Re: [gmx-users] Center of mass restraints
On 11/11/19 3:58 PM, Daniel Burns wrote: Thank you! If I use the coordinates of the center of mass for the spherical restraint, will the ligand remain restrained to that coordinate if the protein rotates or translates the binding site away from that original position? No, that's only possible with the pull code. If you're just trying to do a simple pose refinement, you could apply a light restraint on the backbone or C-alpha atoms to prevent this from happening. Or am I going about this wrong? Can I set up that spherical restraint with a genrestr command without calculating the coordinates of the center of mass from a visualization software? genrestr won't generate what you need. Obtain the COM coordinates of your desired residues with gmx traj -ox -com and a suitable index group. That's the origin of the restraint. Create a (physically unrealistic) coordinate file where all the ligand atoms are set to those coordinates. I haven't been able to find an example of this. Probably good fodder for my next tutorial...there are lots of practical applications to using the flat-bottom restraints. -Justin On Mon, Nov 11, 2019 at 8:25 AM Justin Lemkul wrote: On 11/10/19 2:54 PM, Daniel Burns wrote: Hello, I have identified a set of amino acid residues that surround a small molecule binding site. How would I go about restraining the small molecule ligand to the center of mass of the surrounding residues? I want the molecule to be able to bounce around in the binding site to let if find the most energetically favorable configuration. You could either set up a spherical flat-bottom restraint with the origin of that restraint coincident with the COM of the desired residues, or you could use the pull code to set a restraint between the COM of the protein residues and the COM of the ligand. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.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. -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.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.
Re: [gmx-users] polymer charmm27 parameter
On 11/11/19 10:05 AM, Mijiddorj B wrote: Dear Prof. Justin, Thank you very much for your reply. My target polymer is the branched polyethyleneimine. I copied a figure. I am sorry for furthermore asking. If I understand correctly, the model compound consists of the last two heavy atoms and first two heavy atoms along with the corresponding protons. Is it right? Whatever model compounds you use have to encompass all relevant internal degrees of freedom (bonds, angles, dihedrals). Do I need to make a model N and C terminal atoms? You need termini, but N- and C-termini are protein-specific concepts, so no, not exactly. See e.g. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2009-March/040125.html -Justin Thank you for your time. [image: image.png] Best regards, Mijiddorj -- Message: 1 Date: Sun, 10 Nov 2019 09:20:52 -0500 From: Justin Lemkul To: gmx-us...@gromacs.org Subject: Re: [gmx-users] polymer charmm27 parameter Message-ID: <4ed3e913-bf3d-f79d-e997-fc03d451e...@vt.edu> Content-Type: text/plain; charset=utf-8; format=flowed On 11/10/19 8:52 AM, Mijiddorj B wrote: Dear GMX users, I would like to simulate a long polymer, which consists of the number of units (monomers). I generated the charmm27 parameter for the single unit using swissparam server. However, I need to prepare the parameter for the long polymer chain. If you have any experience, please advise me to build the topology of the long polymer using the parameter of the single unit. Thanks for any guidance. You need a model compound that captures all relevant degrees of freedom, including bonds, angles, and dihedrals between monomer units. You then need to parametrize those interactions so the properties of your chain are correct. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.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.
Re: [gmx-users] 1 particles communicated to PME rank 0 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.
