[gmx-users] Fixing dssp images using m2p file

Dear Gromacs experts, Which option i need to use to correct the dssp image as given in the link. (i have to get full part upto 100 ns in the box) You can see the right side is not full in the box, i marked in the black box https://drive.google.com/file/d/1QkpFOLvOcrSyv1U6HkRorYrKgKxGCskS/view?

[gmx-users] gromacs paper

Hi, does anyone have a copy of this conference paper / the conference proceedings book (below)? If so would you be so kind to mail it to me (copy or similar)? "Bekker, H., Berendsen, H. J. C., Dijkstra, E. J., Achterop, S., van Drunen, R., van der Spoel, D., Sijbers, A., Keegstra, H., Reitsma, B.

Re: [gmx-users] Perturbing Proteins

There are a number of ways to bias a system. Many of them are implemented in gromacs. You will need to be more specific about what you want here. The structures you find in the PDB are in an energy minima but these (lets call them physical) minima may not be (lets call them theoretical) minima of

[gmx-users] gibbs free energy calculation

Hi! Thank you for your previous reply. You were right, my file was getting modified. I had not saved the page directly but had copy-pasted it in a textedit file. I am again stuck, though. I was trying to run job_0.sh and when I gave the command: gmx grompp -f $MDP/EM/em_steep_$LAMBDA.mdp -c $FREE

Re: [gmx-users] Regarding calculation of Spatial Distribution Function

I want to calculate water SDF around C-alpha of glycine molecule. So here i have followed the commands.. Step 2:- gmx trjconv -s nptmd.tpr -f nptmd.xtc -o abc.tng -boxcenter tric -ur compact -pbc none and it asks me Select group for output Group 0 ( System) has 1543 elements Group 1 ( Prot

[gmx-users] Problems with Ionic Liquid Simulations

Hi All, I am currently trying to run a simulation on the ionic liquid 1-butyl-3-methyl-imidazolium hexafluorophosphate ([Bmim][PF6]), but have run into a few errors I am unable to solve. I've used the following steps in my simulation so far: a) Generated the required .pdb files for both the

Re: [gmx-users] Perturbing Proteins

Hi, Good question! The nstcomm is the frequency at which the center of mass motion is removed. My guess is that using short frequency for the nstcomm (e.g. nstcomm=1 while simulation time step is 1 fs, dt=0.001) can perturbe the system. That is, the system may not return to its starting/unpertu

Re: [gmx-users] gmx_mpi works in command line but not in script

Hi Marc, On Tue, Apr 3, 2018 at 4:35 PM, Marc Hoemberger wrote: > Hi Alex, > > I have had a similar issue on our cluster (different module files etc.) for > me it turned out that on the actual compute nodes this module was not > available. Thus if you run it from the command line on e.g. your l

[gmx-users] Perturbing Proteins

Hi all, I was wondering if there is a principled way to perturb molecules and then see its energy converge to the stationary state via the simulation. Perturbation could mean changing the coordinates of the atoms, changing angles dihedrals etc. Anything related to the topology. I want to see this

Re: [gmx-users] gmx_mpi works in command line but not in script

Hi Alex, I have had a similar issue on our cluster (different module files etc.) for me it turned out that on the actual compute nodes this module was not available. Thus if you run it from the command line on e.g. your login node you might have access to this compiler / modulefile, but when movin

Re: [gmx-users] gmx_mpi works in command line but not in script

Hi, I can't help you troubleshoot your use of your cluster's modules (nor guess about what's in the rest of your run script). Talk to the people paid to do it ;-) Mark On Tue, Apr 3, 2018 at 10:15 PM Alex wrote: > On Tue, Apr 3, 2018 at 3:46 PM, Mark Abraham > wrote: > > > Hi, > > > > On Tue,

Re: [gmx-users] gmx_mpi works in command line but not in script

On Tue, Apr 3, 2018 at 3:46 PM, Mark Abraham wrote: > Hi, > > On Tue, Apr 3, 2018 at 8:56 PM Alex wrote: > > > Thanks Marc. > > > > I removed the two EXPORT line in the script but still missing the library > > (removing only the second line also did not help): > > > > ModuleCmd_Load.c(208):ERROR

