Re: [gmx-users] Simulate only one unit of the virus capsid while fixing its surrounding units
Dear Andre, Thank you. We are trying to use an adenovirus as a vaccine. As it is not stable, we want to simulate it to identify the unstable regions (e.g. flexible), so as to either engineering (e.g. mutation) it, or adding excipients. Simulating only one protein of the capsid is of course doable. But do you think simulating one protein without its neighbours could reflect its dynamics? Would its boundary residues behave very differently compared to with neighbours? --Original-- From:"ZHANG Cheng"<272699...@qq.com; Date:Wed, Apr 8, 2020 11:02 AM To:"gromacs.org_gmx-users"http://www.gromacs.org/Documentation/How-tos/Position_Restraints Thank you! Yours sincerely Cheng -- 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] Velocities from the .gro file
On Tue, Apr 7, 2020 at 3:38 PM Mohamed Abdelaal wrote: > No, I use the generate velocity option in the .mdp files. > > However I want now to assign different velocities in the x,y,z directions. > Which I thought it could only be done through the .gro file, but I don't > know If I did that, should I change the value of the generate velocity to > be = NO in the .mdp files ? (otherwise I would have generated the > velocities twice). > That sounds logical. Set it to no if you provide your own initial velocities. > > Moreover, if I added the velocities in the .gro file how can I generate the > velocities in the .gro file from a distribution (Maxwell) with a specific > mean and standard deviation ? > > I have tried to search in different sources (the user list, manual, user > guide, research gate and other platforms) how to solve this velocity > problem but I didn't find a clear way to insert different velocities in the > x,y,z directions using distribution rater than constant velocities. > > There is a good section on this in the manual. For example, section 3.4.1 in the Gromacs 5.1.2 manual. Also, you know that the generate velocities option assigns velocities to atoms from an approximate MB distribution at whatever temperature you specify in the MDP file, right? If I understand you correctly, the generate velocities options should do exactly what you want. With no extra work. > Please guide me how to do it as I am a little bit confused in the velocity > generation mechanisms. > > Many thanks, > Mohamed > > On Mon, Apr 6, 2020 at 6:19 PM Justin Lemkul wrote: > > > > > > > On 4/6/20 12:16 PM, Mohamed Abdelaal wrote: > > > Hello everybody :) > > > > > > Can I use the gmx insert-molecules to insert molecules in my box with > > > velocities by adding the velocities in the .gro file and insert the > > > molecules from this .gro file ? > > > > Have you tried it? > > > > -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. > -- 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] Simulate only one unit of the virus capsid while fixing its surrounding units
Dear Cheng, maybe you should step back and begin the planification of your research project considering how much computer power you have available. If you cannot handle the whole capsid then you have to simplify the model either using some coarse grained force field (MARTINI, for instance) or studying a smaller part of the capsid. but these choices are up to you, they depend on what questions you are trying to answer. Andre On Wed, Apr 8, 2020 at 12:02 AM ZHANG Cheng <272699...@qq.com> wrote: > Dear Justin and Andre, > > > Thank you for the advice. So can I ask how commonly the very large virus > capsid is simulated? A recent paper "Physical properties of the HIV-1 > capsid from all-atom molecular dynamics simulations" is using 3880 GPU > accelerated Cray-XK nodes, which is impossible for our university to > provide. > > > > > --Original-- > From:"ZHANG Cheng"<272699...@qq.com; > Date:Tue, Apr 7, 2020 10:10 PM > To:"ZHANG Cheng"<272699...@qq.com;"gromacs.org_gmx-users"< > gromacs.org_gmx-users@maillist.sys.kth.se; > > Subject:Re:Simulate only one unit of the virus capsid while fixing > its surrounding units > > > > Dear Andre, Thank you for the advice. Can I ask, > > > 1) Could you please clarify the concepts? I know "constraint" and > "restraint" are two different things in gromacs. And "fix" is another term? > How about "freezegrps"? > > > 2) It is okay that the computational time is not reduced, as now only > several proteins are simulated. If I simulate all the several protein > without any fixing, I worry they will lose their conformation. So fixing > the neighbours and only focusing on the protein in the centre could be the > solution. > > > > > > -- Original -- > From:"ZHANG Cheng"<272699...