Farideh, There appears to be a problem with the topology that you are using for the molecule that explodes. Look at the pdb files generated at each time the system has exploded. Work out which group of atoms are moving too far, then look at the topology around those atoms to identify where the problem is located. Where the instability has started, there will be something about the topology around that location which is wrong. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Sat, 9 Nov 2019 at 04:17, Farideh Badalkhani Khamseh < f.badalkh...@modares.ac.ir> wrote: > Dear GROMACS users. > > I am trying to perform MD simulations on a PEGylated dendrimer. At first, > I performed energy minimization with > > emtol = 1000 kJ/mol/nm. > > I did not gent any error in EM, NVT (1 ns), and NPT (1 ns) equilibrations. > But the simulation crashed relatively early (within 1 ns). Therefore, I > performed successive Steep and CG minimizations until the system was > minimized at emtol = 80 kJ/mol/nm. Again, I did not get any error during > NVT and NPT equilibrations. This time production MD crashed after 10 ns and > I got the following error: > > DD step 548 load imb.: force 0.2% >Step Time > 54910980.0 > >Energies (kJ/mol) >Bond AngleProper Dih. Improper Dih. LJ-14 > 2.27616e+037.97871e+036.08238e+033.55375e+012.21395e+03 > Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. > 3.79715e+043.35801e+05 -1.16286e+04 -2.68521e+068.57466e+03 > PotentialKinetic En. Total Energy Conserved En.Temperature >-2.29590e+064.43034e+05 -1.85287e+06 -1.63147e+063.10476e+02 > Pres. DC (bar) Pressure (bar) Constr. rmsd >-1.10990e+029.76046e+013.84574e-06 > > Constraint error in algorithm Lincs at step 5491696 > Wrote pdb files with previous and current coordinates > Constraint error in algorithm Lincs at step 5491698 > Wrote pdb files with previous and current coordinates > Constraint error in algorithm Lincs at step 5491700 > Wrote pdb files with previous and current coordinates > Constraint error in algorithm Lincs at step 5491701 > Wrote pdb files with previous and current coordinates > Constraint error in algorithm Lincs at step 5491702 > Wrote pdb files with previous and current coordinates > Constraint error in algorithm Lincs at step 5491703 > Wrote pdb files with previous and current coordinates > Constraint error in algorithm Lincs at step 5491704 > Wrote pdb files with previous and current coordinates > > --- > Program: gmx mdrun, version 2019.3 > Source file: src/gromacs/ewald/pme-redistribute.cpp (line 282) > MPI rank:0 (out of 2) > > Fatal error: > 1 particles communicated to PME rank 0 are more than 2/3 times the cut-off > out > of the domain decomposition cell of their charge group in dimension x. > This usually means that your system is not well equilibrated. > > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > --- > > > The md.mdp file is as follows: > > title = G3ACE-16PEG MD > ; Run parameters > integrator = md; leap-frog integrator > nsteps = 5000 ; 2 * 5000 = 100 ns > dt = 0.002 ; 2 fs > ; Output control > nstxout = 5000; save coordinates every 10 ps > nstvout = 5000; save velocities every 10 ps > nstfout = 5000 ; nstvout, and nstfout > nstenergy = 5000 ; save energies every 10.0 ps > nstlog = 5000 ; update log file every 10.0 ps > nstxout-compressed = 5000 ; save compressed coordinates every > 10.0 ps > compressed-x-grps = System; save the whole system > ; Bond parameters > continuation= yes ; Restarting after NPT > constraint_algorithm= lincs ; holonomic constraints > constraints = h-bonds ; bonds involving H are constrained > lincs_iter = 1 ; accuracy of LINCS > lincs_order = 4 ; also related to accuracy > ; Neighborsearching > cutoff-scheme = Verlet; Buffered neighbor searching > ns_type = grid ; search neighboring grid cells > nstlist = 10; 20 fs, largely irrelevant with > Verlet scheme > rcoulomb= 1.2 ; short-range electrostatic cutoff (in > nm) > rvdw= 1.2 ;
Re: [gmx-users] Center of mass restraints
Thank you! If I use the coordinates of the center of mass for the spherical restraint, will the ligand remain restrained to that coordinate if the protein rotates or translates the binding site away from that original position? Or am I going about this wrong? Can I set up that spherical restraint with a genrestr command without calculating the coordinates of the center of mass from a visualization software? I haven't been able to find an example of this. On Mon, Nov 11, 2019 at 8:25 AM Justin Lemkul wrote: > > > On 11/10/19 2:54 PM, Daniel Burns wrote: > > Hello, > > > > I have identified a set of amino acid residues that surround a small > > molecule binding site. How would I go about restraining the small > molecule > > ligand to the center of mass of the surrounding residues? I want the > > molecule to be able to bounce around in the binding site to let if find > the > > most energetically favorable configuration. > > You could either set up a spherical flat-bottom restraint with the > origin of that restraint coincident with the COM of the desired > residues, or you could use the pull code to set a restraint between the > COM of the protein residues and the COM of the ligand. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.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. > -- 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] polymer charmm27 parameter
