[gmx-users] REMD queries
Hi friends , I am new to the REMD simulation. I read some thread from archive but they not clarify by queries that why I am asking you on forum I have following Queries: 1. I want to simulate protein by remd at physiological temp ( 310). So my initial temp of replica should be 310 or less than that??? 2. I read some thread for archive but not get the exact protocol : As per the http://www.gromacs.org/Documentation/How-tos/REMD link I have to do the seperate NVT for each replica... But Should for NPT and Production run I have to do the same thing ??? Or please help me to set the proper protocol.. When I used the T-remd http://folding.bmc.uu.se/remd/ for NVT *ERROR*: Can not do constant volume yet! So how to determine temp for the nvt ??? Is it possible to run replica directly in the production run ??? These may be simple question but as new to REMD these question putting me in a great trouble For NPT with constrained I got following result Summary of input and derived variables. VariableValue Pdes0.1 Temperature range310 - 350 Number of water molecules3000 Number of protein atoms284 Including all H~ 431 Number of hydrogens in protein~ 62 Number of constraints~ 284 Number of vsites~ 0 Number of degrees of freedom~ 27568Energy loss due to constraints1.18 (kJ/mol K) Should I have to use these same value for NVT and production MD ??? or for production MD I have to use NPT Constraints in the protein: fully flexible I just confused with these options. So please give me proper protocol. Thank you in advance. With best wishes and regards Rama david, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Concerning a Fatal Error!
On 10/13/12 4:48 AM, Arman Mahboubi Soufiani wrote: Dear all friends, When I want to run a short EM to get my structure more stable for further equilibration and production steps I get the following error as outpu: *Library file in current dir nor not found justPLA-em.tpr_d1.xvgin default directories* I have to note that justPLA-em.tpr is the .tpr file I created by grompp. I would be really thankful if anyone can help me sort this out. Without seeing your mdrun command, it's a bit hard to guess why your .tpr file is being read in as a tabulated dihedral file. Suffice it to say that something about your command line is wrong. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Concerning a Fatal Error!
On 10/13/12 9:05 AM, Arman M. Soufiani wrote: Dear Justin, I appreciate your direction. I will try to find out, however, could not fix it yet. Providing your exact mdrun command, copied and pasted from the terminal, is the fastest way to get a solution. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: small tc-group
Thanks, I'll do some test to compare the different choices regards, Facundo -- View this message in context: http://gromacs.5086.n6.nabble.com/small-tc-group-tp5001927p5001986.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Concerning a Fatal Error!
Dear Justin, The followings are the two successive commands I used: *grompp -f justPLA.mdp -c 20LA-2layer-4chains.gro -p t-PLA.top -o justPLA-em.tpr mdrun -deffnm justPLa-em* BR Arman On Sat, Oct 13, 2012 at 3:07 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/13/12 9:05 AM, Arman M. Soufiani wrote: Dear Justin, I appreciate your direction. I will try to find out, however, could not fix it yet. Providing your exact mdrun command, copied and pasted from the terminal, is the fastest way to get a solution. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] problem with pull code
Hi all, I am trying to do an umbrella sampling of a fairly extended state of the protein along end-to-end distance of it. I am using a rectangular box ( elongated along x ) of dimension 20 nm X 8nm X 8 nm. I am doing the simulation in NVT ensemble. gromacs 4.5.4 is being used. But, even after running for 1 ns, the simulation crashes saying that Program mdrun_5mpi, VERSION 4.5.4 Source code file: pull.c, line: 329 Fatal error: Distance of pull group 1 (2.940209 nm) is larger than 0.49 times the box size (9.00) But if I see the trajectory, it hardly shows any issue with seeing the PBC image . I am not sure how to avoid this issue. Should I make one of the endgroup as freeze group so that it does not get tilted. Any help will be appreciated. Sanku -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Running Gromacs on Rescale
Dear users, At Rescale (www.rescale.com) we have developed a cloud simulation platform to run any type of simulation workflow on-demand. We specifically focus on highly scalable implementations of compute intensive simulation codes along with applied math tools to set up designs of experiment or optimization loops as part of a workflow. Our primary user base is currently in computational fluid dynamics and finite element analysis, but we are now expanding to molecular dynamics codes. We have just added Gromacs to our simulation library and are looking for any feedback on the type of applications that you would like to run, and overall usability of our platform for molecular dynamics. We would really appreciate your help and would be happy to provide any user with 100 free simulation dyno hours to help beta test the Gromacs code capabilities on our platform. You can sign up directly on our website (www.rescale.com), and/or contact me directly (jo...@rescale.com) to get your account set up for beta testing and get 100 free hours credited to your account. Best, Joris Joris Poort Rescale jo...@rescale.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Concerning a Fatal Error!
On 10/13/12 9:49 AM, Arman Mahboubi Soufiani wrote: Dear Justin, The followings are the two successive commands I used: *grompp -f justPLA.mdp -c 20LA-2layer-4chains.gro -p t-PLA.top -o justPLA-em.tpr mdrun -deffnm justPLa-em* These commands would not produce the error posted previously. The error would have resulted from: mdrun -deffnm justPLA-em.tpr The fact that the capitalization is different and the nature of the suffix supports this conclusion. It is better to copy directly from the terminal rather than try to recreate what you did. In any case, proper invocation of the command should solve the issue. mdrun is looking for an .xvg file containing parameters for a tabulated dihedral; it needs to be named appropriately to function correctly. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: LINCS metal-ligand bonds
On 10/12/12 2:50 PM, tarak karmakar wrote: Thanks Justin Chaban. Even I did the simulation for 3 ns and it worked well. Now the issue in my case is , while I was not imposing the M-N constraints, the metal was rattling around (little bit) and the histidine residues were moving back and forth (elongation of M-Nhis length). So I employed constraints to keep them in peace. But I'm bit worried about the dynamics of the entire protein. I'm not sure how accurate results these will produce if I impose these sorts of approximations. Any idea ? Any reference where people have followed the same ? Anything you do is going to suffer from the fact that it's an approximation since MM force fields are not going to preserve coordination geometry for these ions. A constraint is very rigid, but on average, probably describes correct behavior. A harmonic interaction is defined by the force constant, but you'll have a hard time defining proper parameters for that, too. A distance restraint suffers from a similar interaction regarding how hard the interaction is. Surely a few minutes searching will turn up pertinent literature. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] problem with pull code
On 10/13/12 3:17 PM, Sanku M wrote: Hi all, I am trying to do an umbrella sampling of a fairly extended state of the protein along end-to-end distance of it. I am using a rectangular box ( elongated along x ) of dimension 20 nm X 8nm X 8 nm. I am doing the simulation in NVT ensemble. gromacs 4.5.4 is being used. But, even after running for 1 ns, the simulation crashes saying that Program mdrun_5mpi, VERSION 4.5.4 Source code file: pull.c, line: 329 Fatal error: Distance of pull group 1 (2.940209 nm) is larger than 0.49 times the box size (9.00) But if I see the trajectory, it hardly shows any issue with seeing the PBC image . I am not sure how to avoid this issue. The pull code is very sensitive to these motions. Mathematically, I don't understand why mdrun is complaining, but your setup is prone to failure. An extended protein in an elongated box will surely interact with its periodic image at some point. Should I make one of the endgroup as freeze group so that it does not get tilted. I don't think you'll be able to freeze or restrain enough of the protein to make a difference that does not significantly impact the dynamics of the system. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] error: group protein not found in index file
Hi All: I'm trying to set up a small box with only water and ions (no protein) and run MD simulation. The commands I used to set up my system and running MD are as follows: genbox -cs spc216.gro -o water.gro -maxsol 256 -box 2.1 2.1 2.1 pdb2gmx -f water.gro -q water.pdb -n index.ndx grompp -f ions.mdp -c water.gro -p topol.top -o ions.tpr genion -s ions.tpr -o water_ions.gro -pname NA -nname CL -nn 23 -np 23 -rmin 0.44 -p topol.top grompp -f mini.mdp -c water_ions.gro -p topol.top -o em.tpr mdrun -v -deffnm em grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr And then I received the error message Fatal error: Group Protein not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. Then I tried using make_ndx -f water_ions.mdp -o index.ndx to generate index file and tried grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr - index.ndx but still didn't work. In my system, there is no protein, so how can I setup the system correctly and run MD. Thanks! what's in top file: [ system ] ; Name Generated by genbox [ molecules ] ; Compound#mols SOL 210 NA 23 CL 23 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error: group protein not found in index file
On 10/13/12 10:32 PM, Liu, Hanzhong wrote: Hi All: I'm trying to set up a small box with only water and ions (no protein) and run MD simulation. The commands I used to set up my system and running MD are as follows: genbox -cs spc216.gro -o water.gro -maxsol 256 -box 2.1 2.1 2.1 pdb2gmx -f water.gro -q water.pdb -n index.ndx grompp -f ions.mdp -c water.gro -p topol.top -o ions.tpr genion -s ions.tpr -o water_ions.gro -pname NA -nname CL -nn 23 -np 23 -rmin 0.44 -p topol.top grompp -f mini.mdp -c water_ions.gro -p topol.top -o em.tpr mdrun -v -deffnm em grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr And then I received the error message Fatal error: Group Protein not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. Then I tried using make_ndx -f water_ions.mdp -o index.ndx to generate index file and tried grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr - index.ndx but still didn't work. In my system, there is no protein, so how can I setup the system correctly and run MD. Thanks! If there is no protein, don't specify Protein anywhere in your .mdp file. Likely this is one of your tc-grps. You should probably be using System for this setting. -Justin what's in top file: [ system ] ; Name Generated by genbox [ molecules ] ; Compound#mols SOL 210 NA 23 CL 23 -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] error: group protein not found in index file
Thanks! Problem solved!!! From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Saturday, October 13, 2012 10:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] error: group protein not found in index file On 10/13/12 10:32 PM, Liu, Hanzhong wrote: Hi All: I'm trying to set up a small box with only water and ions (no protein) and run MD simulation. The commands I used to set up my system and running MD are as follows: genbox -cs spc216.gro -o water.gro -maxsol 256 -box 2.1 2.1 2.1 pdb2gmx -f water.gro -q water.pdb -n index.ndx grompp -f ions.mdp -c water.gro -p topol.top -o ions.tpr genion -s ions.tpr -o water_ions.gro -pname NA -nname CL -nn 23 -np 23 -rmin 0.44 -p topol.top grompp -f mini.mdp -c water_ions.gro -p topol.top -o em.tpr mdrun -v -deffnm em grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr And then I received the error message Fatal error: Group Protein not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file to the '-n' option of grompp. Then I tried using make_ndx -f water_ions.mdp -o index.ndx to generate index file and tried grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr - index.ndx but still didn't work. In my system, there is no protein, so how can I setup the system correctly and run MD. Thanks! If there is no protein, don't specify Protein anywhere in your .mdp file. Likely this is one of your tc-grps. You should probably be using System for this setting. -Justin what's in top file: [ system ] ; Name Generated by genbox [ molecules ] ; Compound#mols SOL 210 NA 23 CL 23 -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