@qq.com; > Date:Tue, Apr 7, 2020 09:41 PM > To:"gromacs.org_gmx-users" ; > Cc:"ZHANG Cheng"<272699...@qq.com; > Subject:Simulate only one unit of the virus capsid while fixing its > surrounding units > > > > It is a challenge to simulate the entire virus as it is too big and I do > not have such computational resources. So I was thinking to only simulate > one coat protein and its surrounding neighbours, but keep the neighbours > relatively fixed. > > > Can I ask > > > 1) Is this a sensible idea to proceed? > > > 2) To fix the neighbours, should I use "constraints" or "restraints"? > > > 3) At which step should I start to introduce the fixation? > > > 4) If possible, is there a tutorial for this? I feel the information here > is still not straightforward to follow > http://www.gromacs.org/Documentation/How-tos/Position_Restraints > > > Thank you! > > > Yours sincerely > Cheng > -- > 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. > -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- 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] Simulate only one unit of the virus capsid while fixing its surrounding units
Dear Justin and Andre, Thank you for the advice. So can I ask how commonly the very large virus capsid is simulated? A recent paper "Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations" is using 3880 GPU accelerated Cray-XK nodes, which is impossible for our university to provide. --Original-- From:"ZHANG Cheng"<272699...@qq.com; Date:Tue, Apr 7, 2020 10:10 PM To:"ZHANG Cheng"<272699...@qq.com;"gromacs.org_gmx-users"http://www.gromacs.org/Documentation/How-tos/Position_Restraints Thank you! Yours sincerely Cheng -- 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] Velocities from the .gro file
No, I use the generate velocity option in the .mdp files. However I want now to assign different velocities in the x,y,z directions. Which I thought it could only be done through the .gro file, but I don't know If I did that, should I change the value of the generate velocity to be = NO in the .mdp files ? (otherwise I would have generated the velocities twice). Moreover, if I added the velocities in the .gro file how can I generate the velocities in the .gro file from a distribution (Maxwell) with a specific mean and standard deviation ? I have tried to search in different sources (the user list, manual, user guide, research gate and other platforms) how to solve this velocity problem but I didn't find a clear way to insert different velocities in the x,y,z directions using distribution rater than constant velocities. Please guide me how to do it as I am a little bit confused in the velocity generation mechanisms. Many thanks, Mohamed On Mon, Apr 6, 2020 at 6:19 PM Justin Lemkul wrote: > > > On 4/6/20 12:16 PM, Mohamed Abdelaal wrote: > > Hello everybody :) > > > > Can I use the gmx insert-molecules to insert molecules in my box with > > velocities by adding the velocities in the .gro file and insert the > > molecules from this .gro file ? > > Have you tried it? > > -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.
Re: [gmx-users] dt in mdp
Thanks Justin for the response. Please find below the mdp file. The system is a thin film made out of a epoxy molecule, picture in be below link, with water on top and bottom of the film. I even sometimes have the same issue when I simulate the bulk of this system, I mean a cubic box filled by this molecule and no water. I got the force fields from the latest version of ATB repository by which I have previously done some other simulation for the same molecule. https://drive.google.com/open?id=1tJLxh9jQ2v5DDTrVR8IuQz40B3NN0zlb %mdp--- title= Thin-Film integrator = md dt = 0.002 ; 2 fs ;0.001 1 fs nsteps = 2500 ; 50 ns ;5000 ; 50 ns xtc-precision= 500 ; 1000 ;nstlist = 40 %- ;;in .trr file nstxout = 3000 ; 6000 nstvout = 0 nstfout = 0 ;;in energy file.log nstlog = 2000 ; 4000 nstcalcenergy= 2000 ;4000 nstenergy= 2000 ;4000 ;;in xtc file nstxout-compressed = 0 ;compressed-x-grps= non-Water %- continuation = yes gen-vel = no constraint-algorithm = lincs constraints = h-bonds cutoff-scheme= Verlet coulombtype = PME rcoulomb = 1.4 vdwtype = Cut-off rvdw = 1.4 DispCorr = EnerPres tcoupl= v-rescale tc-grps = system tau-t = 1.5 nhchainlength = 10 ref-t = 298.15 pbc = xyz pcoupl = Parrinello-Rahman Pcoupltype = isotropic tau_p= 2.5 compressibility = 4.5e-5 ref_p= 1.0 refcoord-scaling = com energygrps = thin_film SOL comm-mode= Linear nstcomm = 100 comm-grps= Thin_fiml SOL %- Thank you Alex On Tue, Apr 7, 2020 at 5:06 PM Justin Lemkul wrote: > > > On 4/7/20 5:00 PM, Alex wrote: > > Dear all, > > After minimization and equalizations using nvt (v-rescale) and npt (both > > berendsen