Dear Prof. Justin, Thank you very much for your reply. My target polymer is the branched polyethyleneimine. I copied a figure. I am sorry for furthermore asking. If I understand correctly, the model compound consists of the last two heavy atoms and first two heavy atoms along with the corresponding protons. Is it right? Do I need to make a model N and C terminal atoms? Thank you for your time. [image: image.png] Best regards, Mijiddorj > > -- > > Message: 1 > Date: Sun, 10 Nov 2019 09:20:52 -0500 > From: Justin Lemkul > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] polymer charmm27 parameter > Message-ID: <4ed3e913-bf3d-f79d-e997-fc03d451e...@vt.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > > > On 11/10/19 8:52 AM, Mijiddorj B wrote: > > Dear GMX users, > > > > I would like to simulate a long polymer, which consists of the number of > > units (monomers). I generated the charmm27 parameter for the single unit > > using swissparam server. > > However, I need to prepare the parameter for the long polymer chain. > > If you have any experience, please advise me to build the topology of the > > long polymer using the parameter of the single unit. Thanks for any > > guidance. > > You need a model compound that captures all relevant degrees of freedom, > including bonds, angles, and dihedrals between monomer units. You then > need to parametrize those interactions so the properties of your chain > are correct. > > -Justin > > -- 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] Center of mass restraints
On 11/10/19 2:54 PM, Daniel Burns wrote: Hello, I have identified a set of amino acid residues that surround a small molecule binding site. How would I go about restraining the small molecule ligand to the center of mass of the surrounding residues? I want the molecule to be able to bounce around in the binding site to let if find the most energetically favorable configuration. You could either set up a spherical flat-bottom restraint with the origin of that restraint coincident with the COM of the desired residues, or you could use the pull code to set a restraint between the COM of the protein residues and the COM of the ligand. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.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.
Re: [gmx-users] How to set more mpi for the REMD run?
Thank you very much Paul, I got it! --Original-- From:"ZHANG Cheng"<272699...@qq.com; Date:Mon, Nov 11, 2019 09:57 PM To:"gromacs.org_gmx-users"http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B For Stage 1 of the tutorial, when "#$ -pe mpi 4" is used, it can be run successfully: gerun mdrun_mpi -v -multidir ./equil[0123] However, when "#$ -pe mpi 12" is used with the same command, the error message told me as the below. Can I ask how to properly set more mpi? Program: mdrun_mpi, version 2019.3 Source file: src/gromacs/domdec/domdec.cpp (line 2403) MPI rank: 6 (out of 12) Fatal error: There is no domain decomposition for 3 ranks that is compatible with the given box and a minimum cell size of 0.8875 nm Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6 -- 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 set more mpi for the REMD run?
Hello, yes, this is indeed possible (see http://manual.gromacs.org/current/user-guide/mdrun-features.html#running-multi-simulations for more information on multi simulations with GROMACS). It is just the case that the tutorial system is too small to be correctly distributed with domain decomposition. If you use a larger system that will work. Cheers Paul On 11/11/2019 14:57, ZHANG Cheng wrote: Thank you Paul! I want to use more than one mpi processes for each of the REMD, would it be possible? --Original-- From:"ZHANG Cheng"<272699...@qq.com; Date:Mon, Nov 11, 2019 09:39 PM To:"gromacs.org_gmx-users"http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B For Stage 1 of the tutorial, when "#$ -pe mpi 4" is used, it can be run successfully: gerun mdrun_mpi -v -multidir ./equil[0123] However, when "#$ -pe mpi 12" is used with the same command, the error message told me as the below. Can I ask how to properly set more mpi? Program: mdrun_mpi, version 2019.3 Source file: src/gromacs/domdec/domdec.cpp (line 2403) MPI rank: 6 (out of 12) Fatal error: There is no domain decomposition for 3 ranks that is compatible with the given box and a minimum cell size of 0.8875 nm Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6 -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm, SciLifeLab 0046737308594 -- 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 set more mpi for the REMD run?