Re: [gmx-users] gmx_mpi works in command line but not in script

Hi, On Tue, Apr 3, 2018 at 8:56 PM Alex wrote: > Thanks Marc. > > I removed the two EXPORT line in the script but still missing the library > (removing only the second line also did not help): > > ModuleCmd_Load.c(208):ERROR:105: Unable to locate a modulefile for > 'intel/composerxe/2015.1.133'

Re: [gmx-users] gmx_mpi works in command line but not in script

Thanks Marc. I removed the two EXPORT line in the script but still missing the library (removing only the second line also did not help): ModuleCmd_Load.c(208):ERROR:105: Unable to locate a modulefile for 'intel/composerxe/2015.1.133' --

Re: [gmx-users] gmx_mpi works in command line but not in script

Hi, It looks like you are choosing to mismanage LD_LIBRARY_PATH. Try letting the modules do it, since it is their job. Mark On Tue, Apr 3, 2018, 20:29 Alex wrote: > Dear all, > > I have installed the gromacs2018.1 parallel in a cluster, it works > perfectly in the command line, of course after

Re: [gmx-users] Performance

Hi, Your system is exploding, some atoms end up with coordinates of around 10^9 which then throw off the PBC code that tries to put atoms back in the box. This will normally not happen as constraining will already fail with such huge coordinates, I think, so technically it is a bug, we could handl

[gmx-users] gmx_mpi works in command line but not in script

Dear all, I have installed the gromacs2018.1 parallel in a cluster, it works perfectly in the command line, of course after loading some module. But when I put the commands along with loading module commands in a bash script to be submitted in the cluster, it crashes with the below massage: +

Re: [gmx-users] Number of Xeon cores per GTX 1080Ti

On Tue, Apr 3, 2018 at 5:10 PM, Jochen Hub wrote: > > > Am 03.04.18 um 16:26 schrieb Szilárd Páll: > >> On Tue, Apr 3, 2018 at 3:41 PM, Jochen Hub wrote: >>> >>>benchmar >>> >>> Am 29.03.18 um 20:57 schrieb Szilárd Páll: >>> Hi Jochen, For that particular benchmark I only measured

Re: [gmx-users] Number of Xeon cores per GTX 1080Ti

Am 03.04.18 um 16:26 schrieb Szilárd Páll: On Tue, Apr 3, 2018 at 3:41 PM, Jochen Hub wrote: Am 29.03.18 um 20:57 schrieb Szilárd Páll: Hi Jochen, For that particular benchmark I only measured performance with 1,2,4,8,16 cores with a few different kinds of GPUs. It would be easy to do th

Re: [gmx-users] Number of Xeon cores per GTX 1080Ti

On Tue, Apr 3, 2018 at 3:41 PM, Jochen Hub wrote: > > > Am 29.03.18 um 20:57 schrieb Szilárd Páll: > >> Hi Jochen, >> >> For that particular benchmark I only measured performance with >> 1,2,4,8,16 cores with a few different kinds of GPUs. It would be easy >> to do the runs on all possible core co

Re: [gmx-users] Number of Xeon cores per GTX 1080Ti

Am 29.03.18 um 20:57 schrieb Szilárd Páll: Hi Jochen, For that particular benchmark I only measured performance with 1,2,4,8,16 cores with a few different kinds of GPUs. It would be easy to do the runs on all possible core counts with increments of 1, but that won't tell a whole lot more than

Re: [gmx-users] error in index file

On 4/3/18 5:50 AM, Joe Jordan wrote: Gromacs 4.6 is no longer supported, so I would recommend upgrading to 2018 and using gmx select. Short of that, if you just run make_ndx and don't use a selection sting you will get a group corresponding to NAP with the right number of atoms. Neither gmx s

Re: [gmx-users] Possible to extract gro file from a tpr?

