[gmx-users] A question
Hello, I am new user of Gromacs. I did a pdb2gmx command on my pdb file. I got an error below: Residue 'XXX' not found in residue topology database I know that I blindly made my pdb file using Materials Studio 4.2. Let me know there is a special software to make a pdb file? Thank you in advance for your response. Regards, Samad Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ 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] Entropy correction in PMF
Date: Wed, 23 Apr 2008 20:34:40 -0400 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] Entropy correction in PMF That sentence could definitely use some massaging. Try this: Whether one needs to correct for this contribution depends on what the pmf should represent. When one wants to pull a substrate into a protein, this entropic term indeed contributes to the work to get the substrate into the protein. This is because the work required to pull a ligand into a protein binding pocket depends on the concentration of that ligand in the unbound state. The entropic contribution, however, depends on the size of your simulation box if your sampling of the entire box is ergodic. Further, the large computational cost of converging the sampling of large separations between the protein and ligand make it undesirable to target true ergodicity for large separations. It is more efficient to calculate the work required to pull a ligand into a protein from an unbound state that has a defined concentration and then to separately calculate the work required to change that concentration to some standard state, e.g. 1 molar. If any other free energy users care to comment, perhaps we could come up with something based on what I have suggested (or something entirely different) that could go into the new manual. --original message -- I sent the attached message on last March 31 but I didn't get any answer... may be the right people was not available at that time and that is why I am trying again. I would thank a lot to have some more detail about this paragraph in the gromacs manual (version 3.3, chapter 6, page 111): Whether one needs to correct for this contribution depends on what the pmf should represent. When one wants to pull a substrate into a protein, this entropic term indeed contributes to the work to get the substrate into the protein. But when calculating a pmf between two solutes in a solvent, for the purpose of simulating without solvent, the entropic contribution should be removed. Note that this term can be significant; when at 300K the distance is halved the contribution is 3.5 kJ mol-1.� why exactly for a substrate-protein complex shouldn't one correct the pmf? This is not a simple should or should not. It depends on what you want to use the PMF for. You should be aware that there is this simple entropic distance contribution. When a substrate needs to enter into a protein, it has to work against this entropic term. If you include this or not, depends on how your want to present the PMF in a presentation, or how your will use it for further calculation. Berk. _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ 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] A question
I suggest reading the following: http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database /Erik samad ahadian skrev: Hello, I am new user of Gromacs. I did a pdb2gmx command on my pdb file. I got an error below: Residue 'XXX' not found in residue topology database I know that I blindly made my pdb file using Materials Studio 4.2. Let me know there is a special software to make a pdb file? Thank you in advance for your response. Regards, Samad Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ 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 -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 [EMAIL PROTECTED]http://xray.bmc.uu.se/molbiophys ___ 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] A question
samad ahadian wrote: Hello, I am new user of Gromacs. I did a pdb2gmx command on my pdb file. I got an error below: Residue 'XXX' not found in residue topology database I know that I blindly made my pdb file using Materials Studio 4.2. Let me know there is a special software to make a pdb file? Thank you in advance for your response. No, but you can certainly make life hard for yourself by using poor PDB-producing software, or using good software poorly. See http://wiki.gromacs.org/index.php/Errors for some background for this error. You need to generate a structure file whose residues and atoms are defined for the force field you intend to use, and which are named suitably so that pdb2gmx can recognize them. 'XXX' suggests that either MS4.2, or your usage of it, or both, are making life hard. Depending on your level of newness, you should definitely do some background textbook/manual/literature reading, and/or tutorials. 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] position restraints
Hello, I'm trying to run a simulation with one lipid molecule in a fixed simulation box without pbc. I set position restraints on one of the atoms and I seem to keep on getting the following error: ...This usually means your system is exploding... Do you have any idea what may cause this problem? Not without further details. Where did you get the parameters for your lipid? What lipid is it? What did you do to minimize and equilibrate your system? What's in your .mdp file? See here: http://wiki.gromacs.org/index.php/blowing_up -Justin Hello, The lipid is DPPC.The .itp file I got from a coworker that used it before for membrane MD simulations. To minimize the system I used steepest descent with the following parameters: title = TAT cpp = /usr/bin/cpp define = -DPOSRE constraints = none integrator = steep dt = 0.002 ;ps nsteps = 400 nstlist = 10 ns_type = grid rlist = 0.99 coulombtype = PME rcoulomb = 0.99 vdwtype = cut-off rvdw = 0.99 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes emtol = 1000.0 emstep = 0.01 I tried running the steepest descent several times however that did not help. I run an MD simulation with the following parameters: title = dppc cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.001 ;ps nsteps = 10 nstcomm = 1 nstxout = 1000 nstvout = 0 nstfout = 0 nstenergy = 1000 nstlist = 10 pbc = no ns_type = simple rlist = 1.4 coulombtype = cut-off rcoulomb = 1.4 vdwtype = cut-off rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes Tcoupl = berendsen tau_t = 1.0 tc-grps = DPP ref_t = 300 Pcoupl = no gen_vel = yes gen_temp = 300.0 gen_seed = -1 bd_fric = 0 ld_seed = -1 epsilon_r = 80 comm_mode = angular thank you Gadi This message was sent using IMP, the Internet Messaging Program. ___ 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] position restraints
[EMAIL PROTECTED] wrote: Please generate replies to the mailing list sensibly. It's very hard to work out who you are quoting where in this email. It'd be easy just to ignore it, and that's the last thing you should want. Hello, I'm trying to run a simulation with one lipid molecule in a fixed simulation box without pbc. I set position restraints on one of the atoms and I seem to keep on getting the following error: Why do you want MD of a single lipid and a position restraint on one atom? If you just want to see a lipid wiggle around, then don't create more numerical complexity. The lipid is DPPC.The .itp file I got from a coworker that used it before for membrane MD simulations. To minimize the system I used steepest descent with the following parameters: Well if your grompp and mdrun completed successfully and without warnings then you've probably got an OK topology and structure. The combination of all bond constraints, a single lipid in vacuo, temperature coupling and a single position restraint sounds like a recipe for a numerical disaster, i.e. blowing up. Try with fewer of those things applied, or get a more physically-reasonable system, like a whole membrane. 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] position restraints
Hi, I tried using no temperature coupling and no constraints, that did not help. If I run the simulation without the position restraints it works OK. Could there by something wrong with the posre file (I'll attach it at the end of the email). I want one of the atoms in the lipid to stay in one place and the rest to wiggle around it. Is there any other way to do that which is not position restraints. Thanks Gadi [ position_restraints ] ; atom type fx fy fz 1 1 0 0 0 2 1 0 0 0 3 1 0 0 0 4 1 0 0 0 5 1 0 0 0 6 1 0 0 0 7 1 0 0 0 8 1 1000.0 1000.0 1000.0 9 1 0 0 0 10 1 0 0 0 11 1 0 0 0 12 1 0 0 0 13 1 0 0 0 14 1 0 0 0 15 1 0 0 0 16 1 0 0 0 17 1 0 0 0 18 1 0 0 0 19 1 0 0 0 20 1 0 0 0 21 1 0 0 0 22 1 0 0 0 23 1 0 0 0 24 1 0 0 0 25 1 0 0 0 26 1 0 0 0 27 1 0 0 0 28 1 0 0 0 29 1 0 0 0 30 1 0 0 0 31 1 0 0 0 32 1 0 0 0 33 1 0 0 0 34 1 0 0 0 35 1 0 0 0 36 1 0 0 0 37 1 0 0 0 38 1 0 0 0 39 1 0 0 0 40 1 0 0 0 41 1 0 0 0 42 1 0 0 0 43 1 0 0 0 44 1 0 0 0 45 1 0 0 0 46 1 0 0 0 47 1 0 0 0 48 1 0 0 0 49 1 0 0 0 50 1 0 0 0 Quoting Mark Abraham [EMAIL PROTECTED]: [EMAIL PROTECTED] wrote: Please generate replies to the mailing list sensibly. It's very hard to work out who you are quoting where in this email. It'd be easy just to ignore it, and that's the last thing you should want. Hello, I'm trying to run a simulation with one lipid molecule in a fixed simulation box without pbc. I set position restraints on one of the atoms and I seem to keep on getting the following error: Why do you want MD of a single lipid and a position restraint on one atom? If you just want to see a lipid wiggle around, then don't create more numerical complexity. The lipid is DPPC.The .itp file I got from a coworker that used it before for membrane MD simulations. To minimize the system I used steepest descent with the following parameters: Well if your grompp and mdrun completed successfully and without warnings then you've probably got an OK topology and structure. The combination of all bond constraints, a single lipid in vacuo, temperature coupling and a single position restraint sounds like a recipe for a numerical disaster, i.e. blowing up. Try with fewer of those things applied, or get a more physically-reasonable system, like a whole membrane. 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 This message was sent using IMP, the Internet Messaging Program. ___ 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] position restraints
Did your minimization converge to a nice, negative potential energy? Also, what is the full mdrun output when the simulation blows up? You've quoted the last bit, but it would be more informative to see the whole output, or at least a description of it (i.e., LINCS warnings). -Justin Quoting [EMAIL PROTECTED]: Hi, I tried using no temperature coupling and no constraints, that did not help. If I run the simulation without the position restraints it works OK. Could there by something wrong with the posre file (I'll attach it at the end of the email). I want one of the atoms in the lipid to stay in one place and the rest to wiggle around it. Is there any other way to do that which is not position restraints. Thanks Gadi [ position_restraints ] ; atom type fx fy fz 1 1 0 0 0 2 1 0 0 0 3 1 0 0 0 4 1 0 0 0 5 1 0 0 0 6 1 0 0 0 7 1 0 0 0 8 1 1000.0 1000.0 1000.0 9 1 0 0 0 10 1 0 0 0 11 1 0 0 0 12 1 0 0 0 13 1 0 0 0 14 1 0 0 0 15 1 0 0 0 16 1 0 0 0 17 1 0 0 0 18 1 0 0 0 19 1 0 0 0 20 1 0 0 0 21 1 0 0 0 22 1 0 0 0 23 1 0 0 0 24 1 0 0 0 25 1 0 0 0 26 1 0 0 0 27 1 0 0 0 28 1 0 0 0 29 1 0 0 0 30 1 0 0 0 31 1 0 0 0 32 1 0 0 0 33 1 0 0 0 34 1 0 0 0 35 1 0 0 0 36 1 0 0 0 37 1 0 0 0 38 1 0 0 0 39 1 0 0 0 40 1 0 0 0 41 1 0 0 0 42 1 0 0 0 43 1 0 0 0 44 1 0 0 0 45 1 0 0 0 46 1 0 0 0 47 1 0 0 0 48 1 0 0 0 49 1 0 0 0 50 1 0 0 0 Quoting Mark Abraham [EMAIL PROTECTED]: [EMAIL PROTECTED] wrote: Please generate replies to the mailing list sensibly. It's very hard to work out who you are quoting where in this email. It'd be easy just to ignore it, and that's the last thing you should want. Hello, I'm trying to run a simulation with one lipid molecule in a fixed simulation box without pbc. I set position restraints on one of the atoms and I seem to keep on getting the following error: Why do you want MD of a single lipid and a position restraint on one atom? If you just want to see a lipid wiggle around, then don't create more numerical complexity. The lipid is DPPC.The .itp file I got from a coworker that used it before for membrane MD simulations. To minimize the system I used steepest descent with the following parameters: Well if your grompp and mdrun completed successfully and without warnings then you've probably got an OK topology and structure. The combination of all bond constraints, a single lipid in vacuo, temperature coupling and a single position restraint sounds like a recipe for a numerical disaster, i.e. blowing up. Try with fewer of those things applied, or get a more physically-reasonable system, like a whole membrane. 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 This message was sent using IMP, the Internet Messaging Program. ___ 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 Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ 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] position restraints
Hi, The full mdrun output when the simulation blows up is: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max inf (between atoms 6 and 7) rms inf bonds that rotated more than 30 degrees: . . . Warning: 1-4 interaction between 1 and 6 at distance 324490777485109120.000 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Thanks Gadi Quoting Justin A. Lemkul [EMAIL PROTECTED]: Did your minimization converge to a nice, negative potential energy? Also, what is the full mdrun output when the simulation blows up? You've quoted the last bit, but it would be more informative to see the whole output, or at least a description of it (i.e., LINCS warnings). -Justin Quoting [EMAIL PROTECTED]: Hi, I tried using no temperature coupling and no constraints, that did not help. If I run the simulation without the position restraints it works OK. Could there by something wrong with the posre file (I'll attach it at the end of the email). I want one of the atoms in the lipid to stay in one place and the rest to wiggle around it. Is there any other way to do that which is not position restraints. Thanks Gadi [ position_restraints ] ; atom type fx fy fz 1 1 0 0 0 2 1 0 0 0 3 1 0 0 0 4 1 0 0 0 5 1 0 0 0 6 1 0 0 0 7 1 0 0 0 8 1 1000.0 1000.0 1000.0 9 1 0 0 0 10 1 0 0 0 11 1 0 0 0 12 1 0 0 0 13 1 0 0 0 14 1 0 0 0 15 1 0 0 0 16 1 0 0 0 17 1 0 0 0 18 1 0 0 0 19 1 0 0 0 20 1 0 0 0 21 1 0 0 0 22 1 0 0 0 23 1 0 0 0 24 1 0 0 0 25 1 0 0 0 26 1 0 0 0 27 1 0 0 0 28 1 0 0 0 29 1 0 0 0 30 1 0 0 0 31 1 0 0 0 32 1 0 0 0 33 1 0 0 0 34 1 0 0 0 35 1 0 0 0 36 1 0 0 0 37 1 0 0 0 38 1 0 0 0 39 1 0 0 0 40 1 0 0 0 41 1 0 0 0 42 1 0 0 0 43 1 0 0 0 44 1 0 0 0 45 1 0 0 0 46 1 0 0 0 47 1 0 0 0 48 1 0 0 0 49 1 0 0 0 50 1 0 0 0 Quoting Mark Abraham [EMAIL PROTECTED]: [EMAIL PROTECTED] wrote: Please generate replies to the mailing list sensibly. It's very hard to work out who you are quoting where in this email. It'd be easy just to ignore it, and that's the last thing you should want. Hello, I'm trying to run a simulation with one lipid molecule in a fixed simulation box without pbc. I set position restraints on one of the atoms and I seem to keep on getting the following error: Why do you want MD of a single lipid and a position restraint on one atom? If you just want to see a lipid wiggle around, then don't create more numerical complexity. The lipid is DPPC.The .itp file I got from a coworker that used it before for membrane MD simulations. To minimize the system I used steepest descent with the following parameters: Well if your grompp and mdrun completed successfully and without warnings then you've probably got an OK topology and structure. The combination of all bond constraints, a single lipid in vacuo, temperature coupling and a single position restraint sounds like a recipe for a numerical disaster, i.e. blowing up. Try with fewer of those things applied, or get a more physically-reasonable system, like a whole membrane. 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 This message was sent using IMP, the Internet Messaging Program. ___ 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 Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080
Re: [gmx-users] position restraints
Quoting [EMAIL PROTECTED]: Hi, The full mdrun output when the simulation blows up is: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max inf (between atoms 6 and 7) rms inf bonds that rotated more than 30 degrees: . . . Warning: 1-4 interaction between 1 and 6 at distance 324490777485109120.000 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Basic information about this type of error can be found here (as well as several hundred posts in the list archive): http://wiki.gromacs.org/index.php/Errors#LINCS_warnings How did you do your minimization, with or without restraints? Did it converge to an acceptable potential energy? -Justin Thanks Gadi Quoting Justin A. Lemkul [EMAIL PROTECTED]: Did your minimization converge to a nice, negative potential energy? Also, what is the full mdrun output when the simulation blows up? You've quoted the last bit, but it would be more informative to see the whole output, or at least a description of it (i.e., LINCS warnings). -Justin Quoting [EMAIL PROTECTED]: Hi, I tried using no temperature coupling and no constraints, that did not help. If I run the simulation without the position restraints it works OK. Could there by something wrong with the posre file (I'll attach it at the end of the email). I want one of the atoms in the lipid to stay in one place and the rest to wiggle around it. Is there any other way to do that which is not position restraints. Thanks Gadi [ position_restraints ] ; atom type fx fy fz 1 1 0 0 0 2 1 0 0 0 3 1 0 0 0 4 1 0 0 0 5 1 0 0 0 6 1 0 0 0 7 1 0 0 0 8 1 1000.0 1000.0 1000.0 9 1 0 0 0 10 1 0 0 0 11 1 0 0 0 12 1 0 0 0 13 1 0 0 0 14 1 0 0 0 15 1 0 0 0 16 1 0 0 0 17 1 0 0 0 18 1 0 0 0 19 1 0 0 0 20 1 0 0 0 21 1 0 0 0 22 1 0 0 0 23 1 0 0 0 24 1 0 0 0 25 1 0 0 0 26 1 0 0 0 27 1 0 0 0 28 1 0 0 0 29 1 0 0 0 30 1 0 0 0 31 1 0 0 0 32 1 0 0 0 33 1 0 0 0 34 1 0 0 0 35 1 0 0 0 36 1 0 0 0 37 1 0 0 0 38 1 0 0 0 39 1 0 0 0 40 1 0 0 0 41 1 0 0 0 42 1 0 0 0 43 1 0 0 0 44 1 0 0 0 45 1 0 0 0 46 1 0 0 0 47 1 0 0 0 48 1 0 0 0 49 1 0 0 0 50 1 0 0 0 Quoting Mark Abraham [EMAIL PROTECTED]: [EMAIL PROTECTED] wrote: Please generate replies to the mailing list sensibly. It's very hard to work out who you are quoting where in this email. It'd be easy just to ignore it, and that's the last thing you should want. Hello, I'm trying to run a simulation with one lipid molecule in a fixed simulation box without pbc. I set position restraints on one of the atoms and I seem to keep on getting the following error: Why do you want MD of a single lipid and a position restraint on one atom? If you just want to see a lipid wiggle around, then don't create more numerical complexity. The lipid is DPPC.The .itp file I got from a coworker that used it before for membrane MD simulations. To minimize the system I used steepest descent with the following parameters: Well if your grompp and mdrun completed successfully and without warnings then you've probably got an OK topology and structure. The combination of all bond constraints, a single lipid in vacuo, temperature coupling and a single position restraint sounds like a recipe for a numerical disaster, i.e. blowing up. Try with fewer of those things applied, or get a more physically-reasonable system, like a whole membrane. 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 This message was sent using IMP, the Internet Messaging Program. ___
Re: [gmx-users] position restraints
no prob you wait for some time it will write topology file and the proceed further.. On Thu, Apr 24, 2008 at 5:04 PM, [EMAIL PROTECTED] wrote: Hi, The full mdrun output when the simulation blows up is: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max inf (between atoms 6 and 7) rms inf bonds that rotated more than 30 degrees: . . . Warning: 1-4 interaction between 1 and 6 at distance 324490777485109120.000 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Thanks Gadi Quoting Justin A. Lemkul [EMAIL PROTECTED]: Did your minimization converge to a nice, negative potential energy? Also, what is the full mdrun output when the simulation blows up? You've quoted the last bit, but it would be more informative to see the whole output, or at least a description of it (i.e., LINCS warnings). -Justin Quoting [EMAIL PROTECTED]: Hi, I tried using no temperature coupling and no constraints, that did not help. If I run the simulation without the position restraints it works OK. Could there by something wrong with the posre file (I'll attach it at the end of the email). I want one of the atoms in the lipid to stay in one place and the rest to wiggle around it. Is there any other way to do that which is not position restraints. Thanks Gadi [ position_restraints ] ; atom type fx fy fz 1 1 0 0 0 2 1 0 0 0 3 1 0 0 0 4 1 0 0 0 5 1 0 0 0 6 1 0 0 0 7 1 0 0 0 8 1 1000.0 1000.0 1000.0 9 1 0 0 0 10 1 0 0 0 11 1 0 0 0 12 1 0 0 0 13 1 0 0 0 14 1 0 0 0 15 1 0 0 0 16 1 0 0 0 17 1 0 0 0 18 1 0 0 0 19 1 0 0 0 20 1 0 0 0 21 1 0 0 0 22 1 0 0 0 23 1 0 0 0 24 1 0 0 0 25 1 0 0 0 26 1 0 0 0 27 1 0 0 0 28 1 0 0 0 29 1 0 0 0 30 1 0 0 0 31 1 0 0 0 32 1 0 0 0 33 1 0 0 0 34 1 0 0 0 35 1 0 0 0 36 1 0 0 0 37 1 0 0 0 38 1 0 0 0 39 1 0 0 0 40 1 0 0 0 41 1 0 0 0 42 1 0 0 0 43 1 0 0 0 44 1 0 0 0 45 1 0 0 0 46 1 0 0 0 47 1 0 0 0 48 1 0 0 0 49 1 0 0 0 50 1 0 0 0 Quoting Mark Abraham [EMAIL PROTECTED]: [EMAIL PROTECTED] wrote: Please generate replies to the mailing list sensibly. It's very hard to work out who you are quoting where in this email. It'd be easy just to ignore it, and that's the last thing you should want. Hello, I'm trying to run a simulation with one lipid molecule in a fixed simulation box without pbc. I set position restraints on one of the atoms and I seem to keep on getting the following error: Why do you want MD of a single lipid and a position restraint on one atom? If you just want to see a lipid wiggle around, then don't create more numerical complexity. The lipid is DPPC.The .itp file I got from a coworker that used it before for membrane MD simulations. To minimize the system I used steepest descent with the following parameters: Well if your grompp and mdrun completed successfully and without warnings then you've probably got an OK topology and structure. The combination of all bond constraints, a single lipid in vacuo, temperature coupling and a single position restraint sounds like a recipe for a numerical disaster, i.e. blowing up. Try with fewer of those things applied, or get a more physically-reasonable system, like a whole membrane. 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 This message was sent using IMP, the Internet Messaging Program. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please
Re: [gmx-users] position restraints
Quoting chandrabhan seniya [EMAIL PROTECTED]: no prob you wait for some time it will write topology file and the proceed further.. I think that a lipid molecule trying to tear itself apart at step 0 would fall under the category of a problem, and it will not disappear on it's own if we conveniently ignore it... On Thu, Apr 24, 2008 at 5:04 PM, [EMAIL PROTECTED] wrote: Hi, The full mdrun output when the simulation blows up is: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max inf (between atoms 6 and 7) rms inf bonds that rotated more than 30 degrees: . . . Warning: 1-4 interaction between 1 and 6 at distance 324490777485109120.000 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Thanks Gadi Quoting Justin A. Lemkul [EMAIL PROTECTED]: Did your minimization converge to a nice, negative potential energy? Also, what is the full mdrun output when the simulation blows up? You've quoted the last bit, but it would be more informative to see the whole output, or at least a description of it (i.e., LINCS warnings). -Justin Quoting [EMAIL PROTECTED]: Hi, I tried using no temperature coupling and no constraints, that did not help. If I run the simulation without the position restraints it works OK. Could there by something wrong with the posre file (I'll attach it at the end of the email). I want one of the atoms in the lipid to stay in one place and the rest to wiggle around it. Is there any other way to do that which is not position restraints. Thanks Gadi [ position_restraints ] ; atom type fx fy fz 1 1 0 0 0 2 1 0 0 0 3 1 0 0 0 4 1 0 0 0 5 1 0 0 0 6 1 0 0 0 7 1 0 0 0 8 1 1000.0 1000.0 1000.0 9 1 0 0 0 10 1 0 0 0 11 1 0 0 0 12 1 0 0 0 13 1 0 0 0 14 1 0 0 0 15 1 0 0 0 16 1 0 0 0 17 1 0 0 0 18 1 0 0 0 19 1 0 0 0 20 1 0 0 0 21 1 0 0 0 22 1 0 0 0 23 1 0 0 0 24 1 0 0 0 25 1 0 0 0 26 1 0 0 0 27 1 0 0 0 28 1 0 0 0 29 1 0 0 0 30 1 0 0 0 31 1 0 0 0 32 1 0 0 0 33 1 0 0 0 34 1 0 0 0 35 1 0 0 0 36 1 0 0 0 37 1 0 0 0 38 1 0 0 0 39 1 0 0 0 40 1 0 0 0 41 1 0 0 0 42 1 0 0 0 43 1 0 0 0 44 1 0 0 0 45 1 0 0 0 46 1 0 0 0 47 1 0 0 0 48 1 0 0 0 49 1 0 0 0 50 1 0 0 0 Quoting Mark Abraham [EMAIL PROTECTED]: [EMAIL PROTECTED] wrote: Please generate replies to the mailing list sensibly. It's very hard to work out who you are quoting where in this email. It'd be easy just to ignore it, and that's the last thing you should want. Hello, I'm trying to run a simulation with one lipid molecule in a fixed simulation box without pbc. I set position restraints on one of the atoms and I seem to keep on getting the following error: Why do you want MD of a single lipid and a position restraint on one atom? If you just want to see a lipid wiggle around, then don't create more numerical complexity. The lipid is DPPC.The .itp file I got from a coworker that used it before for membrane MD simulations. To minimize the system I used steepest descent with the following parameters: Well if your grompp and mdrun completed successfully and without warnings then you've probably got an OK topology and structure. The combination of all bond constraints, a single lipid in vacuo, temperature coupling and a single position restraint sounds like a recipe for a numerical disaster, i.e. blowing up. Try with fewer of those things applied, or get a more physically-reasonable system, like a whole membrane. 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]
[gmx-users] AFMM parameter refinement
Hi All, Has any body tried doing parameter refinement using Vaiana's python code called afmm.py? A.C. Vaiana, Z. Cournia, I.B. Costescu and J.C. Smith, AFMM: A molecular mechanics force field vibrational parametrization program', Computer Physics Communications, 167 (2005), pp.34-42. I have done a test run using propene setup that came along with the code and came across a problem. It gives me the same minimum and current sigma value in every steps as: Minimum sigma: 5782.258565, current sigma: 5782.258565 Dose anybody know what might be the problem? With regards, Abu _ Be a superhero and win! Play the Iron Man Mashup Game http://www.ironmanmashup.co.uk___ 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] position restraints
chandrabhan seniya wrote: what is yr real prob tell me? On this list, we like constructive criticism. I don't think the above qualifies as such. 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] position restraints
Quoting chandrabhan seniya [EMAIL PROTECTED]: what is yr real prob tell me? No need to get confrontational; my reply was not intended to be insulting. Mark and I have been putting forth some effort to help our friend Gadi here by extracting some detail that may be useful to document in the list archives. Posting advice to ignore the problem, that everything will be fine, etc, may result in someone searching for help, finding your post about ignoring the problem, and trying to proceed. My response was simply that errors that cause simulations to crash typically shouldn't be ignored with the belief that they will resolve themselves. Just my $0.02, and everyone hereafter is free to take it or leave it. -Justin On Thu, Apr 24, 2008 at 5:49 PM, Justin A. Lemkul [EMAIL PROTECTED] wrote: Quoting chandrabhan seniya [EMAIL PROTECTED]: no prob you wait for some time it will write topology file and the proceed further.. I think that a lipid molecule trying to tear itself apart at step 0 would fall under the category of a problem, and it will not disappear on it's own if we conveniently ignore it... On Thu, Apr 24, 2008 at 5:04 PM, [EMAIL PROTECTED] wrote: Hi, The full mdrun output when the simulation blows up is: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max inf (between atoms 6 and 7) rms inf bonds that rotated more than 30 degrees: . . . Warning: 1-4 interaction between 1 and 6 at distance 324490777485109120.000 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Thanks Gadi Quoting Justin A. Lemkul [EMAIL PROTECTED]: Did your minimization converge to a nice, negative potential energy? Also, what is the full mdrun output when the simulation blows up? You've quoted the last bit, but it would be more informative to see the whole output, or at least a description of it (i.e., LINCS warnings). -Justin Quoting [EMAIL PROTECTED]: Hi, I tried using no temperature coupling and no constraints, that did not help. If I run the simulation without the position restraints it works OK. Could there by something wrong with the posre file (I'll attach it at the end of the email). I want one of the atoms in the lipid to stay in one place and the rest to wiggle around it. Is there any other way to do that which is not position restraints. Thanks Gadi [ position_restraints ] ; atom type fx fy fz 1 1 0 0 0 2 1 0 0 0 3 1 0 0 0 4 1 0 0 0 5 1 0 0 0 6 1 0 0 0 7 1 0 0 0 8 1 1000.0 1000.0 1000.0 9 1 0 0 0 10 1 0 0 0 11 1 0 0 0 12 1 0 0 0 13 1 0 0 0 14 1 0 0 0 15 1 0 0 0 16 1 0 0 0 17 1 0 0 0 18 1 0 0 0 19 1 0 0 0 20 1 0 0 0 21 1 0 0 0 22 1 0 0 0 23 1 0 0 0 24 1 0 0 0 25 1 0 0 0 26 1 0 0 0 27 1 0 0 0 28 1 0 0 0 29 1 0 0 0 30 1 0 0 0 31 1 0 0 0 32 1 0 0 0 33 1 0 0 0 34 1 0 0 0 35 1 0 0 0 36 1 0 0 0 37 1 0 0 0 38 1 0 0 0 39 1 0 0 0 40 1 0 0 0 41 1 0 0 0 42 1 0 0 0 43 1 0 0 0 44 1 0 0 0 45 1 0 0 0 46 1 0 0 0 47 1 0 0 0 48 1 0 0 0 49 1 0 0 0 50 1 0 0 0 Quoting Mark Abraham [EMAIL PROTECTED]: [EMAIL PROTECTED] wrote: Please generate replies to the mailing list sensibly. It's very hard to work out who you are quoting where in this email. It'd be easy just to ignore it, and that's the last thing you should want. Hello, I'm trying to run a simulation with one lipid molecule in a fixed simulation box without pbc. I set position restraints on one of the atoms and I seem to keep on getting the following error: Why do you want MD of a single lipid and a position restraint on one atom? If you just want to see a lipid wiggle around, then
Re: [gmx-users] position restraints
Hi, I minimized without restraints, could that be the problem? After the minimization I got a Potential Energy = -6.1434351e+02. Gadi Quoting Justin A. Lemkul [EMAIL PROTECTED]: Quoting [EMAIL PROTECTED]: Hi, The full mdrun output when the simulation blows up is: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max inf (between atoms 6 and 7) rms inf bonds that rotated more than 30 degrees: . . . Warning: 1-4 interaction between 1 and 6 at distance 324490777485109120.000 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Basic information about this type of error can be found here (as well as several hundred posts in the list archive): http://wiki.gromacs.org/index.php/Errors#LINCS_warnings How did you do your minimization, with or without restraints? Did it converge to an acceptable potential energy? -Justin Thanks Gadi Quoting Justin A. Lemkul [EMAIL PROTECTED]: Did your minimization converge to a nice, negative potential energy? Also, what is the full mdrun output when the simulation blows up? You've quoted the last bit, but it would be more informative to see the whole output, or at least a description of it (i.e., LINCS warnings). -Justin Quoting [EMAIL PROTECTED]: Hi, I tried using no temperature coupling and no constraints, that did not help. If I run the simulation without the position restraints it works OK. Could there by something wrong with the posre file (I'll attach it at the end of the email). I want one of the atoms in the lipid to stay in one place and the rest to wiggle around it. Is there any other way to do that which is not position restraints. Thanks Gadi [ position_restraints ] ; atom type fx fy fz 1 1 0 0 0 2 1 0 0 0 3 1 0 0 0 4 1 0 0 0 5 1 0 0 0 6 1 0 0 0 7 1 0 0 0 8 1 1000.0 1000.0 1000.0 9 1 0 0 0 10 1 0 0 0 11 1 0 0 0 12 1 0 0 0 13 1 0 0 0 14 1 0 0 0 15 1 0 0 0 16 1 0 0 0 17 1 0 0 0 18 1 0 0 0 19 1 0 0 0 20 1 0 0 0 21 1 0 0 0 22 1 0 0 0 23 1 0 0 0 24 1 0 0 0 25 1 0 0 0 26 1 0 0 0 27 1 0 0 0 28 1 0 0 0 29 1 0 0 0 30 1 0 0 0 31 1 0 0 0 32 1 0 0 0 33 1 0 0 0 34 1 0 0 0 35 1 0 0 0 36 1 0 0 0 37 1 0 0 0 38 1 0 0 0 39 1 0 0 0 40 1 0 0 0 41 1 0 0 0 42 1 0 0 0 43 1 0 0 0 44 1 0 0 0 45 1 0 0 0 46 1 0 0 0 47 1 0 0 0 48 1 0 0 0 49 1 0 0 0 50 1 0 0 0 Quoting Mark Abraham [EMAIL PROTECTED]: [EMAIL PROTECTED] wrote: Please generate replies to the mailing list sensibly. It's very hard to work out who you are quoting where in this email. It'd be easy just to ignore it, and that's the last thing you should want. Hello, I'm trying to run a simulation with one lipid molecule in a fixed simulation box without pbc. I set position restraints on one of the atoms and I seem to keep on getting the following error: Why do you want MD of a single lipid and a position restraint on one atom? If you just want to see a lipid wiggle around, then don't create more numerical complexity. The lipid is DPPC.The .itp file I got from a coworker that used it before for membrane MD simulations. To minimize the system I used steepest descent with the following parameters: Well if your grompp and mdrun completed successfully and without warnings then you've probably got an OK topology and structure. The combination of all bond constraints, a single lipid in vacuo, temperature coupling and a single position restraint sounds like a recipe for a numerical disaster, i.e. blowing up. Try with fewer of those things applied, or get a more physically-reasonable system, like a whole membrane. 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 This message was sent using IMP, the Internet Messaging Program.
Re: [gmx-users] position restraints
Quoting [EMAIL PROTECTED]: Hi, I minimized without restraints, could that be the problem? After the minimization I got a Potential Energy = -6.1434351e+02. That seems fine. Basically, your lipid's headgroup is shearing itself apart (which you can tell from the LINCS warnings). At this point, I could only guess as to what's going wrong, which probably won't do you much good. If you'd like to send me your structure, topologies, and .mdp file off-list, I'd be happy to have a look at them. -Justin Gadi Quoting Justin A. Lemkul [EMAIL PROTECTED]: Quoting [EMAIL PROTECTED]: Hi, The full mdrun output when the simulation blows up is: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max inf (between atoms 6 and 7) rms inf bonds that rotated more than 30 degrees: . . . Warning: 1-4 interaction between 1 and 6 at distance 324490777485109120.000 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Basic information about this type of error can be found here (as well as several hundred posts in the list archive): http://wiki.gromacs.org/index.php/Errors#LINCS_warnings How did you do your minimization, with or without restraints? Did it converge to an acceptable potential energy? -Justin Thanks Gadi Quoting Justin A. Lemkul [EMAIL PROTECTED]: Did your minimization converge to a nice, negative potential energy? Also, what is the full mdrun output when the simulation blows up? You've quoted the last bit, but it would be more informative to see the whole output, or at least a description of it (i.e., LINCS warnings). -Justin Quoting [EMAIL PROTECTED]: Hi, I tried using no temperature coupling and no constraints, that did not help. If I run the simulation without the position restraints it works OK. Could there by something wrong with the posre file (I'll attach it at the end of the email). I want one of the atoms in the lipid to stay in one place and the rest to wiggle around it. Is there any other way to do that which is not position restraints. Thanks Gadi [ position_restraints ] ; atom type fx fy fz 1 1 0 0 0 2 1 0 0 0 3 1 0 0 0 4 1 0 0 0 5 1 0 0 0 6 1 0 0 0 7 1 0 0 0 8 1 1000.0 1000.0 1000.0 9 1 0 0 0 10 1 0 0 0 11 1 0 0 0 12 1 0 0 0 13 1 0 0 0 14 1 0 0 0 15 1 0 0 0 16 1 0 0 0 17 1 0 0 0 18 1 0 0 0 19 1 0 0 0 20 1 0 0 0 21 1 0 0 0 22 1 0 0 0 23 1 0 0 0 24 1 0 0 0 25 1 0 0 0 26 1 0 0 0 27 1 0 0 0 28 1 0 0 0 29 1 0 0 0 30 1 0 0 0 31 1 0 0 0 32 1 0 0 0 33 1 0 0 0 34 1 0 0 0 35 1 0 0 0 36 1 0 0 0 37 1 0 0 0 38 1 0 0 0 39 1 0 0 0 40 1 0 0 0 41 1 0 0 0 42 1 0 0 0 43 1 0 0 0 44 1 0 0 0 45 1 0 0 0 46 1 0 0 0 47 1 0 0 0 48 1 0 0 0 49 1 0 0 0 50 1 0 0 0 Quoting Mark Abraham [EMAIL PROTECTED]: [EMAIL PROTECTED] wrote: Please generate replies to the mailing list sensibly. It's very hard to work out who you are quoting where in this email. It'd be easy just to ignore it, and that's the last thing you should want. Hello, I'm trying to run a simulation with one lipid molecule in a fixed simulation box without pbc. I set position restraints on one of the atoms and I seem to keep on getting the following error: Why do you want MD of a single lipid and a position restraint on one atom? If you just want to see a lipid wiggle around, then don't create more numerical complexity. The lipid is DPPC.The .itp file I got from a coworker that used it before for membrane MD simulations. To minimize the system I used steepest descent with the following parameters: Well if your grompp and mdrun completed successfully and without warnings then you've probably got an OK topology and structure. The combination of all bond constraints, a single lipid in vacuo, temperature coupling and a single position restraint sounds like a recipe for a numerical disaster, i.e. blowing up. Try with
[gmx-users] Converting OPLS parameters
Dear Gromacs users, I am new to gromacs. I have just installed and read some tutorials. I would like to start reproducing the results I have calculated with another program (Dynamo). My system has a protein, water, ATP and N-acetylglutamate (NAG). The protein and water are trivial to convert. But I would like to use the same ATP and NAG parameters that I already have in my OPLS file (I enclose this file for the ATP at the end of the mail). I know PRODRG can generate the topology files, but it also creates the force field parameters, doesn't it? Is there an automatic way to translate the OPLS format to gromacs? Or could you suggest another work-around? Thanks in advance, Ramon !=== ! OPLS MM Definition File for ATP !=== ! ! . Notes: ! ! !=== MM_Definitions OPLS_AA 1.0 ! . Atom Type Definitions. Types ! Atom Name Atomic Number Sigma Epsilon H 10.0 0.0 HO10.0 0.0 HC12.5 0.03000 CA63.5 0.08000 ! for Adenine CB63.5 0.08000 ! for Adenine CK63.5 0.08000 ! for Adenine CQ63.5 0.08000 ! for Adenine CT63.5 0.06600 N*73.25000 0.17000 N273.25000 0.17000 NB73.25000 0.17000 ! for Adenine NC73.25000 0.17000 ! for Adenine O 83.15000 0.2 OH83.07000 0.17000 OS82.9 0.14000 P153.74000 0.2 End ! . Electrostatics and Lennard-Jones Options. Electrostatics Scale 0.5 Lennard_Jones Scale 0.5 ! . Units specification. Units kcal/mole !=== ! . Residue Definitions. !=== Residues !--- Residue ATP !--- ! # Atoms, bonds and impropers. 44 45 5 N1NC -0.53 ! Impact Adenine C2CQ 0.22 ! Impact Adenine H2HC 0.20 ! Impact Adenine N3NC -0.55 ! Impact Adenine C4CB 0.38 ! Impact Adenine C5CB 0.15 ! Impact Adenine C6CA 0.44 ! Impact Adenine N7NB -0.49 ! Impact Adenine C8CK 0.20 ! Impact Adenine H8HC 0.20 ! Impact Adenine N9N* -0.50 ! Impact Adenine N10 N2 -0.81 ! Impact Adenine H11 H 0.37 ! Impact Adenine H12 H 0.37 ! Impact Adenine C1' CT 0.25 ! adjusted H1' HC 0.10 ! Impact HC hemiacetal C2' CT 0.20 ! Impact CT diols H2' HC 0.10 ! Impact HC hemiacetal O2' OH -0.70 ! Impact OH6 hemiacetal, diol HT2' HO 0.43 ! Impact HO hemiacetal, diol C3' CT 0.20 ! Impact CT diols H3' HC 0.10 ! Impact HC hemiacetal O3' OH -0.70 ! Impact OH6 hemiacetal, diol HT3' HO 0.43 ! Impact HO hemiacetal, diol C4' CT 0.24 ! adjusted O4' OS -0.40 ! Impact OS ether, acetal. H4' HC 0.10 ! Impact HC hemiacetal C5' CT 0.42 ! HF/6-31+G* CHelpG H51' HC -0.10 ! HF/6-31+G* CHelpG H52' HC -0.10 ! HF/6-31+G* CHelpG O5' OS -0.71 ! HF/6-31+G* CHelpG PAP 1.85 ! HF/6-31+G* CHelpG OA1 O -1.07 ! HF/6-31+G* CHelpG OA2 O -1.07 ! HF/6-31+G* CHelpG OA3 OS -0.78 ! HF/6-31+G* CHelpG PBP 1.98 ! HF/6-31+G* CHelpG OB1 O -1.09 ! HF/6-31+G* CHelpG OB2 O -1.09 ! HF/6-31+G* CHelpG OB3 OS -0.74 ! HF/6-31+G* CHelpG PGP 2.04 ! HF/6-31+G* CHelpG OG1 O -1.18 ! HF/6-31+G* CHelpG OG2 O -1.18 ! HF/6-31+G* CHelpG OG3 O -1.18 ! HF/6-31+G* CHelpG N1 C2 ; C2 N3 ; C2 H2 ; N3 C4 ; C4 C5 ; C5 C6 C6 N1 ; C6 N10 ; N10 H11 ; N10 H12 ; C5 N7 ; N7 C8 C8 N9 ; C8 H8 ; N9 C4 ; N9 C1' ; C1' C2' ; C1' H1' C2' C3' ; C2' H2' ; C2' O2' ; O2' HT2'; C3' C4' ; C3' H3' C3' O3' ; O3' HT3'; C4' C5' ; C4' H4' ; C4' O4' ; O4' C1' C5' O5' ; C5' H51'; C5' H52'; O5' PA ; PA OA1 ; PA OA2 PA OA3 ; OA3 PB ; PB OB1 ; PB OB2 ; PB OB3; OB3 PG PG OG1 ; PG OG2 ; PG OG3 N1 N3 C2 H2 ; N1 C5 C6 N10 ; N3 C5 C4 N9 C4 C6 C5 N7 ; N7 N9 C8
[gmx-users] Re: gmx-users Digest, Vol 48, Issue 82
://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php http://www.gromacs.org/mailing_lists/users.php Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search 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 http://www.gromacs.org/mailing_lists/users.php -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20080424/be06fc7f/atta chment.html http://www.gromacs.org/pipermail/gmx-users/attachments/20080424/be06fc7f/att achment.html -- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 48, Issue 82 * ___ 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] Converting OPLS parameters
Hello Ramon, There's no automatic way, and prodrg doesn't deal with OPLS. If you have common residues (protein, water, maybe also ATP and NAG) you can use pdb2gmx. Otherwise, you'll have to write a script or do things by hand. Since you already have the parameters it shouldn't be too difficult. Ran. Ramon Crehuet wrote: Dear Gromacs users, I am new to gromacs. I have just installed and read some tutorials. I would like to start reproducing the results I have calculated with another program (Dynamo). My system has a protein, water, ATP and N-acetylglutamate (NAG). The protein and water are trivial to convert. But I would like to use the same ATP and NAG parameters that I already have in my OPLS file (I enclose this file for the ATP at the end of the mail). I know PRODRG can generate the topology files, but it also creates the force field parameters, doesn't it? Is there an automatic way to translate the OPLS format to gromacs? Or could you suggest another work-around? Thanks in advance, Ramon !=== ! OPLS MM Definition File for ATP !=== ! ! . Notes: ! ! !=== MM_Definitions OPLS_AA 1.0 ! . Atom Type Definitions. Types ! Atom Name Atomic Number Sigma Epsilon H 10.0 0.0 HO10.0 0.0 HC12.5 0.03000 CA63.5 0.08000 ! for Adenine CB63.5 0.08000 ! for Adenine CK63.5 0.08000 ! for Adenine CQ63.5 0.08000 ! for Adenine CT63.5 0.06600 N*73.25000 0.17000 N273.25000 0.17000 NB73.25000 0.17000 ! for Adenine NC73.25000 0.17000 ! for Adenine O 83.15000 0.2 OH83.07000 0.17000 OS82.9 0.14000 P153.74000 0.2 End ! . Electrostatics and Lennard-Jones Options. Electrostatics Scale 0.5 Lennard_Jones Scale 0.5 ! . Units specification. Units kcal/mole !=== ! . Residue Definitions. !=== Residues !--- Residue ATP !--- ! # Atoms, bonds and impropers. 44 45 5 N1NC -0.53 ! Impact Adenine C2CQ 0.22 ! Impact Adenine H2HC 0.20 ! Impact Adenine N3NC -0.55 ! Impact Adenine C4CB 0.38 ! Impact Adenine C5CB 0.15 ! Impact Adenine C6CA 0.44 ! Impact Adenine N7NB -0.49 ! Impact Adenine C8CK 0.20 ! Impact Adenine H8HC 0.20 ! Impact Adenine N9N* -0.50 ! Impact Adenine N10 N2 -0.81 ! Impact Adenine H11 H 0.37 ! Impact Adenine H12 H 0.37 ! Impact Adenine C1' CT 0.25 ! adjusted H1' HC 0.10 ! Impact HC hemiacetal C2' CT 0.20 ! Impact CT diols H2' HC 0.10 ! Impact HC hemiacetal O2' OH -0.70 ! Impact OH6 hemiacetal, diol HT2' HO 0.43 ! Impact HO hemiacetal, diol C3' CT 0.20 ! Impact CT diols H3' HC 0.10 ! Impact HC hemiacetal O3' OH -0.70 ! Impact OH6 hemiacetal, diol HT3' HO 0.43 ! Impact HO hemiacetal, diol C4' CT 0.24 ! adjusted O4' OS -0.40 ! Impact OS ether, acetal. H4' HC 0.10 ! Impact HC hemiacetal C5' CT 0.42 ! HF/6-31+G* CHelpG H51' HC -0.10 ! HF/6-31+G* CHelpG H52' HC -0.10 ! HF/6-31+G* CHelpG O5' OS -0.71 ! HF/6-31+G* CHelpG PAP 1.85 ! HF/6-31+G* CHelpG OA1 O -1.07 ! HF/6-31+G* CHelpG OA2 O -1.07 ! HF/6-31+G* CHelpG OA3 OS -0.78 ! HF/6-31+G* CHelpG PBP 1.98 ! HF/6-31+G* CHelpG OB1 O -1.09 ! HF/6-31+G* CHelpG OB2 O -1.09 ! HF/6-31+G* CHelpG OB3 OS -0.74 ! HF/6-31+G* CHelpG PGP 2.04 ! HF/6-31+G* CHelpG OG1 O -1.18 ! HF/6-31+G* CHelpG OG2 O -1.18 ! HF/6-31+G* CHelpG OG3 O -1.18 ! HF/6-31+G* CHelpG N1 C2 ; C2 N3 ; C2 H2 ; N3 C4 ; C4 C5 ; C5 C6 C6 N1 ; C6 N10 ; N10 H11 ; N10 H12 ; C5 N7 ; N7 C8 C8 N9 ; C8 H8 ;
[gmx-users] Problem with ref_t and tau_t values
Hi List: I am trying to run a MD of a system containing 12256 atoms and grompp gives me that Fatal error about ¨not enough ref_t and tau_t values¨ , I have already tried everything recommended in the mailing list and can not solve my problem. Any new tips? -- Miguel ___ 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 ref_t and tau_t values
Quoting Miguel Fernández Oliva [EMAIL PROTECTED]: Hi List: I am trying to run a MD of a system containing 12256 atoms and grompp gives me that Fatal error about ¨not enough ref_t and tau_t values¨ , I have already tried everything recommended in the mailing list and can not solve my problem. Any new tips? Without seeing your .mdp file, not really. If you can show us that, we might have some idea. -Justin -- Miguel ___ 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 Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ 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] Entropy correction in PMF
Thanks a lot Chris and Berk for your answers. I think that there are (at least) two different and independent corrections that should be performed to estimate absolute binding energies from the pmf (that is indeed my aim) -the correction for the reference state that depends on the concentration of the different species in the solution (this is quite clear in the Gilson's papers) and the entropic correction. I may agree that whether or not the entropic correction should be performed depends on what you want the pmf for but what is the difference between a substrate-protein complex and the interaction between two methane molecules in solution regarding the entropic correction? My confusion comes from these two sentences in the manual: When one wants to pull a substrate into a protein, this entropic term indeed contributes to the work to get the substrate into the protein. But when calculating a pmf between two solutes in a solvent, for the purpose of simulating without solvent, the entropic contribution should be removed. Summing up my concern: Does the entropic term really contribute to the absolute binding energy, or, on the contrary, this absolute binding energy must be calculated from the previously corrected pmf? Angel. On Thu, 2008-04-24 at 09:23 +0200, Berk Hess wrote: __ Date: Wed, 23 Apr 2008 20:34:40 -0400 From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: [gmx-users] Entropy correction in PMF That sentence could definitely use some massaging. Try this: Whether one needs to correct for this contribution depends on what the pmf should represent. When one wants to pull a substrate into a protein, this entropic term indeed contributes to the work to get the substrate into the protein. This is because the work required to pull a ligand into a protein binding pocket depends on the concentration of that ligand in the unbound state. The entropic contribution, however, depends on the size of your simulation box if your sampling of the entire box is ergodic. Further, the large computational cost of converging the sampling of large separations between the protein and ligand make it undesirable to target true ergodicity for large separations. It is more efficient to calculate the work required to pull a ligand into a protein from an unbound state that has a defined concentration and then to separately calculate the work required to change that concentration to some standard state, e.g. 1 molar. If any other free energy users care to comment, perhaps we could come up with something based on what I have suggested (or something entirely different) that could go into the new manual. --original message -- I sent the attached message on last March 31 but I didn't get any answer... may be the right people was not available at that time and that is why I am trying again. I would thank a lot to have some more detail about this paragraph in the gromacs manual (version 3.3, chapter 6, page 111): Whether one needs to correct for this contribution depends on what the pmf should represent. When one wants to pull a substrate into a protein, this entropic term indeed contributes to the work to get the substrate into the protein. But when calculating a pmf between two solutes in a solvent, for the purpose of simulating without solvent, the entropic contribution should be removed. Note that this term can be significant; when at 300K the distance is halved the contribution is 3.5 kJ mol-1.� why exactly for a substrate-protein complex shouldn't one correct the pmf? This is not a simple should or should not. It depends on what you want to use the PMF for. You should be aware that there is this simple entropic distance contribution. When a substrate needs to enter into a protein, it has to work against this entropic term. If you include this or not, depends on how your want to present the PMF in a presentation, or how your will use it for further calculation. Berk. __ Express yourself instantly with MSN Messenger! MSN Messenger ___ 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
[gmx-users] Infinite system PBC and Bonded Interaction
I am simulating a infinite graphene sheet in water. The expected is that the system it is infinite in xy plane. But after the simulation I note that the edges of the box (in particular the graphene) are not replicables, i. e., it do not match with its images. I suspect that I may be wrong in using any option mdp file I got the same result for both full and xyz for option pbd. What have I to do to my system be infinitely replicated, with all its bonded interaction matching? -- ___ Eudes Eterno Fileti Centro de Ciência Naturais e Humanas Universidade Federal do ABC Rua Catequese, 242 - 3º Andar 09090-400 Santo André - SP Brasil Tel: +55 11 4437-1600 ramal 408 skype: eefileti http://cromo.ufabc.edu.br/~fileti/ ___ 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] Ion Parametrization in OPLS-AA forcefield
Dear All, I require the papers in which the original parameters (in ions.itp) for ions in OPLSAA force field was published. Also I would like to if there are any studies in which these ion parameters were benchmarked with experimental values. Thanks a lot. Regards Srinivas -- Srinivas Ramachandran Graduate Student Molecular and Cellular Biophysics Program Department of Biochemistry and Biophysics University of North Carolina at Chapel Hill USA www.unc.edu/~ramachan ___ 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] Defining charges: [atomtypes] vs [atoms]
Looking through the documentation, it seems like the charge of an atom may be defined in one of two ways: in the [atomtypes] directive, or in the [atoms] directive. In the past, I've always made them identical, but I have seen examples where they differ. Why are there two ways to define an atom's charge, and which definition takes precedence? Also, during a free energy calculation where an atom mutates typeA - typeB, are the charge values as defined in the [atomtypes] section or [atoms] section used? Thanks -- Matt ___ 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] about NMR Refinement
Hi users I sent the attached message on last April 16th, but I didn't get any answer... that is why I am trying again. I would thank a lot to have some information about NMR refinement with GROMACS Dear users, I want to do a NMR refinement (with GROMACS) of a protein structure that comes from CYANA, (a program that perform torsion angle dynamics), to include a full physical force field and explicit water to represent the solvent to improve the quality of the structure, my question is about the protocol that i should do, i have read the manual but i dont know if i need to do annealing simulation, or position restricted dynamics or use NMR refinement and how i should choose the parameters, is there any manual to do that? thanks in advance ROGELIO HERNANDEZ - Yahoo! Deportes Beta ¡No te pierdas lo último sobre el torneo clausura 2008! Entérate aquí http://deportes.yahoo.com___ 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] Entropy correction in PMF
Chris, I think you are correct here. For binding calculations there is probably a further trick relating to how to define an unbound state that has a well-defined concentration. This I think depends on how one is pulling -- i.e. doing simple radial PMFs is probably a bad idea, because to even converge the PMF when the ligand is separate from the protein, you by definition need to integrate over all x, y, and z at that r, so you end up needing to sample a spherical shell covering a substantial fraction of the simulation box. For this reason I think it's probably wiser to do pulling along a specified vector away from the protein, for example (this is what people using this strategy have mostly done, I think). Additionally there is the standard state issue, which is important also. I think you may have more or less raised all of these issues already; I'm just trying to put them a slightly different way. David On Wed, Apr 23, 2008 at 5:34 PM, [EMAIL PROTECTED] wrote: That sentence could definitely use some massaging. Try this: Whether one needs to correct for this contribution depends on what the pmf should represent. When one wants to pull a substrate into a protein, this entropic term indeed contributes to the work to get the substrate into the protein. This is because the work required to pull a ligand into a protein binding pocket depends on the concentration of that ligand in the unbound state. The entropic contribution, however, depends on the size of your simulation box if your sampling of the entire box is ergodic. Further, the large computational cost of converging the sampling of large separations between the protein and ligand make it undesirable to target true ergodicity for large separations. It is more efficient to calculate the work required to pull a ligand into a protein from an unbound state that has a defined concentration and then to separately calculate the work required to change that concentration to some standard state, e.g. 1 molar. If any other free energy users care to comment, perhaps we could come up with something based on what I have suggested (or something entirely different) that could go into the new manual. --original message -- I sent the attached message on last March 31 but I didn't get any answer... may be the right people was not available at that time and that is why I am trying again. I would thank a lot to have some more detail about this paragraph in the gromacs manual (version 3.3, chapter 6, page 111): Whether one needs to correct for this contribution depends on what the pmf should represent. When one wants to pull a substrate into a protein, this entropic term indeed contributes to the work to get the substrate into the protein. But when calculating a pmf between two solutes in a solvent, for the purpose of simulating without solvent, the entropic contribution should be removed. Note that this term can be significant; when at 300K the distance is halved the contribution is 3.5 kJ mol-1. why exactly for a substrate-protein complex shouldn't one correct the pmf? ___ 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 thewww 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] RE: x2top error in CNT simulation on Gromacs 3.3.3 (Christopher Stiles)
Jue, Please read over this wiki article that I sent to you just the other day: http://wiki.gromacs.org/index.php/Carbon_Nanotube Please to special note of the sending e-mails to the mailing list and not individuals, while then every one can benefit. On my site I set it up so that you can check to make sure you are doing things correctly every step of the way by providing copies of files that you should have at each step and a complete copy of my output with each step. Please take some time to learn how *.pdb file should look like and its format. Since I do not have version 3.3.3 I can not really offer any better advice. Take care, ~Christopher Stiles -Original Message- From: Hero [mailto:[EMAIL PROTECTED] Sent: Thursday, April 24, 2008 12:42 PM To: [EMAIL PROTECTED] Subject: x2top error in CNT simulation on Gromacs 3.3.3 (Christopher Stiles) Dear Mr. Stiles, Thank you so much for your reply! Sorry I keep on bugging you on CNT! But I do have problems making it run on Gromacs 3.3.3. I have spent a lot of time trying to figure out the problems, unfortunately I still do not know what happened using the new version. The files are attached and I sincerely appreciate your kind help and time! Very best regards, Jue Message: 3 Date: Wed, 23 Apr 2008 22:27:57 -0400 From: Christopher Stiles [EMAIL PROTECTED] Subject: RE: [gmx-users] x2top error in CNT simulation on Gromacs 3.3.3 To: 'Discussion list for GROMACS users' gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain;charset=us-ascii Send a copy of your ffgmx.n2t, ffgmxbon.itp, and SWNT_6_6_144.pdb files please, if the following does not work. Also I think that the information updated in ffgmxbon.itp might be found in a different file with the 3.3.3 version (I think from looking at previous e-mails that it is ffencadvbon.itp). If any one could let me know I will make an addendum to my site for this new version. (I am about done using GROMACS due to the fact that I am graduating, so I will not be updating mine) ~Christopher Stiles College of Nanoscale Science and Engineering (CNSE) State University of New York, Albany, New York 12203, USA -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Hero Sent: Wednesday, April 23, 2008 5:44 PM To: gmx-users@gromacs.org Subject: [gmx-users] x2top error in CNT simulation on Gromacs 3.3.3 Dear All, I am trying to simulate water flow in CNT and just followed the website: http://cs86.com/CNSE/SWNT.htm I did the following: 1. ffgmx.n2t must change this files name to ffencadv.n2t and add the following 2 lines: C C 1 C ; CNT Carbon with one bond C C 2 C C ; CNT double bonded Carbon 2. ffgmxbon.itp add the following line to it: # [ bondtypes ] ; i j func b0 kb C C 1 0.14210 478900. # [ angletypes ] ; i j k func th0 cth C C C 1 120.000 397.480 # [ dihedraltypes ] ; i l func q0 cq C C 1 0.000 167.360 # But when I ran: x2top -f SWNT_6_6_144.pdb -o SWNT_6_6_144.top -r SWNT_6_6_144.rtp Error message appeared: Can not find forcefield for atom C-1 with 2 bonds . Can not find forcefield for atom C-143 with 2 bonds Can not find forcefield for atom C-144 with 2 bonds --- Program x2top, VERSION 3.3.3 Source code file: x2top.c, line: 206 Fatal error: Could only find a forcefield type for 0 out of 144 atoms --- Could you please tell me what is the problem? This works on Gromacs 3.3.1 Thank you very much! Jue ___ _ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ 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] Infinite system PBC and Bonded Interaction
Eudes Fileti wrote: I am simulating a infinite graphene sheet in water. The expected is that the system it is infinite in xy plane. But after the simulation I note that the edges of the box (in particular the graphene) are not replicables, i. e., it do not match with its images. I suspect that I may be wrong in using any option mdp file I got the same result for both full and xyz for option pbd. What have I to do to my system be infinitely replicated, with all its bonded interaction matching? There's some advice here for an analogous problem that might help - http://wiki.gromacs.org/index.php/Carbon_Nanotube 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] Ion Parametrization in OPLS-AA forcefield
srinivas ramachandran wrote: Dear All, I require the papers in which the original parameters (in ions.itp) for ions in OPLSAA force field was published. Also I would like to if there are any studies in which these ion parameters were benchmarked with experimental values. require is a dangerous word to use when asking for help from people you don't know! :-) There are literature references to the force fields in the GROMACS manual - I suggest you start by reading them. 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] Defining charges: [atomtypes] vs [atoms]
Matt Wyczalkowski wrote: Looking through the documentation, it seems like the charge of an atom may be defined in one of two ways: in the [atomtypes] directive, or in the [atoms] directive. In the past, I've always made them identical, but I have seen examples where they differ. Why are there two ways to define an atom's charge, and which definition takes precedence? Having two ways allows for more flexibility. Some force fields might be prescriptive about charges for certain atom types, some might not be. Accordingly, [atoms] takes precedence. Also, during a free energy calculation where an atom mutates typeA - typeB, are the charge values as defined in the [atomtypes] section or [atoms] section used? I don't know, but I expect [atoms]. 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] about NMR Refinement
Rogelio Hernández wrote: Hi users I sent the attached message on last April 16th, but I didn't get any answer... that is why I am trying again. I would thank a lot to have some information about NMR refinement with GROMACS There's nothing to say - you should search the manual for NMR and read about what it has to say there. Then search the literature for people who've done NMR refinement using MD programs and learn from that. 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] A question
Dear Mark, Thanks for your invaluable advice. I solved my problem. Samad --- On Thu, 4/24/08, Mark Abraham [EMAIL PROTECTED] wrote: From: Mark Abraham [EMAIL PROTECTED] Subject: Re: [gmx-users] A question To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Thursday, April 24, 2008, 12:37 AM samad ahadian wrote: Hello, I am new user of Gromacs. I did a pdb2gmx command on my pdb file. I got an error below: Residue 'XXX' not found in residue topology database I know that I blindly made my pdb file using Materials Studio 4.2. Let me know there is a special software to make a pdb file? Thank you in advance for your response. No, but you can certainly make life hard for yourself by using poor PDB-producing software, or using good software poorly. See http://wiki.gromacs.org/index.php/Errors for some background for this error. You need to generate a structure file whose residues and atoms are defined for the force field you intend to use, and which are named suitably so that pdb2gmx can recognize them. 'XXX' suggests that either MS4.2, or your usage of it, or both, are making life hard. Depending on your level of newness, you should definitely do some background textbook/manual/literature reading, and/or tutorials. 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 Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ ___ 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] problem running parallel simulation regarding the md log file
Dear GROMACS users and developers, I've encountered a problem when tying to do a parallel simulation for my protein structure. I tried so many times but the problem still with the log file. Can someone help me out here please?. I changed the log filename, but still got this error: --- Program mdrun_mpi, VERSION 3.3.2 Source code file: futil.c, line: 313 File input/output error: tg1_md.log --- You Own the Sun (Throwing Muses) Halting program mdrun_mpi gcq#111: You Own the Sun (Throwing Muses) [0] MPI Abort by user Aborting program ! [0] Aborting program! p0_2442: p4_error: : -1 p4_error: latest msg from perror: No such file or directory Muhammad Alif Mohammad Latif Department of Chemistry Faculty of Science Universiti Putra Malaysia 43400 UPM Serdang, Selangor MALAYSIA Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ___ 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] negative eigenvalues occured and not nearly zero
Hello gmx-users: I'm recently using Normal Mode Analysis(NMA) of GROMACS package to calculate the foundamental frequency of graphite systems. But I got some results that are unexplainable, and I can not continue my work now. For all the examples below, I use the double precision GROMACS functions: grompp_d, mdrun_d, and g_nmeig_d. For the EM part, I used the conjugated-gradients algorism, and for the NMA part, I used nm integrator and included the full precision structure file: em.trr into the .tpr input file. For the systems that I applied no restraints, the first six eigenvalues should be zero, or at least nearly zero if we considering the accuracy of numerical calculating. But the typical first twelve eigenvalues I got have the values below: (after EM, the Fmax5e-4) 1-0.37993 2 -0.335177 3 -0.206887 4 -0.111813 5 -0.0381566 6 -0.0211911 7 0.0189381 8 0.0370517 9 0.0385126 100.093188 110.132927 120.169143 the first eigenvalue has larger absolute value than the 7th eigenvalue, which should not happen for an unrestrained system. WHY the first six eigenvalues are not zero or nearly zero? I guess there might by something wrong in my input files, but I can not figure out where it is. By the way, the topology files and coordinate files are surely correct. Another problem is: For the system that I applied restraints to, which removed the translation and rotation about the center of mass, the eigenvalues should be all positive. But I still found that negative values occured. 1 -0.135621 2 -0.074 3 -0.0390086 4 -0.0108285 5 0.0101438 6 0.0553579 70.146471 80.162898 90.344921 100.396553 110.486316 120.544625 WHY? If anyone used the NMA of GROMACS before and got correct output, it will be very helpful if you can send me your parameters or input files or give me some advice. If you need any more information, please e-mail me. I really need your help, thanks. Yours Sincerely Yue Shao E-mail: [EMAIL PROTECTED] ___ ___ Shao Yue Institue of Biomechanics and Biomedical Engineering Department of Engineering Mechanics Tsinghua University P.R. China ___ 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