Thank you Paul! I want to use more than one mpi processes for each of the REMD, would it be possible? --Original-- From:"ZHANG Cheng"<272699...@qq.com; Date:Mon, Nov 11, 2019 09:39 PM To:"gromacs.org_gmx-users"http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B For Stage 1 of the tutorial, when "#$ -pe mpi 4" is used, it can be run successfully: gerun mdrun_mpi -v -multidir ./equil[0123] However, when "#$ -pe mpi 12" is used with the same command, the error message told me as the below. Can I ask how to properly set more mpi? Program: mdrun_mpi, version 2019.3 Source file: src/gromacs/domdec/domdec.cpp (line 2403) MPI rank: 6 (out of 12) Fatal error: There is no domain decomposition for 3 ranks that is compatible with the given box and a minimum cell size of 0.8875 nm Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6 -- 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 set more mpi for the REMD run?
Hello, you have set the -mpi option correctly (I think), but the small test system used for the tutorial can not be split up over more domains (as the error message tells you). The idea of the tutorial are here to run on system for each mpi process. Are you trying to do the same (and run 12 different simulations), or do you want to use several mpi processes for each of the REMD simulations? Cheers Paul On 11/11/2019 14:39, ZHANG Cheng wrote: I am using the same files based onMark Abraham's REMD tutorial, except using a recent Gromacs version (gromacs/2019.3).http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B For Stage 1 of the tutorial,when "#$ -pe mpi 4" is used, it can be run successfully: gerun mdrun_mpi -v -multidir ./equil[0123] However, when "#$ -pe mpi 12" is used with the same command, the error message told me as the below. Can I ask how to properly set more mpi? Program: mdrun_mpi, version 2019.3 Source file: src/gromacs/domdec/domdec.cpp (line 2403) MPI rank: 6 (out of 12) Fatal error: There is no domain decomposition for 3 ranks that is compatible with the given box and a minimum cell size of 0.8875 nm Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6 -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm, SciLifeLab 0046737308594 -- 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] How to set more mpi for the REMD run?
I am using the same files based onMark Abraham's REMD tutorial, except using a recent Gromacs version (gromacs/2019.3).http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B For Stage 1 of the tutorial,when "#$ -pe mpi 4" is used, it can be run successfully: gerun mdrun_mpi -v -multidir ./equil[0123] However, when "#$ -pe mpi 12" is used with the same command, the error message told me as the below. Can I ask how to properly set more mpi? Program: mdrun_mpi, version 2019.3 Source file: src/gromacs/domdec/domdec.cpp (line 2403) MPI rank: 6 (out of 12) Fatal error: There is no domain decomposition for 3 ranks that is compatible with the given box and a minimum cell size of 0.8875 nm Change the number of ranks or mdrun option -rcon or -dds or your LINCS settings Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6 -- 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] Webinar on mdp file settings
Hello @ all GROMACS users, on December 5th 2019, Christian from core developer team in Stockholm will give a webinar explaining the different options available in mdp files, and showing how they influence your simulations. You can find more information about the event here: https://bioexcel.eu/webinar-a-walk-through-simulation-parameter-options-mdp-files-for-gromacs-2019-12-05/ or sign up for it here: https://attendee.gotowebinar.com/register/5648316978867324429 Hope this will be useful for the community! Cheers Paul -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm, SciLifeLab 0046737308594 -- 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] gromacs.org_gmx-users Digest, Vol 187, Issue 21
