Re: [gmx-users] is it necessary to mdrun posre_npt.mdp first and then posre_nvt.mdp

No, what Mark means is that if you equilibrated temperature AND pressure (NpT) there's no point in an NVT step, in which the pressure may go off again, even though it's unlikely to matter much, because the volume is already within proper range. However, there's the 'posre' part still, which

Re: [gmx-users] QM calculation

Thank you very much Justin for your helpful answer. On Thursday, March 31, 2016 3:40 PM, Justin Lemkul wrote: On 3/31/16 12:19 AM, mohammad r wrote: > Thank you Justin, I want to do QM calculationbefore running equilibration > then run the MD simulation by GROMACS. Do

Re: [gmx-users] Number of simulated annealing points

Hi, My guess is that you're fine. MAXPTR is probably just a hangover from someone who didn't want to allocate memory dynamically. Mark On Fri, 1 Apr 2016 00:50 Tim Moore wrote: > I went back and tried to change MAXPTR to a larger value - I then get a > different error

Re: [gmx-users] Number of simulated annealing points

I went back and tried to change MAXPTR to a larger value - I then get a different error saying input lines can only contain 4095 characters. After digging around the source code a bit more, I found this came from a defined constant STRLEN in src/gromacs/utility/cstringutil.h

Re: [gmx-users] Error: Lost Particles while sorting

On Thu, Mar 31, 2016 at 9:25 PM, Smith, Micholas D. wrote: > Hi, > > Good to know. I'll ask the supercomputing folks to update gromacs from > 5.0.4 to 5.0.7 at the next scheduled downtime. > I don't think the machine needs to be offline just to install a version of GROMACS. ;)

[gmx-users] Rotation of single moleculae in vacuum

I simulate a single flexible molecule with no PBC starting from its optimized configuration (L_BFGS) and immediately turning T-coupling on. >From the very beginning, the molecule starts to rotate around COM. Although this motion may not matter for an isolated molecule, I'd be happy to understand a

Re: [gmx-users] Suggestion to update online .mdp options for pull code

On Thu, Mar 31, 2016 at 8:37 PM, Mark Abraham wrote: > Hi, > > On Thu, 31 Mar 2016 19:23 Christopher Neale > wrote: > > > Dear developers: > > > > The online manual lists pull-code options here: > >

Re: [gmx-users] Error: Lost Particles while sorting

Hi, Good to know. I'll ask the supercomputing folks to update gromacs from 5.0.4 to 5.0.7 at the next scheduled downtime. -Micholas From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf

Re: [gmx-users] Error: Lost Particles while sorting

Hi, I was thinking of http://redmine.gromacs.org/issues/1153 but on general principles that should not have showed up in 5.0. Nonetheless the early 5.0 versions had enough GPU-related issues that you still want to follow my suggestion and see how you go. Mark On Thu, 31 Mar 2016 20:11 Smith,

Re: [gmx-users] Error: Lost Particles while sorting

Thanks, Mark. I didn't see this bug noted in the bug list so I thought I was just going crazy === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics

Re: [gmx-users] Suggestion to update online .mdp options for pull code

Indeed, sorry that I missed that stamp in the upper right. I was confused by the word "current" in the html address, I guess. Searching "pull" on http://manual.gromacs.org/documentation/5.1.2/index.html did pull up what I wanted:

Re: [gmx-users] Error: Lost Particles while sorting

Hi, Starting a new series of calculations on the earliest of a series of patch releases means you have chosen to accept all the bugs that have been fixed since. ;-) This indeed looks like one of them. Get e.g. 5.0.7 installed. Mark On Thu, 31 Mar 2016 19:40 Smith, Micholas D.

[gmx-users] Error: Lost Particles while sorting

Dear other users (and developers) I moved some simulations that were working pretty well on one supercomputer to another (the previous one did not have gpu nodes) to take advantage of some gpus, but I am now getting a sporadic error: Program gmx_mpi, VERSION 5.0 Source code file:

Re: [gmx-users] Suggestion to update online .mdp options for pull code

Hi, On Thu, 31 Mar 2016 19:23 Christopher Neale wrote: > Dear developers: > > The online manual lists pull-code options here: > http://manual.gromacs.org/current/online/mdp_opt.html#pull No, because those pages are version stamped e.g. 5.0.7 because that version

[gmx-users] Suggestion to update online .mdp options for pull code

Dear developers: The online manual lists pull-code options here: http://manual.gromacs.org/current/online/mdp_opt.html#pull that seem to have not been updated since: http://manual.gromacs.org/documentation/5.1/ReleaseNotes/new-features.html#changed-the-way-pull-directions-are-selected It took

Re: [gmx-users] Looking for the source of the H-REMD slowdown when decoupling a lot of atoms

> One more question: why does the free energy code have to use its own kernel? > I realize that I'm going to sound like an idiot here, but why can't one just > tweak parameters outside of the kernel and then have the optimized kernel do > the dynamics? I presume that one has to step outside of

Re: [gmx-users] -pbc nojump failure

I think the problem is that I can’t seem to start from an unfragmented structure. I start from the .pdb file, where the protein is a whole, and end up with a .tpr file that is fragmented. The interesting thing is, this did not happen with version 4.6.5 (I now use 5.1.2). Do I have to do

Re: [gmx-users] Looking for the source of the H-REMD slowdown when decoupling a lot of atoms

Dear Szilárd, Mark, and Michael: Thank you for your suggestions. 1. I did use the icc compiler 2. I tested usage of nstlist=10 by setting verlet-buffer-tolerance=-1 (I had already set nstlist=10 but mdrun changes that to 25 in my previous setup) -- this did not improve the performance 3. I

Re: [gmx-users] a question related to minim.mdp

It depends on what you want to do. If you simply want to minimize the system so that the dynamics will be stable in MD, then I have never needed more than 500 steps of minimization (though in some cases I find it necessary to use flexible waters and solutes via the mdp options define=-DFLEXIBLE

[gmx-users] a question related to minim.mdp

Dear all, Following is a minim.mdp from the website, in which "nsteps = 5". Here what I want to ask is, does it mean the larger the protein, the larger the value of nsteps? Or for any size of protein regardless of mw, as for it has specified "emtol = 500.0", " nsteps =

Re: [gmx-users] is it necessary to mdrun posre_npt.mdp first and then posre_nvt.mdp

can i use only one equilibrium(only posre_npt.mdp) i.e if after em.mdp if i run posre_npt file and use the output of posre_npt file for final mdrun? On 31 March 2016 at 20:32, Pradip Kaur wrote: > Hi , > I started mdrun with posre_npt .mdp and I have ignored

Re: [gmx-users] -pbc nojump failure

No! You can't do that, because fitting will cause the PBC and the coordinates to mismatch. So 'nojump' after that will for sure screw up the coordinates. Check the trjconv workflow on the Gromacs site. Cheers, Tsjerk On Mar 31, 2016 14:23, "Francesco Carbone" wrote: >

Re: [gmx-users] -pbc nojump failure

Hi, Thanks. If I do that, the reference structure would be what’s in the .tpr file, right? Best, Irem > On Mar 31, 2016, at 8:22 AM, Francesco Carbone wrote: > > You could try to fit first (-fit rot+trans) and fix pbc (-pbc nojump) later. > > Cheers, > > Fra > > On

Re: [gmx-users] -pbc nojump failure

Hi, Thanks for your suggestion. Unsurprisingly, the structure in nvt_water_frozen.tpr is also fragmented. Is there a way to use the input .pdb file as reference, somehow? Best, Irem > On Mar 31, 2016, at 12:45 AM, Tsjerk Wassenaar wrote: > > Hi Irem, > > Check the

Re: [gmx-users] pdb2gmx & terminal residues

On 3/31/16 10:41 AM, Brett wrote: Dear Justin and All, The full screen output was as following and I am looking forward to getting a reply from you. gmx pdb2gmx -f practice.pdb -o target_processed.gro -ignh :-) GROMACS - gmx pdb2gmx, VERSION 5.1.2 (-:

Re: [gmx-users] pdb2gmx & terminal residues

Dear Justin and All, The full screen output was as following and I am looking forward to getting a reply from you. gmx pdb2gmx -f practice.pdb -o target_processed.gro -ignh :-) GROMACS - gmx pdb2gmx, VERSION 5.1.2 (-: GROMACS is written by:

Re: [gmx-users] pdb2gmx & terminal residues

On 3/31/16 8:18 AM, Brett wrote: Dear Justin and All, For terminal residue, regardless I select 0, 1, 2, the error messages always exist. I have opened the pdb by swiss deep view and resaved it, the same error message still exist. However if I choose force field 6: AMBER99SB-ILDN

Re: [gmx-users] Own coarse-grained forcefield

On 3/31/16 9:35 AM, Michał Kadlof wrote: I would like to build my own coarse-grained forcefield for virtual beads-on-chain polymer. All I want for now is LJ Potential, and a spring between neighbours. Below are files that I have already have in my ff. The last file is my experimental

[gmx-users] Own coarse-grained forcefield

I would like to build my own coarse-grained forcefield for virtual beads-on-chain polymer. All I want for now is LJ Potential, and a spring between neighbours. Below are files that I have already have in my ff. The last file is my experimental structure in PDB format. When I run: gmx pdb2gmx

Re: [gmx-users] pdb2gmx & terminal residues

Dear Justin and All, For terminal residue, regardless I select 0, 1, 2, the error messages always exist. I have opened the pdb by swiss deep view and resaved it, the same error message still exist. However if I choose force field 6: AMBER99SB-ILDN protein, the error message disappear. Will

Re: [gmx-users] -pbc nojump failure

You could try to fit first (-fit rot+trans) and fix pbc (-pbc nojump) later. Cheers, Fra On 31 March 2016 at 05:45, Tsjerk Wassenaar wrote: > Hi Irem, > > Check the structure in nvt_water_frozen.tpr: > > gmx editconf -f nvt_water_frozen.tpr -o ref.pdb > > Cheers, > > Tsjerk

Re: [gmx-users] pdb2gmx & terminal residues

On 3/30/16 10:41 PM, Brett wrote: Dear All, When I do "mx pdb2gmx -f practice.pdb -o target_processed.gro -ignh" with force field, it gave me the warning as following, "WARNING: WARNING: Residue 1 named ASP of a molecule in the input file was mapped to an entry in the topology database,

Re: [gmx-users] QM calculation

On 3/31/16 12:19 AM, mohammad r wrote: Thank you Justin, I want to do QM calculationbefore running equilibration then run the MD simulation by GROMACS. Do you knowwhich software is appropriate and compatible with GROMACS that after QM calculation I can run the rest of simulation? Again, for

Re: [gmx-users] virtual site - algorithmic reasons

On 3/31/16 6:06 AM, Samith Rathnayake wrote: Hi everyone, Recently i was used to started Bevan Lab tutorial and gone through specially with virtual site tutorial.In this tutorial Dr.Justin emphasized that co2 cannot effectively build in traditional sense because of algorithmic reasons.

Re: [gmx-users] Generate diagram/figure with information about protein-ligand interactions

On 3/31/16 6:58 AM, bio hpc wrote: My problem is not excel or whatever graphical program. I just need the data, in an automatic way. Then I can use either matplotlib or similar to get the plots automatically. But my question is if there is somewhere a repository of gromacs scripts with a

Re: [gmx-users] Generate diagram/figure with information about protein-ligand interactions

Hi biohpc, For this you need to combine output from gmx hbond, gmx sasa, and gmx saltbr. Cheers, Tsjerk On Mar 31, 2016 12:58, "bio hpc" wrote: > My problem is not excel or whatever graphical program. I just need the > data, in an automatic way. Then I can use either

Re: [gmx-users] Use pdb file generated with Maestro, in Gromacs

On 3/31/16 6:55 AM, bio hpc wrote: Thanks. Apart from this, is is there some script that keeps my original hydrogens from Maestro? Rename with sed according to what the force field expects. -Justin El 30/3/2016, a las 19:43, Tsjerk Wassenaar escribió: Hey :) -ignh

Re: [gmx-users] Generate diagram/figure with information about protein-ligand interactions

My problem is not excel or whatever graphical program. I just need the data, in an automatic way. Then I can use either matplotlib or similar to get the plots automatically. But my question is if there is somewhere a repository of gromacs scripts with a script doing an analysis of the

Re: [gmx-users] Use pdb file generated with Maestro, in Gromacs

Thanks. Apart from this, is is there some script that keeps my original hydrogens from Maestro? > El 30/3/2016, a las 19:43, Tsjerk Wassenaar escribió: > > Hey :) > > -ignh does ignore the hydrogens in the input file. It builds those > hydrogens that are specified in the

[gmx-users] virtual site - algorithmic reasons

Hi everyone, Recently i was used to started Bevan Lab tutorial and gone through specially with virtual site tutorial.In this tutorial Dr.Justin emphasized that co2 cannot effectively build in traditional sense because of algorithmic reasons. And cant hold 180 degree during a simulation.Could

Re: [gmx-users] Umbrella sampling along PCA eigenvector using make_edi

Dear Hendrik, that indeed looks a bit strange. If you provide the necessary input files for a test, I could have a look at what might be wrong. You can put them somewhere for download or email them directly to me (not to the list, they will not be accepted). Carsten > On 30 Mar 2016, at 16:11,