and ;Parrinello-Rahman), a simulation of mine could run well > for > > 200 ns using dt =0.001 while it would crash after 3 ns If I used dt = > 0.002 > > with the particles communication fatal error. > > > > Fatal error: > > 2 particles communicated to PME rank 12 are more than 2/3 times the > cut-off > > out of the domain decomposition cell of their charge group in dimension > y. > > This usually means that your system is not well equilibrated. > > > > So, if the system would not be well equlibrated, then I would expect that > > with dt = 0.001 the simulation wouldn't run well for 200 ns. But I expect > > that it also crashes for example around 6 ns as the with the dt = 0.002 > the > > simulation last only 3 ns. > > > > Any comment that helps to understand the problem would be highly > > appreciated. > > Please provide a description of what your system is and a full .mdp > file. While most of the time these crashes come from poor equilibration, > an inadequately parametrized topology or bad combination/misuse of > algorithms can also cause crashes. > > -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] dt in mdp
Dear all, After minimization and equalizations using nvt (v-rescale) and npt (both berendsen and ;Parrinello-Rahman), a simulation of mine could run well for 200 ns using dt =0.001 while it would crash after 3 ns If I used dt = 0.002 with the particles communication fatal error. Fatal error: 2 particles communicated to PME rank 12 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. So, if the system would not be well equlibrated, then I would expect that with dt = 0.001 the simulation wouldn't run well for 200 ns. But I expect that it also crashes for example around 6 ns as the with the dt = 0.002 the simulation last only 3 ns. Any comment that helps to understand the problem would be highly appreciated. Regards, 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.
Re: [gmx-users] restarting a simulation
On 4/7/20 11:47 AM, Daniel Burns wrote: You should also have an "md10.cpt" in addition to the "md10_prev.cpt"? If so, replace it in your command with just the md10.cpt file. If you don't have it, try renaming your "_prev.cpt" file to just "md10.cpt". The issue is not with the naming of the checkpoint file but with the output files specified within the checkpoint. The simplest workaround here is simply to use -noappend and concatenate output later. If one moves files around, sometimes the appending mechanism can break for reasons that are still unclear to me. -Justin Dan On Mon, Apr 6, 2020 at 11:06 AM Sadaf Rani wrote: Dear Gromacs users I am restarting a simulation with the following command:- mpirun gmx_mpi mdrun -s md10.tpr -cpi md10_prev.cpt -append However, I am getting following error message. All the below-named files are there in my directory but it still complains the same. Inconsistency in user input: Some output files listed in the checkpoint file md10_prev.cpt are not present or not named as the output files by the current program:)Expected output files that are present: Expected output files that are not present or named differently: md10.log md10.xtc md10.trr md10.edr md10.xvg To keep your simulation files safe, this simulation will not restart. Either name your output files exactly the same as the previous simulation part (e.g. with -deffnm), or make sure all the output files are present (e.g. run from the same directory as the previous simulation part), or instruct mdrun to write new output files with mdrun -noappend. In the last case, you will not be able to use appending in future for this simulation. I also tried without -append option. Please correct me if I am wrong somewhere. Thanks. Sadaf -- 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] restarting a simulation
You should also have an "md10.cpt" in addition to the "md10_prev.cpt"? If so, replace it in your command with just the md10.cpt file. If you don't have it, try renaming your "_prev.cpt" file to just "md10.cpt". Dan On Mon, Apr 6, 2020 at 11:06 AM Sadaf Rani wrote: > Dear Gromacs users > I am restarting a simulation with the following command:- > mpirun gmx_mpi mdrun -s md10.tpr -cpi md10_prev.cpt -append > > However, I am getting following error message. All the below-named files > are there in my directory but it still complains the same. > > Inconsistency in user input: > Some output files listed in the checkpoint file md10_prev.cpt are not > present > or not named as the output files by the current program:)Expected output > files > that are present: > > Expected output files that are not present or named differently: > md10.log > md10.xtc > md10.trr > md10.edr > md10.xvg > To keep your simulation files safe, this simulation will not restart. > Either > name your > output files exactly the same as the previous simulation part (e.g. with > -deffnm), or > make sure all the output files are present (e.g. run from the same > directory > as the > previous simulation part), or instruct mdrun to write new output files with > mdrun -noappend. > In the last case, you will not be able to use appending in future for this > simulation. > > I also tried without -append option. > Please correct me if I am wrong somewhere. > Thanks. > > Sadaf > -- > 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] Simulate only one unit of the virus capsid while fixing its surrounding units
Dear Cheng, I also think that freezing introduces more artifacts than benefits, since you are probably beginning your simulation from a crystallographic structure and fixing most of the molecules will provide a crystal-like structure, not a relaxed structure closer to the typical physiological conditions. Andre On Tue, Apr 7, 2020 at 11:29 AM Justin Lemkul wrote: > > > On 4/7/20 10:10 AM, ZHANG Cheng wrote: > > Dear Andre, Thank you for the advice. Can I ask, > > > > > > 1) Could you please clarify the concepts? I know "constraint" and > "restraint" are two different things in gromacs. And "fix" is another term? > How about "freezegrps"? > > I would not use "fix" and "restrain" interchangeably. Fixing a quantity > means it cannot vary. With a restraint, movement is disfavored but not > prevented. Freezing is totally artificial and requires you to ignore > nonbonded interactions between the frozen groups. > > > > > 2) It is okay that the computational time is not reduced, as now only > several proteins are simulated. If I simulate all the several protein > without any fixing, I worry they will lose their conformation. So fixing > the neighbours and only focusing on the protein in the centre could be the > solution. > > > > Your approach assumes that the conformations of the proteins are not > dependent on their neighbors. I do not think that is a justifiable > assumption. If you simulate one protein freely and restrain its > neighbors, you're doing a glorified simulation of a crystal, which is > not reflective of biological reality for a virus capsid. > > -Justin > > > > > > > > > --Original-- > > From:"ZHANG Cheng"<272699...@qq.com; > > Date:Tue, Apr 7, 2020 09:41 PM > > To:"gromacs.org_gmx-users"< > gromacs.org_gmx-users@maillist.sys.kth.se; > > Cc:"ZHANG Cheng"<272699...@qq.com; > > Subject:Simulate only one unit of the virus capsid while fixing > its surrounding units > > > > > > > > It is a challenge to simulate the entire virus as it is too big and I do > not have such computational resources. So I was thinking to only simulate > one coat protein and its surrounding neighbours, but keep the neighbours > relatively fixed. > > > > > > Can I ask > > > > > > 1) Is this a sensible idea to proceed? > > > > > > 2) To fix the neighbours, should I use "constraints" or "restraints"? > > > > > > 3) At which step should I start to introduce the fixation? > > > > > > 4) If possible, is there a tutorial for this? I feel the information > here is still not straightforward to follow > > http://www.gromacs.org/Documentation/How-tos/Position_Restraints > > > > > > Thank you! > > > > > > Yours sincerely > > Cheng > > -- > == > > 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. > -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- 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] Simulate only one unit of the virus capsid while fixing its surrounding units
On 4/7/20 10:10 AM, ZHANG Cheng wrote: Dear Andre, Thank you for the advice. Can I ask, 1) Could you please clarify the concepts? I know "constraint" and "restraint" are two different things in gromacs. And "fix" is another term? How about "freezegrps"? I would not use "fix" and "restrain" interchangeably. Fixing a quantity means it cannot vary. With a restraint, movement is disfavored but not prevented. Freezing is totally artificial and requires you to ignore nonbonded interactions between the frozen groups. 2) It is okay that the computational time is not reduced, as now only several proteins are simulated. If I simulate all the several protein without any fixing, I worry they will lose their conformation. So fixing the neighbours and only focusing on the protein in the centre could be the solution. Your approach assumes that the conformations of the proteins are not dependent on their neighbors. I do not think that is a justifiable assumption. If you simulate one protein freely and restrain its neighbors, you're doing a glorified simulation of a crystal, which is not reflective of biological reality for a virus capsid. -Justin --Original-- From:"ZHANG Cheng"<272699...@qq.com; Date:Tue, Apr 7, 2020 09:41 PM To:"gromacs.org_gmx-users"http://www.gromacs.org/Documentation/How-tos/Position_Restraints Thank you! Yours sincerely Cheng -- == 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] Simulate only one unit of the virus capsid while fixing its surrounding units
