Re: [gmx-users] problem: gromacs run on gpu

Can you try to open the script in vi, delete the mdrun line and then manually retype it? On 7/12/2017 11:03 PM, leila karami wrote: Dear Gromacs users, I am doing md simulation on Gromacs 5.1.3. on GPU in Rocks cluster system using command: gmx_mpi mdrun -nb gpu -v -deffnm gpu -ntomp 16

[gmx-users] problem: gromacs run on gpu

Dear Gromacs users, I am doing md simulation on Gromacs 5.1.3. on GPU in Rocks cluster system using command: gmx_mpi mdrun -nb gpu -v -deffnm gpu -ntomp 16 -gpu_id 0 -pin on All things are ok. When I use this command in a script to do md simulation by queuing system:

Re: [gmx-users] Periodic Molecule's Free Energy Calculation Error

I wonder if the "couple-intramol = yes" is a must. Does it have any influence on the output results if we turn off the intra-molecular non-bonded interactions of a large infinite molecule? The answer to your question has nothing to do with Gromacs, but with understanding the difference

Re: [gmx-users] Periodic Molecule's Free Energy Calculation Error

Hi Alex, Thank you for your reply. Here below is my response to your comments. hBN is hardly a common subject of simulation for Gromacs folks, but let's see... 1. When you run the simulation in vacuum, do you get the same error? Does a 300K vacuum simulation

Re: [gmx-users] gmx select

Hi, Can you please copy, paste and post your actual commands. I don't think your use of quote marks would have led to a valid shell command. The whole selection text will need to be inside some quotes. Mark On Wed, 12 Jul 2017 23:47 Pandya, Akash wrote: > I have

Re: [gmx-users] what is the difference between the 2016.x and the 5.x series?

Additionally, if you care about getting the best performance on your hardware be aware that distro-packaged GROMACS versions are generally optimized for the lowest common denominator CPU architectural capabilities and will not be able to make the best use of modern CPU instructions sets. Hence, if

Re: [gmx-users] gmx select

I have used the same name in my coordinate file. For Glycine it is spelt as Glyci, so the word has been cut off. I know this is correct because I use the same name in VMD. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se

Re: [gmx-users] gmx select

Hi, What are the residue names in your coordinate file? Glyci probably doesn't fit Mark On Wed, Jul 12, 2017 at 10:36 PM Pandya, Akash wrote: > Hi all, > > > I am trying to select all the glycine molecules with 0.5nm of my protein. > I tried both of these commands I

[gmx-users] gmx select

Hi all, I am trying to select all the glycine molecules with 0.5nm of my protein. I tried both of these commands I got from the gromacs website: gmx select -f output.gro -select "Close to protein" resname Glyci and within 0.5 of group "Protein"' -ofpdb gmx select -f output.xtc -s output.tpr

[gmx-users] Non-periodic COM Pulling

Hello, Is it possible to do non-periodic COM pulling using the distance function in GMX 5.14 (i.e. where the distance between the two groups is calculated ignoring pbc)? In the tutorials/online the solution seems to be to simply use a box twice the size of the largest pulling distance, but that

Re: [gmx-users] Help on MD performance, GPU has less load than CPU.

Hi, Sure. But who has data that shows that e.g. a free-energy calculation with the defaults produces lower quality observables than you get with the defaults? Mark On Wed, Jul 12, 2017 at 5:59 PM Téletchéa Stéphane < stephane.teletc...@univ-nantes.fr> wrote: > Le 11/07/2017 à 15:24, Mark

Re: [gmx-users] (no subject)

Hi, You need to have a file that contains the frame you want to start from, and give that to gmx grompp -t Mark On Wed, Jul 12, 2017 at 5:54 PM CLARK NICOLAS Joan wrote: > Dear gmx users, > > > I am trying to extend a finished simulation from a frame which is not the

Re: [gmx-users] Help on MD performance, GPU has less load than CPU.

Le 11/07/2017 à 15:24, Mark Abraham a écrit : Guessing wildly, the cost of your simulation is probably at least double what the defaults would give, and for that cost, I'd want to know why. Estimated colleague, Since this is a wild guess, I'd think to add some guesses myself. I remember

[gmx-users] (no subject)

Dear gmx users, I am trying to extend a finished simulation from a frame which is not the last one in my trajectory. I have tried convert-tpr but I think it's only modifying the number of steps because the resulting tpr file starts the simulation from the first or the last frame depending on

Re: [gmx-users] what is the difference between the 2016.x and the 5.x series?

will do, thanks for the tip. On Wed, Jul 12, 2017 at 11:42 AM, Mark Abraham wrote: > Hi, > > That kind of information is in the release notes, e.g. at > http://manual.gromacs.org/documentation/. Perhaps you want to start with > the 2016 ones :-) > > Mark > > On Wed,

Re: [gmx-users] RDF

Dear Vidya.R Its very difficult to answer this question.It depends on your system .If you run more time of your system, RDF will be more smooth Saikat Pal IIT GUWAHATI On Wednesday 12 July 2017, 10:02:30 AM IST, Vidya R wrote: Hi, I want to calculate RDF of my

Re: [gmx-users] what is the difference between the 2016.x and the 5.x series?

