
I BioKid wrote: Hi BioKid, what about the links to the Gromacs workshop at CSC that were send around in this list only one hour before your request? Best, BioGramps Dear all, I am new to the field of simulation and dynamics. I am an undergraduate student with background in physics , biology and computer science. Planning to work on Biomolecular Dynamics and simulation for my thesis work. Can you please recommend me some starting point (reading material, ppts, webs )to scale up my knowledge about the field Thanks, S Khadar ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Where to start ? Gmx Newb !!
Dear all, I am new to the field of simulation and dynamics. I am an undergraduate student with background in physics , biology and computer science. Planning to work on Biomolecular Dynamics and simulation for my thesis work. Can you please recommend me some starting point (reading material, ppts, webs )to scale up my knowledge about the field Thanks, S Khadar ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Question on analyzing REMD simulation
N-J.M. Macaluso wrote: Hello, Thanks for your responses on the demux.pl script. I have some more basic questions on how to analyze an REMD simulation in Gromacs. (1) How can I find the acceptance ratio? Look carefully at the output in the log file :-) You will need to do some averaging over log files if you ran more than one job for the simulation. (2) Does anyone know how to graph the temperature or potential energy of a single replica as a function of time? Yup, write it down and graph it. :-) Seriously, though, I (and doubtless others) have perl scripts that do tasks like these when fed a set of .log files. I'm not interested in following single replicas, so they wouldn't be any good to you unless you can modify them. There were some van der Spoel scripts that he threatened to publish on the webpage a year or more ago... have they seen the light of day David? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] fwspider and drug-enzyme tutorials
Hi John, Thank you so much for your efforts - it's a great tutorial, in particular compared to the somewhat old/crappy/undocumented ones we provide in the distribution ;-) Cheers, Erik On May 10, 2007, at 2:20 PM, John E. Kerrigan wrote: Hi All, I've updated the fwspider and drug-enzyme tutorials. The mdp files have been revised per Mark's excellent suggestion in regard to temperature coupling groups. The Gromacs Biomolecular simulations workshop recently held this past February in Finland and now posted online (see http://www.csc.fi/english/research/sciences/chemistry/courses/ gmx2007 ) was very helpful in the revision of these tutorials. I highly recommend the gromacs workshop at CSC. A number of bugs and errors in the drug-enzyme tutorial have been fixed. Even still, these basic tutorials have become rather large and unwieldy. There might still remain some typos and errors of omission. I hope not. Please do feel free to contact me if you find a bug or error and I will try to resolve quickly. Thanks so much for your continued use of my tutorials and very helpful input. Regards, John ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] fwspider and drug-enzyme tutorials
Hi All, I've updated the fwspider and drug-enzyme tutorials. The mdp files have been revised per Mark's excellent suggestion in regard to temperature coupling groups. The Gromacs Biomolecular simulations workshop recently held this past February in Finland and now posted online (see http://www.csc.fi/english/research/sciences/chemistry/courses/gmx2007 ) was very helpful in the revision of these tutorials. I highly recommend the gromacs workshop at CSC. A number of bugs and errors in the drug-enzyme tutorial have been fixed. Even still, these basic tutorials have become rather large and unwieldy. There might still remain some typos and errors of omission. I hope not. Please do feel free to contact me if you find a bug or error and I will try to resolve quickly. Thanks so much for your continued use of my tutorials and very helpful input. Regards, John begin:vcard fn:John Kerrigan n:Kerrigan;John org:UMDNJ;IST/AST adr:;;675 Hoes Lane, SB-11;Piscataway;NJ;08854;USA email;internet:[EMAIL PROTECTED] tel;work:(732) 235-4473 tel;fax:(732) 235-5252 url:http://www2.umdnj.edu/~kerrigje version:2.1 end:vcard ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] EM steep Total Energy
Dear GROMACS Developers, I have noticed that while doing Steep Energy Minimization, the Total Energy in the log file is zero. The potential energy is calculated as it should. In Conjugate Gradient or MD the total energy is calculated correctly. Is this a bug or a feature? I suppose that, under these circumstances, the total energy in steep energy minimization equals the potential energy. Yours Sincerely, Nikos __ Yahoo! Clever: Stellen Sie Fragen und finden Sie Antworten. Teilen Sie Ihr Wissen. www.yahoo.de/clever ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Question on analyzing REMD simulation
Hello, Thanks for your responses on the demux.pl script. I have some more basic questions on how to analyze an REMD simulation in Gromacs. (1) How can I find the acceptance ratio? (2) Does anyone know how to graph the temperature or potential energy of a single replica as a function of time? Thanks! Max Macaluso ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] change the ligand in pdb file
Dear Erik and Florian, Thanks for your reply.In my pdb file, the ligand has has been bound with the enzyme(there is a bond between them), and I just want change the side chain of the ligand, should I use a docking? On Wednesday, 9. May 2007 10:45, Rui Li wrote: > Dear all, > I want to change the ligand in pdb file(add,delete atoms and change > conformation),Who can introduce a software to me? > Any reply is appreciated.Thanks in advance >As Erik said pymol is a possible solution, but i don`t think that you can >easily change conformation of the ligand, for this i would use a docking >suite like autodock or something similar, cause you want valid or bioactive >conformations of your ligand. >greetings, >Florian ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] cosine content
Dear Tsjerk Thanks for answering last question on finding eigenvectors. Till now I have not received any answer for the following question. What do you suggest for this? Best regards, Sunita > Dear users, > > I am trying to calculate cosine content of the principal components using > g_analyze. > > I am using time versus projection of trajectory along eigenvector 1 > (extracted from proj.xvg of g_anaeig) as an input file for g_analyze. > When I calculated the same for eigenvector 2, got memory allocation > problem. > How can I fix it? The second question is, am I doing correctly the calculation of cosine content? > > Regards, > Sunita > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
