Re: [gmx-users] pdb2gmx and periodic molecule
Well, none of us in this project have the scripting skills necessary for this, that's sort of the problem... Thanks, Alex Hi Alex, I think the best way is to extend the chain, such that you get an overlap between both ends. So for a stretch of DNA ACGT You would generate TACGTA Then you strip off the terminal atoms and rewire the links over the boundary. It requires renumbering the topology and at first looks a bit cumbersome, but this ensures all the links are correct and the modifications of the termini have no effect, and it's not very hard to script. And, of course, scripting it is a one time effort to avoid doing it manually later. Cheers, Tsjerk On Apr 26, 2015 5:55 AM, "Alex" nedoma...@gmail.com wrote: JL The force field parameters for a phosphodiester are the same in a linear, finite JL DNA as they will be in your infinite chain. I didn't mean that anything would need to be changed in the description of residues. The FF handles a finite chain perfectly. JL The problem is in telling pdb2gmx JL "don't link i,i+1 here, instead link i,i+(some number of intervening nucleotides)." This is exactly what I meant, the linking. Is there a way to achieve this without messing with the code? I just haven't looked at the code, so if you think I'm being a cheeky little bastard, I'll accept that. :) Thanks, Alex -- Gromacs Users mailing list * Please search the archive athttp://www.gromacs.org/Support/Mailing_Lists/GMX-Users_Listbefore posting! * Can't post? Readhttp://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor send a mail togmx-users-requ...@gromacs.org. -- Best regards, Alex mailto:nedoma...@gmail.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] on the MDP options
Dear All, In the on-line lysozyme tutorial, it gives a series of mdp files. But it meantioned for different force fields the options should be different. Will you please tell me regardless of force fields, whether all the cutoff-scheme can be Verlet? Besides I can change the rcoulomb and rvdw fom 1.0 to 1.4, what else should I change on the basis of the on-line tutorial MDP files, with the difference of the force fields? I am looking forward to getting your reply. Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] how to name HIS in the input pdb for the pdb2gmx
Hi, Files in fixed-column formats use the column widths to separate elements. They don't use white space at the same time, for the same job! Try it and see ;-) Mark On 26/04/2015 6:29 am, Brett brettliu...@163.com wrote: Dear All， If we change HIS188 in Chain B to HISE188 in Chain B, before change the PDB looks like HIS B 188, but after change the PDB will look like HISEB 188, which makes thereis no space between HISE and Bchain. I do not know whether pdb2gmx can recognize HISEB 188, or we process it in some other way. I am looking forward to getting a reply from you. Brett At 2015-04-26 11:08:19, Justin Lemkul jalem...@vt.edu wrote: On 4/25/15 11:05 PM, Brett wrote: Dear All, For gromacs, for HIS residues there are HISD,HISE and HISH. In the original PDB file, are HIS residues are written as HIS. If based on necessity, I change exactly some HIS to HISD, some HIS to HISE and some HIS to HISH,the coordinate lines contaning HISD,HISE and HISH will not aling with all the other coordinate lines. Does pdb2gmx recognize these non-aligned coordinate lines? Or what other strategy you recommend me to take so that pdb2gmx can recognize HISD,HISE and HISH? Do the replacement properly and don't screw up column alignment. It needs to be correct for proper interpretation of the coordinates. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pdb2gmx and periodic molecule
Hi Alex, I think the best way is to extend the chain, such that you get an overlap between both ends. So for a stretch of DNA ACGT You would generate TACGTA Then you strip off the terminal atoms and rewire the links over the boundary. It requires renumbering the topology and at first looks a bit cumbersome, but this ensures all the links are correct and the modifications of the termini have no effect, and it's not very hard to script. And, of course, scripting it is a one time effort to avoid doing it manually later. Cheers, Tsjerk On Apr 26, 2015 5:55 AM, Alex nedoma...@gmail.com wrote: JL The force field parameters for a phosphodiester are the same in a linear, finite JL DNA as they will be in your infinite chain. I didn't mean that anything would need to be changed in the description of residues. The FF handles a finite chain perfectly. JL The problem is in telling pdb2gmx JL don't link i,i+1 here, instead link i,i+(some number of intervening nucleotides). This is exactly what I meant, the linking. Is there a way to achieve this without messing with the code? I just haven't looked at the code, so if you think I'm being a cheeky little bastard, I'll accept that. :) Thanks, Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Molecule specific explosion