Hi, As Justin observed, editconf -f your.tpr -o your.pdb just works. Mark -- 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)subscri

Re: [gmx-users] Possible to extract gro file from a tpr?

We haven't yet moved to Discourse ;-) On Tue, Apr 3, 2018, 10:54 Viveca Lindahl wrote: > Wish I could +1 the best response here :) Thanks. > > -- > Viveca > > > On Fri, Mar 30, 2018 at 8:35 PM, Mark Abraham > wrote: > > > Just say No! :-) > > > > On Fri, Mar 30, 2018, 19:58 Alex wrote: > > > >

Re: [gmx-users] Compute average forces along a trajectory

Dear Mark, Thanks. I did not specify that parameter, as you correctly suggested. I'm re-running the simulations and see what happens. Thanks Simone Il lun 2 apr 2018, 17:44 Mark Abraham ha scritto: > Hi, > > Probably you didn't use nstfout to save forces - use gmx check -f on your > trajectory

[gmx-users] Possible to extract gro file from a tpr?

Hi A quick question here, before to read this response I thought (but never tested) that it was possible to extract a pdb from a tpr since we use one to generate a tpr with grompp. So how is store the atomic coordinates of a system in a tpr file ? Thanks ---

Re: [gmx-users] error in index file

Gromacs 4.6 is no longer supported, so I would recommend upgrading to 2018 and using gmx select. Short of that, if you just run make_ndx and don't use a selection sting you will get a group corresponding to NAP with the right number of atoms. On Tue, Apr 3, 2018 at 11:41 AM, abhisek Mondal wrote:

Re: [gmx-users] error in index file

I'm using v4.6.2 $make_ndx -f npt.gro > r 306 (residue num of ligand) > name 24 Ligand This should do the work right ? On Tue, Apr 3, 2018 at 3:07 PM, Joe Jordan wrote: > I got a group with the right number of atoms when I tried it. What version > of gromacs are you using and what selection s

Re: [gmx-users] error in index file

I got a group with the right number of atoms when I tried it. What version of gromacs are you using and what selection string are you using? On Tue, Apr 3, 2018 at 11:32 AM, abhisek Mondal wrote: > Location of the files: > https://drive.google.com/drive/u/0/folders/0B6O- > L5Y7BiGJfmQ4N2FpblBEcF

Re: [gmx-users] error in index file

Location of the files: https://drive.google.com/drive/u/0/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU On Tue, Apr 3, 2018 at 2:53 PM, Joe Jordan wrote: > Can you post the gro file and the resulting index file? > > On Tue, Apr 3, 2018 at 11:20 AM, abhisek Mond

Re: [gmx-users] error in index file

Can you post the gro file and the resulting index file? On Tue, Apr 3, 2018 at 11:20 AM, abhisek Mondal wrote: > Hi, > > I'm just having some issue creating index file for umbrella sampling. > > I have a ligand: > Group20 (NAP) has73 elements > > Now when I run following command: > gmx m

[gmx-users] error in index file

Hi, I'm just having some issue creating index file for umbrella sampling. I have a ligand: Group20 (NAP) has73 elements Now when I run following command: gmx make_ndx -f npt.gro and try to add NAP for index.ndx, only 6 elements were being added. I don't understand the problem here. NA

[gmx-users] Regarding calculation of Spatial Distribution Function

Hello, I want to do the Spatial Distribution Function, I tried to follow the manual gmx spatial. I am following the five-step protocol which is given in gmx spatial manual.. 1) I have an index file ndx_CaOw.ndx (which contains the C-alpha and all the Ow's of water molecules, Is this index good

Re: [gmx-users] Possible to extract gro file from a tpr?

Wish I could +1 the best response here :) Thanks. -- Viveca On Fri, Mar 30, 2018 at 8:35 PM, Mark Abraham wrote: > Just say No! :-) > > On Fri, Mar 30, 2018, 19:58 Alex wrote: > > > Or, and that is a very peculiar option, genion with -conc 0. :) > > > > Alex > > > > > > On 3/30/2018 4:28 AM,