[gmx-users] Simulation of aggregated proteins
Dear all I have a PDB entry having 10 models(Aggregated structure). Here I want to carry out the molecular dynamic simulation as such in aggregated form. But gromacs is considering only one model in the PDB structure. How can I simulate it as a whole.? Thank you -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- 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] Simulation of aggregated proteins
If the PDB has each protein with separate chain entries (A, B, etc) then this shouldn't be a problem. pdb2gmx will produce separate topologies for each chain and an overall topology that reads from each of the individual topologies and contains the other directives about FF, water model, posre, etc. J On Fri, Dec 22, 2017 at 9:29 AM, RAHUL SURESH wrote: > Dear all > > I have a PDB entry having 10 models(Aggregated structure). Here I want to > carry out the molecular dynamic simulation as such in aggregated form. But > gromacs is considering only one model in the PDB structure. How can I > simulate it as a whole.? > > Thank you > > -- > *Regards,* > *Rahul Suresh* > *Research Scholar* > *Bharathiar University* > *Coimbatore* > -- > 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] to post on mailing list
stud.l_mafak...@pasteur.ac.ir -- 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] Simulation of aggregated proteins
Hi, Judicious reading of the documentation will show that you can get pdb2gmx to consider TER and chain ID changes as breaking molecules, or not. But if there are pdb model fields then you need input that does not use them any more. Mark On Fri, Dec 22, 2017, 8:11 PM João Henriques wrote: > If the PDB has each protein with separate chain entries (A, B, etc) then > this shouldn't be a problem. pdb2gmx will produce separate topologies for > each chain and an overall topology that reads from each of the individual > topologies and contains the other directives about FF, water model, posre, > etc. > > J > > On Fri, Dec 22, 2017 at 9:29 AM, RAHUL SURESH > wrote: > > > Dear all > > > > I have a PDB entry having 10 models(Aggregated structure). Here I want to > > carry out the molecular dynamic simulation as such in aggregated form. > But > > gromacs is considering only one model in the PDB structure. How can I > > simulate it as a whole.? > > > > Thank you > > > > -- > > *Regards,* > > *Rahul Suresh* > > *Research Scholar* > > *Bharathiar University* > > *Coimbatore* > > -- > > 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] Volume-Temperature Replica Exchange
Hi, There's currently no support for any kind of control variables for replica exchange in more than one dimension. Mark On Fri, Dec 22, 2017, 10:24 AM Daniel Kozuch wrote: > Hello, > > I am performing constant pressure replica exchange across a phase > transition, and as one might expect the associated change in volume is > causing exchange issues and many of my replicas are not efficiently > crossing the phase transition. > > I noticed some papers that claim volume-temperature replica exchange > (VTREMD) can help solve this issue (https://doi.org/10.1063/1.1652015 and > https://doi.org/10.1016/j.cpc.2014.11.021). The main idea is to have a > grid > of replicas in volume-temperature space that can exchange. Dietmar Paschek > published a code some time ago for performing VTREMD with GROMACS 3, but I > have not seen any recent activity. > > My question: is there an easy way of implementing VTREMD with recent > versions of GROMACS? If not, is there a better way of tackling this issue? > > Best regards, > Dan Kozuch > -- > 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] Gromacs 2018 beta: g_membed broken?
Hi,
Sounds like we might have made a bug in membed, which would be good to fix.
If you can file an issue at https://redmine.gromacs.org that would be
welcome.
Mark
On Wed, Dec 20, 2017, 5:43 AM Daniel Bauer
wrote:
> Hello,
>
> Im using g_membed to insert potassium channels into POPC membranes. My
> "standard protocol" which worked very well for me on all proteins I used
> so far seems to not work with gromacs 2018 (using the exact same input
> files).
>
>
> This is what I am doing:
>
> 1) orienting the protein onto the membrane (lambada)
>
> 2) Merging the topology files for the membrane and protein
>
> 3) grompp: gmx grompp -f g_membed.mdp -n -c input.gro -r input.gro -o
> g_membed.tpr --maxwarn 2
>
> 4) gmx mdrun -deffnm g_membed -membed embed.dat -mn index.ndx -mp
> embedded.top -c embedded.top # selecting protein and membrane group
>
>
> First thing I noticed is that the number of warnings i have to ignore
> during grompp increased by one because of the new PME warning for
> charged systems. My protein has a net charge, so I have to choose if i
> insert counter ions before or after protein insertion (and I chose to do
> it after insertion).
>
> So the warnings I get are:
>
> WARNING 1: You are using Ewald electrostatics in a system with net
> charge // I think I can ignore this since I neutralize right after
> insertion.
>
> WARNING 2: Can not exclude the lattice Coulomb energy between energy
> groups // g_membed does not support verlet
>
>
> Finally when I run the insertion simulation on the 2018 beta I get the
> following error:
>
> step 0: One or more water molecules can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Back Off! I just backed up step0b.pdb to ./#step0b.pdb.1#
>
> Back Off! I just backed up step0c.pdb to ./#step0c.pdb.1#
> Wrote pdb files with previous and current coordinates
> step 0Warning: Only triclinic boxes with the first vector parallel to
> the x-axis and the second vector in the xy-plane are supported.
> Box (3x3):
> Box[0]={-nan, -nan, -nan}
> Box[1]={-nan, -nan, -nan}
> Box[2]={-nan, -nan, -nan}
> Can not fix pbc.
>
> This seems to happen independent of my system (I tried several of my
> membrane patches and proteins that worked previously). All of them
> insert into the membrane with 2016 successfully but fail on the 2018
> version. So far I tried to increase the number of steps, reduced the
> timestep and played arround with xyinit and zinit as well as setting
> -DFLEXIBLE in the mdp, but no success.
>
> Any idea whats wrong? Or should I move this issue directly to redmine
> since its related to a version update?
>
>
> This is my embed.dat file:
>
> nxy= 1000
> xyinit= 0.1
> xyend= 1.0
> rad= 0.22
> ndiff= 0
> asymmetry= no
> pieces= 1
> maxwarn= 1
>
>
> And my mdp:
>
> ; Run parameters
> integrator= md
> nsteps= 1000
> dt= 0.002
>
> ; I have posres for the protein enabled, although this is irrelevant
> because the protein group coords are frozen. Same issue if i disable
> this and remove posres!
> refcoord_scaling = all
>
> ;define = -DFLEXIBLE ; does not help
>
> ; membed options
> energygrps=insertion_group
> freezegrps=insertion_group
> freezedim=Y Y Y
> energygrp_excl=insertion_group insertion_group
>
> ; OUTPUT CONTROL OPTIONS
> nstxout = 0
> nstvout = 0
> nstfout = 0
> nstlog = 1000
> nstenergy= 100
> nstxtcout= 1000
>
> ; Bond parameters
> continuation= no
> constraint_algorithm = lincs
> lincs_iter= 2
> lincs_order= 8
>
> ; CHARMM36 params
> constraints = h-bonds
> cutoff-scheme = Group; Verlet is not supported by g_membed
> vdwtype = Cut-off
> vdw-modifier = force-switch
> rlist = 1.2
> rvdw = 1.2
> rvdw-switch = 0.8
> coulombtype = PME
> rcoulomb = 1.2
> DispCorr = no
>
> ; Temperature coupling
> tcoupl= V-rescale
> tc-grps= Other Water_and_ions Protein
> tau_t= 0.10.1 0.1
> ref-t = 298.0 298.0 298.0
>
>
> ; Pressure coupling
> pcoupl = Berendsen
> pcoupltype = semiisotropic
> tau_p = 5.0
> compressibility = 4.5e-5 4.5e-5
> ref_p = 1.0 1.0
>
>
> ; Periodic boundary conditions
> pbc= xyz
>
>
> ; Velocity generation
> gen_vel= yes
> gen_temp= 298.0
> gen_seed= -1
>
> ; COM motion removal
> ; These options remove motion of the protein/bilayer relative to the
> solvent/ions
> comm-mode= Linear
> comm-grps= Other Water_and_ions Protein
>
>
> Best regards,
>
> Daniel
>
>
> --
> Daniel Bauer, M.Sc.
>
> TU Darmstadt
> Computational Biology & Simulation
> Schnittspahnstr. 2
> 64287 Darmstadt
> ba...@cbs.tu-darmsta
Re: [gmx-users] computing electric field for triclinic system
Hi, You want to compute and plot the potential at particular points in space? Why is periodicity a concern? Mark On Wed, Dec 20, 2017, 3:54 AM Mariia Savenko wrote: > Dear all, > I have system in triclinic box. I'd like to plot a potential map on XY axes > for a given Z in triclinic box, i.e. For a fixed value of Z I want to have > plot of values in this plane. > My system is a periodic "planar" molecule. Scripts using variations of the > Ewald summation are mainly intended for orthogonal boxes. I concluded that > only script which exists for my purpose is the one used internally by > Gromacs. I know that Gromacs converts any triclinic box to a rectangular > one. To ensure periodicity Gromacs uses shifted images of the unit cell > along the triclinic axis. I'd like to understand how the PME algorithm of > Gromacs manages with this issue and if anyone has been doing that. > Sincerely, > Mariia > -- > 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] Umbrella sampling
- Message from "Jefferies D.F." - Date: Tue, 19 Dec 2017 20:56:34 + From: "Jefferies D.F." Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Umbrella sampling To: gmx-us...@gromacs.org, gromacs.org_gmx-users@maillist.sys.kth.se Out of curiosity, how did you manage to identify and subsequently remove the extra space? I have been having similar problems and the tools I've used haven't fixed this problem. Thanks, From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of sp...@iacs.res.in [sp...@iacs.res.in] Sent: Tuesday, December 19, 2017 6:21 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Umbrella sampling - Message from Dhaniram Mahato - Date: Tue, 19 Dec 2017 21:30:05 +0800 From: Dhaniram Mahato Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Umbrella sampling To: gmx-us...@gromacs.org Hi, There could be format problem. You can create your own .dat files by typing it. You have probably copied it from somewhere. I hope it will work then. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096839.html Thanks -- 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 visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. Hii I have solved the problem. It was just because of one extra space added in the tpr-files.dat file. Now its running properly. - End message from Dhaniram Mahato - -- 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 visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. Hii In my tpr-files.dat file as I showed in the first mail, one extra blank line was added at the bottom of the file. I just deleted that line and the problem has been solved. You just open your .dat file and do shift+g then see if there is a extra line or not. Sunipa - End message from "Jefferies D.F." - -- 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] Umbrella sampling
- Message from Mark Abraham - Date: Fri, 22 Dec 2017 00:42:31 + From: Mark Abraham Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Umbrella sampling To: gmx-us...@gromacs.org Cc: gromacs.org_gmx-users@maillist.sys.kth.se Hi, Yes, the parsing of that file looks like it doesn't handle blank lines gracefully, at least. Use a text editor and clean things up. And make sure the file endings are unix style, e.g. with dos2unix if relevant. Mark On Wed, Dec 20, 2017 at 7:57 AM Jefferies D.F. wrote: Out of curiosity, how did you manage to identify and subsequently remove the extra space? I have been having similar problems and the tools I've used haven't fixed this problem. Thanks, From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of sp...@iacs.res.in [sp...@iacs.res.in] Sent: Tuesday, December 19, 2017 6:21 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Umbrella sampling - Message from Dhaniram Mahato - Date: Tue, 19 Dec 2017 21:30:05 +0800 From: Dhaniram Mahato Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Umbrella sampling To: gmx-us...@gromacs.org Hi, There could be format problem. You can create your own .dat files by typing it. You have probably copied it from somewhere. I hope it will work then. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096839.html Thanks -- 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 visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. Hii I have solved the problem. It was just because of one extra space added in the tpr-files.dat file. Now its running properly. - End message from Dhaniram Mahato - -- 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 visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. Thank you Mark for your suggestion. - End message from Mark Abraham - -- 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] computing electric field for triclinic system
Yes, I'd like to compute potential in particular plane in my box. What I find to be a problem, that computing PME in triclinic box is not so trivial. If I understand rightly FFT requires orthonormal space as "input". 22 груд. 2017 р. 11:32 дп "Mark Abraham" пише: > Hi, > > You want to compute and plot the potential at particular points in space? > Why is periodicity a concern? > > Mark > > On Wed, Dec 20, 2017, 3:54 AM Mariia Savenko > wrote: > > > Dear all, > > I have system in triclinic box. I'd like to plot a potential map on XY > axes > > for a given Z in triclinic box, i.e. For a fixed value of Z I want to > have > > plot of values in this plane. > > My system is a periodic "planar" molecule. Scripts using variations of > the > > Ewald summation are mainly intended for orthogonal boxes. I concluded > that > > only script which exists for my purpose is the one used internally by > > Gromacs. I know that Gromacs converts any triclinic box to a rectangular > > one. To ensure periodicity Gromacs uses shifted images of the unit cell > > along the triclinic axis. I'd like to understand how the PME algorithm of > > Gromacs manages with this issue and if anyone has been doing that. > > Sincerely, > > Mariia > > -- > > 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] Umbrella sampling
All sorted now. Thanks, Damien From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of sp...@iacs.res.in [sp...@iacs.res.in] Sent: Friday, December 22, 2017 11:49 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Umbrella sampling - Message from Mark Abraham - Date: Fri, 22 Dec 2017 00:42:31 + From: Mark Abraham Reply-To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Umbrella sampling To: gmx-us...@gromacs.org Cc: gromacs.org_gmx-users@maillist.sys.kth.se > Hi, > > Yes, the parsing of that file looks like it doesn't handle blank lines > gracefully, at least. Use a text editor and clean things up. And make sure > the file endings are unix style, e.g. with dos2unix if relevant. > > Mark > > On Wed, Dec 20, 2017 at 7:57 AM Jefferies D.F. > wrote: > >> Out of curiosity, how did you manage to identify and subsequently remove >> the extra space? I have been having similar problems and the tools I've >> used haven't fixed this problem. >> >> Thanks, >> >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ >> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of >> sp...@iacs.res.in [sp...@iacs.res.in] >> Sent: Tuesday, December 19, 2017 6:21 PM >> To: gromacs.org_gmx-users@maillist.sys.kth.se >> Subject: Re: [gmx-users] Umbrella sampling >> >> - Message from Dhaniram Mahato - >> Date: Tue, 19 Dec 2017 21:30:05 +0800 >> From: Dhaniram Mahato >> Reply-To: gmx-us...@gromacs.org >> Subject: Re: [gmx-users] Umbrella sampling >> To: gmx-us...@gromacs.org >> >> Hi, >> >> There could be format problem. You can create your own .dat files by >> typing >> it. You have probably copied it from somewhere. I hope it will work then. >> >> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096839.html >> >> Thanks >> -- >> 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 >> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >> or send a mail to gmx-users-requ...@gromacs.org. >> >> Hii >> I have solved the problem. It was just because of one extra space added >> in >> the tpr-files.dat file. Now its running properly. >> >> - End message from Dhaniram Mahato - >> -- >> 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 > visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or send a mail to gmx-users-requ...@gromacs.org. Thank you Mark for your suggestion. - End message from Mark Abraham - -- 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] Regarding protocol of g_lie module
Dear users, I want to calculate linear interaction energy for my protein-ligand complex using g_lie module in Gromacs. I have ran two different simulations of ligand, one with protein and other with water. But I am getting same values for GBind while using g_lie for both simulations. Can anyone help me about the exact usage protocol of g_lie? Thanks -- 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] Regarding protocol of g_lie module
Den 2017-12-22 kl. 13:26, skrev neha chaudhary: Dear users, I want to calculate linear interaction energy for my protein-ligand complex using g_lie module in Gromacs. I have ran two different simulations of ligand, one with protein and other with water. But I am getting same values for GBind while using g_lie for both simulations. Can anyone help me about the exact usage protocol of g_lie? Thanks Then Delta G = 0 -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- 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 sign of deuterium order parameter calculated by g_order
Dear All, I am studying the effects of cholesterols in POPC lipid bilayer. The Gromacs is the version 4.6.5 in my simulations. By using the g_order, I could output the deuterium order parameter of POPC lipids for a long-term equilibration. "g_order_mpi -s msd.tpr -f msd-mol.xtc -n sn1.ndx -d z -od deuter_sn1.xvg -o order_sn1.xvg" The results in the file of "deuter_sn1.xvg" are given as below: @title "Deuterium order parameters" @xaxis label "Atom" @yaxis label "Scd" @TYPE xy 1 0.204493 2 0.223424 3 0.222852 4 0.228435 5 0.230187 6 0.229785 7 0.223191 8 0.217353 9 0.204112 10 0.193993 11 0.176565 12 0.162058 130.13807 14 0.112887 As in the experimental papers about the deuterium order parameter measured by NMR, the Scd is negative and round -0.2. I understand the sign of the deuterium order parameter is not measurable in conventional NMR. I am wondering the values calculated and output by g_order in Gromacs is the absolute value (|Scd|) or the opposite value (-Scd) by default. Sorry to bother you with this simple question. But I didn't find any clear answer from mail list or manual. It would be appreciated if you could give your insights or comments. Best, Wenpeng Zhu -- 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] The sign of deuterium order parameter calculated by g_order
On 12/22/17 10:14 AM, Jason Zhu wrote: Dear All, I am studying the effects of cholesterols in POPC lipid bilayer. The Gromacs is the version 4.6.5 in my simulations. By using the g_order, I could output the deuterium order parameter of POPC lipids for a long-term equilibration. "g_order_mpi -s msd.tpr -f msd-mol.xtc -n sn1.ndx -d z -od deuter_sn1.xvg -o order_sn1.xvg" The results in the file of "deuter_sn1.xvg" are given as below: @title "Deuterium order parameters" @xaxis label "Atom" @yaxis label "Scd" @TYPE xy 1 0.204493 2 0.223424 3 0.222852 4 0.228435 5 0.230187 6 0.229785 7 0.223191 8 0.217353 9 0.204112 10 0.193993 11 0.176565 12 0.162058 130.13807 14 0.112887 As in the experimental papers about the deuterium order parameter measured by NMR, the Scd is negative and round -0.2. I understand the sign of the deuterium order parameter is not measurable in conventional NMR. I am wondering the values calculated and output by g_order in Gromacs is the absolute value (|Scd|) or the opposite value (-Scd) by default. Sorry to bother you with this simple question. But I didn't find any clear answer from mail list or manual. It would be appreciated if you could give your insights or comments. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2017-July/114678.html -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] The sign of deuterium order parameter calculated by g_order
Hi, It outputs -Scd not |Scd|. A couple of points worth considering for your analysis: Firstly, g_order/gmx order doesn't work correctly for the unsaturated carbons and so you will not be able to analyse the oleoly tail properly using the default program. Secondly, if you are using an all-atom force field, you are better off using a different method. This program assumes you don't have explicit hydrogen atoms in your tails (as per a united-atom force field) and tries to predict where they will be. It does a decent job for saturated groups but you are better off using a method that uses the actual hydrogen atom positions. For more info, you can see my recent work (http://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00643) (apologies for the shamless plug!). This work also comes with a modified version of g_order that fixes the unsaturated carbon problems and also gives you the splitting of the order parameters in an CH2 group for united-atom force fields. Cheers Tom On 22/12/17 15:15, Justin Lemkul wrote: On 12/22/17 10:14 AM, Jason Zhu wrote: Dear All, I am studying the effects of cholesterols in POPC lipid bilayer. The Gromacs is the version 4.6.5 in my simulations. By using the g_order, I could output the deuterium order parameter of POPC lipids for a long-term equilibration. "g_order_mpi -s msd.tpr -f msd-mol.xtc -n sn1.ndx -d z -od deuter_sn1.xvg -o order_sn1.xvg" The results in the file of "deuter_sn1.xvg" are given as below: @ title "Deuterium order parameters" @ xaxis label "Atom" @ yaxis label "Scd" @TYPE xy 1 0.204493 2 0.223424 3 0.222852 4 0.228435 5 0.230187 6 0.229785 7 0.223191 8 0.217353 9 0.204112 10 0.193993 11 0.176565 12 0.162058 13 0.13807 14 0.112887 As in the experimental papers about the deuterium order parameter measured by NMR, the Scd is negative and round -0.2. I understand the sign of the deuterium order parameter is not measurable in conventional NMR. I am wondering the values calculated and output by g_order in Gromacs is the absolute value (|Scd|) or the opposite value (-Scd) by default. Sorry to bother you with this simple question. But I didn't find any clear answer from mail list or manual. It would be appreciated if you could give your insights or comments. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2017-July/114678.html -Justin -- Dr Thomas Piggot Visiting Fellow University of Southampton, UK. -- 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] Fatal error from grommp in gromacs 5.0.4
Hi All, I've run into a perplexing problem. I take an initial .gro file, do an energy minimization on it, and then begin an MD simulation. File-wise, the sequence of events is: file_to_minimize.gro -> file_for_md.gro -> frame_1.gro -> frame_2.gro Everything is fine up until frame_2.gro, which is written with only 6 atom columns (the atom coordinates and velocities), whereas frame_1.gro had 9-10 columns (residue number and name, and atom number and name, plus the other 6). The non-atom lines (title, atom count, and the last line for the bounding box) are fine. And, the atom columns that are present seem fine. The formats are as they should be, with no excessively large numbers or corruption. I'm not even sure the missing columns are the issue, so I guess the first question is: Should a .gro file work with only the atom coordinates and velocities (plus the appropriate header and footer lines)? Regardless, this is what I am getting when grommp tries to process frame_2.gro: === gromacs-5.0.4/src/gromacs/fileio/confio.c, at line 1040: Fatal error: Something is wrong in the coordinate formatting of file frame_2.gro. === In looking at confio.c, it seems that a line in frame_2.gro is failing the test at line 1038, which appears to be looking for 2 floating point numbers (why 2? I would think it would be 3, one each for X, Y, and Z). If it got that far (handling of the other columns occurs earlier in confio.c), that implies to me that perhaps the missing columns are not the issue. But if not, I don't know why its failing. And, either way, I don't know why the columns are missing. Has anyone seen this behavior before, or have a theory? By the way, in case any of the developers see this, an error that says "Something is wrong..." isn't all that informative (but better than nothing!). It would be great if sanity checks provided more information upon failure. In this case, knowing what line of the .gro file was causing the error, and printing the values for BUF, &x1, and &x2, would be really helpful. (That being said, I don't mean to sound too critical -- gromacs is a great tool and I realize there aren't enough resources to make everything perfect.) Sincerely, James -- 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] protein peptide interaction
Hi Gromacs folks, Does it make sense to combine the protein and peptide in one pdb file for minimization if I want to study the protein peptide interaction? They will belong to two different chains in one pdb file. Ming -- 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] Fatal error from grommp in gromacs 5.0.4
Hi, On Sat, Dec 23, 2017 at 1:16 PM James wrote: > Hi All, > > I've run into a perplexing problem. I take an initial .gro file, do an > energy minimization on it, and then begin an MD simulation. File-wise, the > sequence of events is: > > file_to_minimize.gro -> file_for_md.gro -> frame_1.gro -> frame_2.gro > > Everything is fine up until frame_2.gro, which is written with only 6 atom > columns (the atom coordinates and velocities), whereas frame_1.gro had 9-10 > columns (residue number and name, and atom number and name, plus the other > 6). The non-atom lines (title, atom count, and the last line for the > bounding box) are fine. And, the atom columns that are present seem fine. > The formats are as they should be, with no excessively large numbers or > corruption. > That sounds impossible for either modern or 5.0.4 GROMACS. What commands are you running? > I'm not even sure the missing columns are the issue, so I guess the first > question is: Should a .gro file work with only the atom coordinates and > velocities (plus the appropriate header and footer lines)? > No. > Regardless, this is what I am getting when grommp tries to process > frame_2.gro: > > === > gromacs-5.0.4/src/gromacs/fileio/confio.c, at line 1040: > > Fatal error: > Something is wrong in the coordinate formatting of file > frame_2.gro. > === > > In looking at confio.c, it seems that a line in frame_2.gro is failing the > test at line 1038, which appears to be looking for 2 floating point numbers > (why 2? I would think it would be 3, one each for X, Y, and Z). If it got > that far (handling of the other columns occurs earlier in confio.c), that > implies to me that perhaps the missing columns are not the issue. But if > not, I don't know why its failing. And, either way, I don't know why the > columns are missing. > The best thing one can say about that code is that it seems to work if you give it a valid .gro file... Since there's an outer loop over dimensions, and the string has already been null terminated, the second float in the sscanf format is merely checking for some kind of mis-formatted input. > Has anyone seen this behavior before, or have a theory? > > By the way, in case any of the developers see this, an error that says > "Something is wrong..." isn't all that informative (but better than > nothing!). It would be great if sanity checks provided more information > upon failure. In this case, knowing what line of the .gro file was causing > the error, and printing the values for BUF, &x1, and &x2, would be really > helpful. (That being said, I don't mean to sound too critical -- gromacs is > a great tool and I realize there aren't enough resources to make everything > perfect.) > Yeah, it's not very nice. The best one can do is say "this line "%s" number %d in file %s wasn't formatted correctly." However, if the reading code is correct, the values in BUF, x1 or x2 are useless to a user. In your case, it would probably fire on the first atom line, and you'd still be writing this email :-) The real problem is how you managed to get a broken format written, not whether the reading code does anything good with that broken file. Mark Sincerely, > James > -- > 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.