Hi, That kind of information is in the release notes, e.g. at http://manual.gromacs.org/documentation/. Perhaps you want to start with the 2016 ones :-) Mark On Wed, Jul 12, 2017 at 5:39 PM Jose Borreguero wrote: > Dear Gromacs users, > > I'm a relatively new user of

[gmx-users] what is the difference between the 2016.x and the 5.x series?

Dear Gromacs users, I'm a relatively new user of Gromacs and recently realized there is a "2016" branch that is still being updated. What is the difference with the 5.x branch? I ask because I could find RPM packages only for the 2016 version, much easier to install than building from source.

Re: [gmx-users] LINCS warning during constrained md

Hi, I would avoid using the combination of position restraints and constrained bonds with an input structure that is not necessarily consistent with the constraints. That's a recipe for large forces. I wouldn't use position restraints in such a process unless I had some reason to believe that my

Re: [gmx-users] LINCS warning during constrained md

hi, I've seen with vmd the gro file generated after the transformation, and after the 2 steps of minimization, it seems that they have no problem, while if I see the step_n.pdb file generated before the crash, there are some atoms far away from the rest of the protein, while this is not

[gmx-users] Solvent Accessible Surface Area (SASA): Separate Hydrophobic and Hydrophilic components

Hi, I want to measure the Hydrophobic and Hydrophilic components of the Solvent Accessible Surface Area. In the Tool Changes for 5.0 I found these command: gmx sasa -s md.tpr -f md_traj.trr -surface 'group "A"' -output '"Hydrophobic" group "A" and charge {-0.2 to 0.2}; "Hydrophilic" group "B"

Re: [gmx-users] LINCS warning during constrained md

Hi, Those are all good things, but have you actually got out a molecular viewer and looked at the input and output of your resolution conversion? Mark On Wed, Jul 12, 2017 at 4:25 PM edesantis wrote: > Hi, > thanks for the prompt answer, > > > I've found the same

Re: [gmx-users] LINCS warning during constrained md

Hi, thanks for the prompt answer, I've found the same problem even if I try to convert the coarse grained pdb obtained from martinize.py, so in that case it should be not a problem to have the conversion, for this reason I though it is a methodological problem... I've seen the blowing-up

Re: [gmx-users] LINCS warning during constrained md

Hi, Sounds like you might be http://www.gromacs.org/Documentation/Terminology/Blowing_Up because the conversion doesn't work for your configuration. You should start by doing a visual check of the configuration for sanity, then follow the advice in that link. Mark On Wed, Jul 12, 2017 at 3:04

[gmx-users] Walls and PME for long range electrostatics

Dear all, I am simulating a Au(111) slab with explicit electrons inside (included as a "free electron gas"). The gold atoms are frozen, the electrons are free but confined inside the slab by a more repulsive pair interaction with the Au-surface atoms. This works fine and simulations are

[gmx-users] LINCS warning during constrained md

dear all, I am facing a problem with the conversion from Martini CG representation to All-atomistic one. I am using the initram.sh wrapper around the backward.py. There is a LINCS warning problem when the energy relaxation is performed using position restrained md (I've also tried to run

Re: [gmx-users] ACETONITRILE with CHARM ff

> > Message: 3 > Date: Tue, 11 Jul 2017 12:57:05 -0400 > From: Justin Lemkul > > Moreover, I observed that this time I got lower values for P during the NPT > > equilibration, but still is too far from 1 bar. I really don't understand > > why for the NVT simulation I get a T

Re: [gmx-users] output pdb reformatted

Hi, Please stop doing that. You're risking wasting your own time as well. ;-) Mark On Tue, Jul 11, 2017 at 11:52 PM Alex wrote: > You are absolutely right once again. I've been glancing over that topology, > looking right at what the problem was, and not seeing it. The

[gmx-users] topology servers versus ff

Hello, If you want to use CHARMM for your simulations, do not use PRODRUG to construct your parameters but use ParamChem, instead. https://www.paramchem.org/ Stéphane -- Message: 2 Date: Wed, 12 Jul 2017 14:36:27 +0500 From: maria khan

[gmx-users] topology servers versus ff.

Dear gromacs users.. while using charmm27 can i use PRODRUG for topology building.?? when im using prodrug pdb2gmx gives me error of missing atoms but when i use charmm ff,it doesnt give me that error,so proceeding with charmm27 i made ligand topology by prodrug and used it for further

[gmx-users] Benchmarks v5.0

Hi there, where can I find the benchmark input files for the 2 cases reported in this paper (ion channel and ethanol-water system)? http://www.gromacs.org/@api/deki/files/240/=gromacs-5.0-benchmarks.pdf Many thanks. Jony Dr Jony Castagna Sci-Tech Daresbury Keckwick Lane Daresbury Warrington

Re: [gmx-users] Add missing residues

http://www.charmm-gui.org/ -- Regards, Nikhil Maroli -- 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

[gmx-users] Add missing residues

Hello everyone, Can someone post the best tool available for building missing residues in the crystal structure? I need the complete structure (2 missing residues) for carrying out simulation studies. Thank you *Khadija Amine* Ph.D. Biology and Health Biochemistry & Bioinformatics -- Gromacs