Dear Andre, Thank you for the advice. Can I ask, 1) Could you please clarify the concepts? I know "constraint" and "restraint" are two different things in gromacs. And "fix" is another term? How about "freezegrps"? 2) It is okay that the computational time is not reduced, as now only several proteins are simulated. If I simulate all the several protein without any fixing, I worry they will lose their conformation. So fixing the neighbours and only focusing on the protein in the centre could be the solution. --Original-- From:"ZHANG Cheng"<272699...@qq.com; Date:Tue, Apr 7, 2020 09:41 PM To:"gromacs.org_gmx-users"http://www.gromacs.org/Documentation/How-tos/Position_Restraints Thank you! Yours sincerely Cheng -- 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] Simulate only one unit of the virus capsid while fixing its surrounding units
Dear Cheng, Either fixing or constraining the other units will not decrease the computational cost of the simulation since you will still be computing the interactions between the unit that can move and all the other fixed/constrained units. Andre On Tue, Apr 7, 2020 at 10:41 AM ZHANG Cheng <272699...@qq.com> wrote: > It is a challenge to simulate the entire virus as it is too big and I do > not have such computational resources. So I was thinking to only simulate > one coat protein and its surrounding neighbours, but keep the neighbours > relatively fixed. > > > Can I ask > > > 1) Is this a sensible idea to proceed? > > > 2) To fix the neighbours, should I use "constraints" or "restraints"? > > > 3) At which step should I start to introduce the fixation? > > > 4) If possible, is there a tutorial for this? I feel the information here > is still not straightforward to follow > http://www.gromacs.org/Documentation/How-tos/Position_Restraints > > > Thank you! > > > Yours sincerely > Cheng > -- > 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. > -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- 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] Simulate only one unit of the virus capsid while fixing its surrounding units
It is a challenge to simulate the entire virus as it is too big and I do not have such computational resources. So I was thinking to only simulate one coat protein and its surrounding neighbours, but keep the neighbours relatively fixed. Can I ask 1) Is this a sensible idea to proceed? 2) To fix the neighbours, should I use "constraints" or "restraints"? 3) At which step should I start to introduce the fixation? 4) If possible, is there a tutorial for this? I feel the information here is still not straightforward to follow http://www.gromacs.org/Documentation/How-tos/Position_Restraints Thank you! Yours sincerely Cheng -- 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] restarting a simulation
Hi, Have you read and try what mdrun tells you, like -deffnm option? in recent version of gromacs, if you do not want to append the output to old output files, use option -noappend. On Mon, Apr 6, 2020 at 6:06 PM Sadaf Rani wrote: > Dear Gromacs users > I am restarting a simulation with the following command:- > mpirun gmx_mpi mdrun -s md10.tpr -cpi md10_prev.cpt -append > > However, I am getting following error message. All the below-named files > are there in my directory but it still complains the same. > > Inconsistency in user input: > Some output files listed in the checkpoint file md10_prev.cpt are not > present > or not named as the output files by the current program:)Expected output > files > that are present: > > Expected output files that are not present or named differently: > md10.log > md10.xtc > md10.trr > md10.edr > md10.xvg > To keep your simulation files safe, this simulation will not restart. > Either > name your > output files exactly the same as the previous simulation part (e.g. with > -deffnm), or > make sure all the output files are present (e.g. run from the same > directory > as the > previous simulation part), or instruct mdrun to write new output files with > mdrun -noappend. > In the last case, you will not be able to use appending in future for this > simulation. > > I also tried without -append option. > Please correct me if I am wrong somewhere. > Thanks. > > Sadaf > -- > 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.