Hi, Look at the whole molecule topology. Don't ignore any warnings. Mark On 26/04/2015 9:38 am, Eric Smoll ericsm...@gmail.com wrote: Hello Gromacs Users, I have constructed a multi-component solution and, during energy minimization, one molecule type is radically deforming under ~ 0.2 ps. All molecules of this type explode simultaneously. Looking over the topology, all the atoms in this molecules appear to have correct forcefield assignments. I am writing to ask if anyone might have a suggestion on how I can identify the origin of this problem. Best, Eric -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Molecule specific explosion
Hello Gromacs Users, I have constructed a multi-component solution and, during energy minimization, one molecule type is radically deforming under ~ 0.2 ps. All molecules of this type explode simultaneously. Looking over the topology, all the atoms in this molecules appear to have correct forcefield assignments. I am writing to ask if anyone might have a suggestion on how I can identify the origin of this problem. Best, Eric -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] on the xmgrac for gromacs
Dear All, For the grpmacs analysis purpose, from the official GRACE site I have downloaded and installed different versions of GRACE, some was said to definitely contains xmgrace. But after installation, none contains xmgrace, they contain grace or gr in the bin folder. After I invoke the grace or gr, both needs me input commands, and if I input grace -nxy potential.xvg, they did not work. My workstation is a red hat linux system, and I do not know whether there is X windows installed. Will you please let me know how to have my xmgrace -nxy potential.xvg function works? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] on the xmgrac for gromacs
The issue is, no mater grace or xmggrace I download, I cannot have the xmgrace exe file in the corresponding bin folder produced. Thus will you tell me which version of grace has the xmgrace after unpack and installation? Brett At 2015-04-26 23:09:23, abhijit Kayal abhijitchemi...@gmail.com wrote: the command is xmgrace, try with xmgrace -nxy. On Sun, Apr 26, 2015 at 7:01 AM, Brett brettliu...@163.com wrote: Dear All, For the grpmacs analysis purpose, from the official GRACE site I have downloaded and installed different versions of GRACE, some was said to definitely contains xmgrace. But after installation, none contains xmgrace, they contain grace or gr in the bin folder. After I invoke the grace or gr, both needs me input commands, and if I input grace -nxy potential.xvg, they did not work. My workstation is a red hat linux system, and I do not know whether there is X windows installed. Will you please let me know how to have my xmgrace -nxy potential.xvg function works? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] free energy
On 4/26/15 8:54 AM, fatemeh ramezani wrote: Dear gmx-usersI want to calculate free energy of binding of ligand to Au surface in 8 ns simulation. I considered 7 lambda (lambda= 0, 0.2, 0.4, 0.6, 0.8, 0.9, 1) and for every lambda a mdp file. for example lambda-0 mdp file: title = n.pdb restraining cpp = /lib/cpp constraints = all-bonds constraint_algorithm = lincs lincs_order = 4 lincs_iter = 1 integrator = sd dt = 0.0008 nsteps = 250 nstcomm = 100 nstcalcenergy = 100 nstdhdl = 100 comm_mode = nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstlist = 10 ns_type = grid rlist = 1.4 ;rlistlong = 2 coulombtype = PME rcoulomb= 1.4 rcoulomb-switch = 0.8 rvdw= 1 vdwtype = shift rvdw-switch = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in three groups Tcoupl = V-rescale tau_t = 0.1 0.1 tc-grps= Protein Non-Protein ref_t = 300 300 ; Pressure coupling is on ;Pcoupl = berendsen Pcoupl = Parrinello-Rahman Pcoupltype = isotropic tau_p = 5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 energygrps = Protein Sol freezegrps = AU AUI AUC freezedim = Y Y Y Y Y Y Y Y Y free-energy = yes couple-moltype = Protein2 init-lambda = 0 sc-power= 1 sc-sigma= 0.3 sc-alpha= 1 couple-intramol = no couple-lambda1 = vdwq couple-lambda0 = none foreign-lambda = ALL_LAMBDAS$ As you can see dt= 0.0008, for 8 ns simulation, I should take the nstep of each Lambda 1 ( or I should divide 8 ns between 7 Lambda)? In other words, the simulation time for each of the 7 lambda should be 8 ns or every lambda simulation time should be considered so that the total simulation time of lambdas be 8 ns? How have you predetermined that you want 8 ns total, split over 7 states? You should do some test runs to assess convergence and determine how much sampling per state is necessary, rather than just assume a certain time. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using thermostats to create temperature gradient in system
Hi Agnivo, Temperature gradient means non-equilibrium MD (NEMD) See notes from Prof. Martini: https://nanohub.org/resources/7582/download/Martini_L10_NonequilibruimMD.pdf What observable would you like to measure? Lets say you want to measure observable A. One procedure I can think of: 1. You can run all system at T=300K with NVT. After equilibrium, continue running all system at T=400K with freezing solvent group. See, to how to freeze a group, http://manual.gromacs.org/online/mdp_opt.html#neq To get a good statistic, you need to repeat this procedure K times as solvent thermal wall configuration would be different at each simulation. 100ps? Where did you get that? You need to see how observable A behaves to see if 100ps is enough, A time average. And see how A behaves in K different cases. 2. Similar to previous procedure but this time after freezing solvent group, run system in NVE. Again, you need to repeat this many times to get a good statistic. Similarly monitor observable A to see if 500ps is enough. However, I suggest you to talk to someone having NEMD experience as this procedure is just a heuristic approach. -m -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] a question related to gmx energy minimization
Dear Tsjerk, Will you please explain to me why the RMSD in this step is so large? For this reason I think there is something wrong. I am looking forward to getting a reply from you. Brett At 2015-04-26 20:59:59, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Brett, Too high for what? You do EM because you just built (part of) your system, and in doing so introduced clashes and non-ideal geometries. These lead to high potential energy, so you relax them with EM. What you see is how much the system relaxed. Noone usually cares how much potential energy was lost during EM. The thing that matters is whether the resulting system is relaxed enough to run the simulation. Cheers, Tsjerk On Sun, Apr 26, 2015 at 2:43 PM, Brett brettliu...@163.com wrote: Dear All, I just run the command gmx energy -f em.edr -o potential.xvg for my energy minimization step MD, but I find the RMSD given by this command is 142611, which I regard to be too high. Will you please explain to me what leads to the so high RMSD (Err.Est is 53000, Tot-Drift is -341107 KJ/mol)? I am looking forward to getting your reply. Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] on the xmgrac for gromacs
the command is xmgrace, try with xmgrace -nxy. On Sun, Apr 26, 2015 at 7:01 AM, Brett brettliu...@163.com wrote: Dear All, For the grpmacs analysis purpose, from the official GRACE site I have downloaded and installed different versions of GRACE, some was said to definitely contains xmgrace. But after installation, none contains xmgrace, they contain grace or gr in the bin folder. After I invoke the grace or gr, both needs me input commands, and if I input grace -nxy potential.xvg, they did not work. My workstation is a red hat linux system, and I do not know whether there is X windows installed. Will you please let me know how to have my xmgrace -nxy potential.xvg function works? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] a question related to gmx energy minimization
On 4/26/15 9:53 AM, Brett wrote: Dear Tsjerk, Will you please explain to me why the RMSD in this step is so large? For this reason I think there is something wrong. No, there's nothing wrong; the analysis in this case is meaningless. Energy minimization inherently makes large (orders of magnitude in many cases) changes to the potential as the structure is relaxed. An average energy over the course of this process has absolutely no physical meaning. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] a question related to gmx energy minimization
Hi Brett, Too high for what? You do EM because you just built (part of) your system, and in doing so introduced clashes and non-ideal geometries. These lead to high potential energy, so you relax them with EM. What you see is how much the system relaxed. Noone usually cares how much potential energy was lost during EM. The thing that matters is whether the resulting system is relaxed enough to run the simulation. Cheers, Tsjerk On Sun, Apr 26, 2015 at 2:43 PM, Brett brettliu...@163.com wrote: Dear All, I just run the command gmx energy -f em.edr -o potential.xvg for my energy minimization step MD, but I find the RMSD given by this command is 142611, which I regard to be too high. Will you please explain to me what leads to the so high RMSD (Err.Est is 53000, Tot-Drift is -341107 KJ/mol)? I am looking forward to getting your reply. Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] a question related to gmx energy minimization
Dear All, I just run the command gmx energy -f em.edr -o potential.xvg for my energy minimization step MD, but I find the RMSD given by this command is 142611, which I regard to be too high. Will you please explain to me what leads to the so high RMSD (Err.Est is 53000, Tot-Drift is -341107 KJ/mol)? I am looking forward to getting your reply. Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] free energy
Dear gmx-usersI want to calculate free energy of binding of ligand to Au surface in 8 ns simulation. I considered 7 lambda (lambda= 0, 0.2, 0.4, 0.6, 0.8, 0.9, 1) and for every lambda a mdp file. for example lambda-0 mdp file: title = n.pdb restraining cpp = /lib/cpp constraints = all-bonds constraint_algorithm = lincs lincs_order = 4 lincs_iter = 1 integrator = sd dt = 0.0008 nsteps = 250 nstcomm = 100 nstcalcenergy = 100 nstdhdl = 100 comm_mode = nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstlist = 10 ns_type = grid rlist = 1.4 ;rlistlong = 2 coulombtype = PME rcoulomb = 1.4 rcoulomb-switch = 0.8 rvdw = 1 vdwtype = shift rvdw-switch = 0.9 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in three groups Tcoupl = V-rescale tau_t = 0.1 0.1 tc-grps = Protein Non-Protein ref_t = 300 300 ; Pressure coupling is on ;Pcoupl = berendsen Pcoupl = Parrinello-Rahman Pcoupltype = isotropic tau_p = 5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 energygrps = Protein Sol freezegrps = AU AUI AUC freezedim = Y Y Y Y Y Y Y Y Y free-energy = yes couple-moltype = Protein2 init-lambda = 0 sc-power = 1 sc-sigma = 0.3 sc-alpha = 1 couple-intramol = no couple-lambda1 = vdwq couple-lambda0 = none foreign-lambda = ALL_LAMBDAS$ As you can see dt= 0.0008, for 8 ns simulation, I should take the nstep of each Lambda 1 ( or I should divide 8 ns between 7 Lambda)? In other words, the simulation time for each of the 7 lambda should be 8 ns or every lambda simulation time should be considered so that the total simulation time of lambdas be 8 ns? I hope I could correctly ask my question. I would greatly appreciate your response to my question. Fatemeh Ramezani -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using thermostats to create temperature gradient in system
Hi Agnivo; Yes, the idea of freezing the solvent or the protein in many times is to sample the non-equilibrium thermal process. It will remain in the target temperature on average, over many fixed configurations obtained by different NVT runs (equilibrium runs). But you may need to run this many K times to get a good statistic as I said. Concerning NVE, yes, do the same fixing approach with the protein. But as I mentioned earlier, this is quite heuristic approach, I suggest you to talk with any faculty member having background in non-equilibrium processes if this approach mimics what you need. Best, -m -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using thermostats to create temperature gradient in system
Hello Users, This is in relation to my previous posts. I am looking to replicate the figure below : tempgradient.png https://docs.google.com/file/d/0B-U8uULVZjfRQWlHeHVJdDJjcms/edit?usp=drive_web Basically I am following this paper for my work : Lervik_ProtWatInterHT_2009.pdf https://docs.google.com/file/d/0B-U8uULVZjfRU2haRkNHd2wwNTA/edit?usp=drive_web Look at figure 6 of the paper. My system has water at 300 K and protein at 400 K. The authors of the paper describe that they removed the thermostat from the protein and let it relax keeping the solvent (water) at 300 K. But if I remove thermostat , I get GROMACS error and using freeze groups I am not getting any temperatures as the molecules are not moving. I can not understand how to model this system. Any suggestions will be helpful. I am doing a literature search but till now it is not fruitful. Best, Thanks Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] a question related to gmx energy minimization