Dear GMX users group Message 4 > I am using GROMOS 43a force field, I have typed by protein and got the > ligand file from PRODRG. *Don't use PRODRG; its topologies are not of sufficient quality for running MD simulations*. How to generate ligand topology (GROMOS 43a force field) Does your ligand have a +1 charge? -Justin My ligand does not have a charge. I simulated the same protein-ligand complex for 10ns using GROMACS 5.1.4 on my standalone system. The server at the institute has GROMACS 2018.1. I want to extend my simulation run now on server. > Dear All, > > I m trying to do a protein-ligand simulation, > I am using GROMOS 43a force field, I have typed by protein and got the > ligand file from PRODRG. Don't use PRODRG; its topologies are not of sufficient quality for running MD simulations. > I prepared the complex and added solvent. *The protein has -8.0 charge by > when i m neutralizing it only adds 7 positive charge.* > > > > * 3328 OM336VAL O1 1492 -0.63515.9994 ; > qtot -7.365 3329 OM336VAL O2 1492 -0.635 > 15.9994 ; qtot -8* > Does your ligand have a +1 charge? -Justin > When i added 8 positive charge using the below command > gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL > -np 8 > > > > > > > > *[ molecules ]; Compound#molsProtein_chain_B 11IN >1SOL 22473NA 8* > > Again in the minimization step it is showing a list of > *errors and warnings. * > NOTE 1 [file em.mdp]: >With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note >that with the Verlet scheme, nstlist has no effect on the accuracy of >your simulation. > > Setting the LD random seed to 787146813 > Generated 279 of the 1225 non-bonded parameter combinations > Excluding 3 bonded neighbours molecule type 'Protein_chain_B' > Excluding 3 bonded neighbours molecule type '1IN' > Excluding 2 bonded neighbours molecule type 'SOL' > Excluding 1 bonded neighbours molecule type 'NA' > > NOTE 2 [file topol.top, line 21027]: > > *System has non-zero total charge: 1.00 Total charge should normally > be an integer. *See >http://www.gromacs.org/Documentation/Floating_Point_Arithmetic >for discussion on how close it should be to an integer. > > WARNING 1 [file topol.top, line 21027]: >*You are using Ewald electrostatics in a system with net charge*. This can >lead to severe artifacts, such as ions moving into regions with low >dielectric, due to the uniform background charge. We suggest to >neutralize your system with counter ions, possibly in combination with a >physiological salt concentration. > > Removing all charge groups because cutoff-scheme=Verlet > Analysing residue names: > There are: 335Protein residues > There are: 1 Other residues > There are: 22473 Water residues > There are: 8Ion residues > Analysing Protein... > Analysing residues not classified as Protein/DNA/RNA/Water and splitting > into groups... > Analysing residues not classified as Protein/DNA/RNA/Water and splitting > into groups... > Number of degrees of freedom in T-Coupling group rest is 145023.00 > Calculating fourier grid dimensions for X Y Z > Using a fourier grid of 80x80x80, spacing 0.113 0.113 0.113 > Estimate for the relative computational load of the PME mesh part: 0.20 > This run will generate roughly 6 Mb of data > > There were 2 notes > > There was 1 warning > Please suggests how can overcome these errors. Thanks & Regards, Dr. Pooja Kesari Post Doctoral Fellow Department Of Biosciences and Bioengineering Indian Institute of Technology Bombay INDIA On Fri, Nov 8, 2019 at 9:32 PM < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > >1. Re: Regarding multiple ligands' topology (Justin Lemkul) >2. Problem running simulation on gromacs 2018.8 version > (pooja kesari) >3. Re: gmx trjorder (Christian Blau) >4. Re: Problem running simulation on gromacs 2018.8 version > (Justin Lemkul) >5. Re: (no subject) (Christian Blau) >6. Re: (no subject) (shakuntala dhurua) > > > -- > > Message: 1 > Date: Fri, 8 Nov 2019 06:21:29 -0500 > From: Justin Lemkul > To: gmx-us...@gromacs.org > Subject:
