Dear Justin, I am using the velocities from the NPT run. Could you please explain on the .cpt file you mentioned?
Kind Regards, Antara -- Junior research fellow(project) Systems biology group CSIR-Institute of Genomics & Integrative Biology South Campus New Delhi - 110020 M : +91-9717970040 -- On Sun, May 15, 2016 at 10:51 AM, < 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. COM-Pull along a direction (Pengzhi Zhang) > 2. Re: error in running mdrun of membrane protein in a mixed > bilayer with MARTINI MODEL (Justin Lemkul) > 3. Umbrella Sampling - choice of pull-coord?-dim (Lukas Zimmermann) > 4. PCA and FEL (sun) > 5. Re: PCA and FEL (Tsjerk Wassenaar) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 14 May 2016 14:58:37 -0500 > From: Pengzhi Zhang <pzha...@central.uh.edu> > To: <gromacs.org_gmx-users@maillist.sys.kth.se> > Subject: [gmx-users] COM-Pull along a direction > Message-ID: <5737836d.8010...@central.uh.edu> > Content-Type: text/plain; charset="utf-8"; format=flowed > > Dear Gromacs users, > > I am trying to pull an ion out of a protein using Gromacs/5.0.4. I pull > the ion along specific pre-determined paths. > > From my understanding, pulling along a direction _V guarantees that the > dumb bead would move only at direction _V. The position of the dumb bead > is simply: _r(t) = _r(0) + _V*speed*time (_ means vector). And if the > spring constant is sufficiently large, the pulled atom (a single ion) > would also follow the dumb bead (with fluctuations). However, I found > that no matter how large the spring constant is (I vary it from 100 to > 1,000,000 kJ/mol/nm**2), the pulled atom deviates from the direction _V > in a certain amount of time (usually after the pulled bead unbinds), > sometimes it even goes perpendicular to _V and moves out of the box, > terminating the simulation. > > Does the direction _V (pull-coord1-vec) mean the direction of > instantaneous pull force or the direction of the path that the dumb bead > follows? > > Thank you very much in advance! > > > Here is the pull part of my mdp file. > ; COM PULLING > ; Pull type: no, umbrella, constraint or constant-force > pull = umbrella > pull-geometry = direction > pull-ngroups = 2 > pull-ncoords = 1 > pull-group1-name = binding_site_atoms > pull-group2-name = pull_ion ; pull group > pull-start = yes > pull-coord1-vec = -0.07 -0.04 0.99 > pull-coord1-groups = 1 2 > pull_coord1_rate = 0.001 ; nm/ps > pull-coord1-k = 10000 ; kJ/mol/nm^2 > pull-nstxout = 10 ; 0.02 ps > pull-nstfout = 10 > pull-print-reference = yes > > > Sincerely, > Pengzhi > > > ------------------------------ > > Message: 2 > Date: Sat, 14 May 2016 18:33:08 -0400 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] error in running mdrun of membrane protein in > a mixed bilayer with MARTINI MODEL > Message-ID: <5b732333-0517-e66f-2e4b-7a9cf337e...@vt.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > > > On 5/14/16 2:34 PM, Mark Abraham wrote: > > Hi, > > > > Please keep the discussion on the mailing list, so others can help and > > learn. > > > >> Antara said: > >> I have pasted the mdrun command i used to run it in parallel with the > > number of processors i used which was 16. The command is : > >> > >> > >> /app/setups/gromacs-5.1.1/build/bin -deffnm MD -pin on -rdd 1.8 > > > > That still isn't a command you've copied and pasted from a terminal or a > > script. You needed a call that might include mpirun -np 16 gmx_mpi mdrun, > > etc. > > > >> In the pbs script, i used 16 in the number of processors option. > > > > What happens when you run on one rank? > > > >> For the production tpr, i used the gro file from the last equilibration > > step(step6.6) The command used was : > >> > >> gmx grompp -c step6.6equilibration.gro -p system.top -n new_index.ndx -f > > MD.mdp -o MD.tpr > > > > That looks like it could be reasonable, but as with any equilibration you > > need to look at observables to judge that it's equilibrated. Their > builder > > should provide reasonable defaults, but you can't assume they're perfect, > > either. In particular, if the last equilibration ensemble doesn't match > the > > production ensemble, that could be the problem. > > > > Failing to pass the .cpt file to grompp -t after equilibration is a great > way to > do that. The production simulation is starting from some unpredictable > ensemble, without velocities, etc.. > > -Justin > > > Mark > > > > On Sat, May 14, 2016 at 5:10 PM Mark Abraham <mark.j.abra...@gmail.com> > > wrote: > > > >> Hi, > >> > >> On Sat, May 14, 2016 at 4:34 PM Antara mazumdar < > antara.mazum...@igib.in> > >> wrote: > >> > >>> Dear users, > >>> > >>> I am trying to run a coarse grained simulation of a membrane protein > in a > >>> mixed lipid billayer using martini model 2.2. I have already performed > all > >>> the equilibration steps successfully on my desktop with GROMACS 5.1.0. > >>> However, when i try to execute its production run in parallel(having > >>> gromacs 5.1 version installed) it complains of LINCS warning and > >>> terminates at step 0. The lincs warning error is coming from BB and SC1 > >>> atoms of one of the protein residues. > >>> > >> > >> There are lots of possible places to go wrong, including not making your > >> production .tpr based on the outputs of your equilibration. This seems > >> quite a likely possibility. > >> > >> You should also consider further equilibration - whether using Martini > or > >> not, it is sometimes necessary to use a small time step when relaxing > >> problem configurations. > >> > >> > >>> But on the contrary, it runs on the desktop successfully. *My > production > >>> run mdp file details are below :* > >>> > >>> > >>> . > >>> > >>> This is the MD.mdp file :ntegrator = md > >>> tinit = 0.0 > >>> dt = 0.020 > >>> nsteps = 2500000000 > >>> > >>> nstxout = 2000 > >>> nstvout = 2000 > >>> nstfout = 2000 > >>> nstlog = 2000 > >>> nstenergy = 2000 > >>> nstxtcout = 2000 > >>> xtc_precision = 100 > >>> > >>> ns_type = grid > >>> pbc = xyz > >>> nstlist = 10 > >>> cutoff-scheme = Verlet > >>> rlist = 1.2 > >>> vdwtype = Cut-off > >>> vdw-modifier = none > >>> rvdw_switch = 1.0 > >>> rvdw = 1.2 > >>> coulombtype = pme > >>> rcoulomb = 1.2 > >>> > >>> tcoupl = v-rescale > >>> tc-grps = protein CHOL_POPC_DPSM_DPCE W_ION > >>> > >>> tau_t = 1.0 1.0 1.0 > >>> ref_t = 303.15 303.15 303.15 > >>> > >>> ; Pressure coupling: > >>> Pcoupl = berendsen > >>> Pcoupltype = semiisotropic > >>> tau_p = 5.0 5.0 > >>> compressibility = 3e-4 3e-4 > >>> ref_p = 1.0 1.0 > >>> ; GENERATE VELOCITIES FOR STARTUP RUN: > >>> gen_vel = no > >>> refcoord_scaling = all > >>> > >>> *the command used for mdrun :* > >>> > >>> -deffnm MD -pin on -rdd 1.8 -np 16 > >>> > >> > >> mdrun 5.1 won't accept -np, so I don't know what you are actually doing. > >> Please don't edit and filture things, copy and paste whole actual > things. > >> :-) > >> > >> Mark > >> > >> I would also like to mention that i generated the initial structure of > the > >>> system using CHARMM GUI MARTINI MAKER protein-membrane system option. I > >>> have followed the exact builder protocol for the equilibration and > >>> minimisation. > >>> > >>> Kindly suggest something! > >>> > >>> Thanks, > >>> Antara > >>> > >>> -- > >>> Junior research fellow(project) > >>> Systems biology group > >>> CSIR-Institute of Genomics & Integrative Biology > >>> South Campus > >>> New Delhi - 110020 > >>> M : +91-9717970040 > >>> -- > >>> -- > >>> 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. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > > > ------------------------------ > > Message: 3 > Date: Sun, 15 May 2016 00:55:23 +0200 > From: Lukas Zimmermann <luk.zi...@gmail.com> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] Umbrella Sampling - choice of pull-coord?-dim > Message-ID: > <CAPSKXTqEZw4= > 1ccab3ftbpvtzfvrzlghz6d5ecq1yaq2ytg...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Dear GROMACS users, > > I am interested in the role of the mdp parameter pull-coord?-dim when > sampling > a particular umbrella window after having generated initial configurations > for, say, the > COM distance between two groups being the reaction coordinate. > > I know that these options can be controlled to restrict the actual pulling, > say with geometry distance, to a subset of the pull vector components, for > instance to enable > aligment of the pull vector with the box dimensions. > > However, I do not understand its role when performing umbrella sampling > along the reaction coordinate. > I know that the pull-code then controls the COM distance between the pull > groups with a (usually) harmonic potential, but what effect will > pull-coord?-dim have? > > I observe different behavior for my toy system consisting of two methanol > molecules in vacuum. > With all components enables, I need to correct the PMF for entropic > decrease in the PMF, > since the methanol is sampled on a sphere with increasing radius. > If only allowing one component, the PMF will be flat, but different values > for delta G > result. > > Also, in the US Tutorial by Justin, the US code uses: > > pull_coord1_dim = N N Y > > Is there any particular reason, not to set > > pull_coord1_dim = Y Y Y > > here? Would this setting also be justified? Since, as far as I understood > the procedure, pulling > > is just there for generating the initial configurations and US is more or > less independent of this. > > > > Many thanks in advance! > > Lukas > > > ------------------------------ > > Message: 4 > Date: Sun, 15 May 2016 09:03:34 +0530 > From: sun <sun.i...@gmail.com> > To: gmx-us...@gromacs.org > Subject: [gmx-users] PCA and FEL > Message-ID: <ec81ef15-0fcc-4ba7-b3aa-84d789822...@gmail.com> > Content-Type: text/plain; charset=us-ascii > > Hello everyone > I am using Gromacs 5.0 for protein-ligand MD. I want to do FEL analysis > for the stability of my pro-lig complex. In a 2015 paper, The group > calculated two principal component, PC1 and PC2 and then prepared an.xvg > file to be used as input for g_sham. My question is, when we use g_anaeig; > we get eigenvec.xvg. from -comp flag. Now how shall one select two > principal components from that data? I am sorry if my question is wrong but > please help me. > > My second question is, can we use any two parameters like rmsd and Rg for > input in g_sham to probe the stability of complex? Is that valid? > > With Regards > Suniba > > Sent from my iPhone > > ------------------------------ > > Message: 5 > Date: Sun, 15 May 2016 07:21:37 +0200 > From: Tsjerk Wassenaar <tsje...@gmail.com> > To: Discussion list for GROMACS users <gmx-us...@gromacs.org> > Subject: Re: [gmx-users] PCA and FEL > Message-ID: > < > cabze1sg4ez1ytdbjsmc_z-x3hon3u1zqv74cof4nsoaykss...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi Suniba, > > No, with gmx anaeig you can select -2d, which does a 2D projection onto the > selected eigenvectors. Alternatively, you can combine any two projections > onto eigenvectors, which you get using the option -proj. The quickest way > to do that is something like: > > paste <(grep -v '^[@#]' proj1.xvg) <(proj2.xvg) | awk '{print $2, $4}' > > combined.xvg > > You will loose the labels, but that should be fine. > > You can combine other variables in a similar manner. > > Hope it helps, > > Tsjerk > > On Sun, May 15, 2016 at 5:33 AM, sun <sun.i...@gmail.com> wrote: > > > Hello everyone > > I am using Gromacs 5.0 for protein-ligand MD. I want to do FEL analysis > > for the stability of my pro-lig complex. In a 2015 paper, The group > > calculated two principal component, PC1 and PC2 and then prepared an.xvg > > file to be used as input for g_sham. My question is, when we use > g_anaeig; > > we get eigenvec.xvg. from -comp flag. Now how shall one select two > > principal components from that data? I am sorry if my question is wrong > but > > please help me. > > > > My second question is, can we use any two parameters like rmsd and Rg for > > input in g_sham to probe the stability of complex? Is that valid? > > > > With Regards > > Suniba > > > > Sent from my iPhone > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > > ------------------------------ > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > End of gromacs.org_gmx-users Digest, Vol 145, Issue 55 > ****************************************************** > -- 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.