On 4/26/15 7:42 PM, Brett wrote: Dear Justin, I mean why the RMSD is such huge. Does it mean in the energy mminimization step the protein has moved from point A to point B which is long long distance away from point A but, although the protein has been continously embedded in water? If the RMSD is above several thousands, it would mean the protein conformation after energy minimization would be absolutely different from the input pdb for the pdb2gmx. I am looking forward to getting a clarification. Don't confuse the RMSD of the coordinates with the RMSD of the potential energy data series. What gmx energy is printing is what you asked for - an analysis of the potential energy, so RMSD here is the RMSD of the energy values. Even small changes in the structure can have very large effects on the energy. You may go from +10^6 before EM to -10^6 after EM. That's 12 orders of magnitude difference in the energy, but your protein's RMSD is probably a fraction of an Angstrom. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using thermostats to create temperature gradient in system
Hello all, Thanks to Dr. Lemkul for asking. This is what I did to reach my present state : (a) Prepared the topology of the system using GROMOS96 43a2 ff and energy minimized the system after solvation using steepest descent algorithm. (b) Did a position restrained ( protein ) 5 ns Fatal error: 2936 atoms are not part of any of the T-Coupling groups For more information and tips for troubleshooting, please check the GROMACS Thanks Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using thermostats to create temperature gradient in system
Hello all, Thanks to Dr. Lemkul for asking. This is what I did to reach my present state : (a) Prepared the topology of the system using GROMOS96 43a2 ff and energy minimized the system after solvation using steepest descent algorithm. (b) Did a position restrained ( protein restrained ) 5 ns NVT equilibration using V-rescale thermostat at target temp. of 300 K. (c) Then I kept the solvent at 300 K in a NVT ensemble and heated the protein only by simulated annealing over 500 ps , to 400K. I checked the individual temperatures and found that it was achieved. (d) Then as mentioned in the paper if I remove the thermostat on the protein then grompp gives the following error :- Fatal error: 2936 atoms are not part of any of the T-Coupling groups For more information and tips for troubleshooting, please check the GROMACS I want to let my protein loose heat and thus go down a temp. gradient while the solvent i.e. water stays at 300 K. However , I am unable to do this. If I do not specify any thermostat in a NVT ensemble it becomes NVE and I only get a single temperature profile. Any hints as to how I can achieve my objective ? Sorry for the previous incomplete post. Thanks Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] a question related to gmx energy minimization
Dear Justin, I mean why the RMSD is such huge. Does it mean in the energy mminimization step the protein has moved from point A to point B which is long long distance away from point A but, although the protein has been continously embedded in water? If the RMSD is above several thousands, it would mean the protein conformation after energy minimization would be absolutely different from the input pdb for the pdb2gmx. I am looking forward to getting a clarification. Brett At 2015-04-27 00:00:22, Justin Lemkul jalem...@vt.edu wrote: On 4/26/15 9:53 AM, Brett wrote: Dear Tsjerk, Will you please explain to me why the RMSD in this step is so large? For this reason I think there is something wrong. No, there's nothing wrong; the analysis in this case is meaningless. Energy minimization inherently makes large (orders of magnitude in many cases) changes to the potential as the structure is relaxed. An average energy over the course of this process has absolutely no physical meaning. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using thermostats to create temperature gradient in system
On 4/26/15 7:07 PM, Agnivo Gosai wrote: Hello Users, This is in relation to my previous posts. I am looking to replicate the figure below : tempgradient.png https://docs.google.com/file/d/0B-U8uULVZjfRQWlHeHVJdDJjcms/edit?usp=drive_web Basically I am following this paper for my work : Lervik_ProtWatInterHT_2009.pdf https://docs.google.com/file/d/0B-U8uULVZjfRU2haRkNHd2wwNTA/edit?usp=drive_web Look at figure 6 of the paper. My system has water at 300 K and protein at 400 K. The authors of the paper describe that they removed the thermostat from the protein and let it relax keeping the solvent (water) at 300 K. But if I remove thermostat , I get GROMACS error and using freeze groups I am not getting any temperatures as the molecules are not moving. You'll have to show us what you're doing to get GROMACS error (what error? what were your input settings? Don't make us guess!) Freezing groups means they have no temperature and they don't move. This certainly isn't what you want. I can not understand how to model this system. Any suggestions will be helpful. I am doing a literature search but till now it is not fruitful. Setting tau_t = -1 for the protein tc-grp will remove the thermostat; e.g. not couple it. This sounds like what you want. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using thermostats to create temperature gradient in system
On 4/26/15 8:14 PM, Agnivo Gosai wrote: Hello all, Thanks to Dr. Lemkul for asking. This is what I did to reach my present state : (a) Prepared the topology of the system using GROMOS96 43a2 ff and energy minimized the system after solvation using steepest descent algorithm. (b) Did a position restrained ( protein ) 5 ns Fatal error: 2936 atoms are not part of any of the T-Coupling groups For more information and tips for troubleshooting, please check the GROMACS This means your tc-grps are set up incorrectly, but again you haven't provided your actual settings (copy and paste your .mdp when reporting problems - always). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using thermostats to create temperature gradient in system
Hello, I am copy pasting my mdp file for the last step of my procedure : Here I am not using any freeze group. ; Run parameters integrator = md; leap-frog integrator nsteps = 5; 100 ps dt = 0.002 ; 2 fs energygrps = Protein Non-Protein ; Output control nstxout = 10 nstvout = 10 nstlog = 10 nstenergy = 10 nstxtcout = 50 ; Bond parameters continuation= yes ; after trial 400 K constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.4 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.4 ; short-range electrostatic cutoff (in nm) rvdw= 1.4 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ewald_rtol = 1e-5 ; relative strength of Ewald - shifted direct potential optimize_fft= yes ; saves computation time ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Non-Protein tau_t = 0.1 ; time constant, in ps ref_t = 300 ; reference temperature,in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; COM motion removal ; These options remove COM motion of the system nstcomm = 100 comm-mode = Linear comm-grps = System Plz have a look. Thanks Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using thermostats to create temperature gradient in system
Dr. Lemkul Thanks for such an easy fix to my problem. I guess I have been doing all sort of weird stuff since last night instead of thinking logically and reading the relevant portion of the manual. Thanks Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using thermostats to create temperature gradient in system
Hello users, Thanks a lot Suzen for an insightful suggestion. My protein and solvent have been equilibrated at 300 K in an NVT ensemble. I raised the temperature of protein gradually by using simulated annealing to 400 K and the solvent has been kept at 300 K. Now I wish to get a temperature gradient such that the temperature of the protein comes down by exchanging heat with the solvent to 300 K. So as per your suggestion , do I need to freeze the solvent group so that its position will not be updated and hence it will have the same temperature ?? For the protein if I do not use a thermostat , GROMACS will give error message. So how do I fix this problem ? Or, should I freeze the protein instead and use a thermostat on the solvent ? I am trying both of these as I write this mail. Thanks Regards Agnivo Gosai Grad Student, Iowa State University. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Constraints and Energy Minimization
On 4/26/15 3:40 PM, Eric Smoll wrote: Hello Dr Lemkul, Thank you for the clarification. To summarize: If I have a bond between two atoms and one of the atoms has a topology atom field that begins with the letter H, constraints=h-bonds will transform it into a constraint. Exactly. I have another question. When specifying this constrained bond, I have an equilibrium distance but I do not have a force-constant. Is it irrelevant what value I choose for the force constant if I apply constraints to that bond? Yes. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Constraints and Energy Minimization
Hello Dr Lemkul, Thank you for the clarification. To summarize: If I have a bond between two atoms and one of the atoms has a topology atom field that begins with the letter H, constraints=h-bonds will transform it into a constraint. I have another question. When specifying this constrained bond, I have an equilibrium distance but I do not have a force-constant. Is it irrelevant what value I choose for the force constant if I apply constraints to that bond? Best, Eric On Sat, Apr 25, 2015 at 9:07 PM, Justin Lemkul jalem...@vt.edu wrote: On 4/25/15 11:01 PM, Eric Smoll wrote: Hello Dr Lemkul, Thank you for the rapid response. It is much appreciated. On the subject of specifying constraints, how does the mdp keyword-value pair: constraints=h-bonds work? How are the bonds with hydrogen detected? By atom name. If the first character is 'H' it is converted to a constraint. Here are a few lines from ffnonbonded.itp in the oplsaa.ff. The atoms shown are for custom hydrogen additions to the opls forcefield. Note that the bond_type field begins with the element letter (in this case, C and H) and has a suffix. [ atomtypes ] ; full atom descriptions are available in ffoplsaa.atp ; name bond_typemasscharge ptype sigma epsilon opls_972CA_C 6 12.01100-0.130 A3.55000e-01 2.92880e-01 ;SIG opls_973HA_C 1 1.00800 0.210 A2.42000e-01 1.25520e-01 ;SIG This is only relevant for specifying, e.g. a bond in [bondtypes] between CA_C and HA_C. If I understand your original question right, there are no parameters for these bonds, so this really isn't relevant. Similarly, here are a few lines from the topology I have built. Note that I prefer to have the atom field list the chemical element (again C and H) followed by a numerical suffix. In general my ffnonbonded bond_type field and the topology atom field do not match and are never just labeled with the element name. [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1096 opls_972 42CCC C5332 -0.13 12.011 ; qtot -13.07 1097 opls_973 42CCC H6332 0.21 1.008 ; qtot -12.86 Will constraints=h-bonds correctly identify C-H bonds in my system without manually adding to the topology? Yes. If a bond is listed between the atoms, it will be converted. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] difference of calculation time between the numbers of fep-lambdas values
Dear Gromacs Users, I would appreciate you to give me any comments or hints about the question below. What makes the calculation time much longer when I calculate a solvation free energy using the mdp input1 compared to the mdp input2? Input1 Free_energy = yes Couple-lambda0= vdw-q Couple-lambda1= none Couple-intramol = no Init-lambda-state = 2 Fep-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 Calc-lambda-neighbors = 1 Input2 Free_energy = yes Couple-lambda0= vdw-q Couple-lambda1= none Couple-intramol = no Init-lambda-state = 2 Fep-lambdas = 0.0 0.1 0.2 Calc-lambda-neighbors = 1 It takes three times longer when I write down 36 lambda values compared to 3 lambda values even if there is no difference between mdp inputs other than the value of fep-lambdas and it is a normal free energy calculation not like Hamiltonian replica exchange calculation. Thanks in advance and best regards, Nao -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] the relationship between mdp file and the force field
Dear All, In the on-line Justin tutorial on lysozyme, the several mdp files are for the specific force field OPLS-AA force field. It specifically mentioned Settings, particularly nonbonded interaction settings, will be different for other force fields. Will you please introduce to me how to modify mdp files based on the difference of the force fields? For example, if I use force field 6, what should I modify based on the mdps of the lysozyme tutorial? I am looking forward to getting your reply. Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
