[gmx-users] Range of block lengths in gmx energy error estimate only gives one value

Good morning, With gmx energy one can specify a range of block lengths to use for the error estimate using "-nbmin" and "-nbmax". When I specify a range I still only get one estimate. I would have expected a different estimate for each block length in the range to be printed to the screen. I'm

Re: [gmx-users] Methanol geometry parameters

On Fri, 2015-12-04 at 09:43 +0100, Daniele Veclani wrote: > Dear Peter Stern. > > Yes, I need the starting coordination for methanol, but are there specific > coordinates like for spce water or tip3p water? > > Where can I find the files .gro or .pdb for methanol ? Creating a methanol pdb file

Re: [gmx-users] Help with Gromacs-5.1.1 installation in Cluster

On Fri, 2015-12-04 at 03:32 -0500, Ashalatha Sreshty wrote: > Dear Gromacs Users, > > I need help with installation of gromacs-5.1.1 which is mpi enabled to run > it in a cluster. Although, I was able to compile the the source code > without any errors, I am unable to find the executables in the

Re: [gmx-users] Multi-node Replica Exchange Segfault

   1.0 Replica Exchange Order Replica 0: Replica 1: Atom distribution over 16 domains: av 1207 stddev 26 min 1165 max 1238 On Fri, 2015-10-30 at 13:08 +, Barnett, James W wrote: > Hey Mark, > > On Fri, 2015-10-30 at 08:14 +, Mark Abraham wrote: > > Hi, >

Re: [gmx-users] Multi-node Replica Exchange Segfault

Hey Mark, On Fri, 2015-10-30 at 08:14 +, Mark Abraham wrote: > Hi, > > I've never heard of such. You could try a multisim without -replex, to help > diagnose. A multidir simulation runs without issue when -replex is omitted. > > On Fri, 30 Oct 2015 03:33 Barne

Re: [gmx-users] Multi-node Replica Exchange Segfault

but after further testing when it reaches a successful exchange I still get the segmentation fault. >  > > On Fri, Oct 30, 2015 at 2:32 PM Barnett, James W <jbarn...@tulane.edu> > wrote: > > > I added the -debug flag to my two replica test. The end of my mdrun log > &g

[gmx-users] Multi-node Replica Exchange Segfault

Good evening here, I get a segmentation fault with my GROMACS 5.1 install only for replica exchange simulations right at the first successful exchange on a multi-node run. Normal simulations across multiple nodes work fine, and replica exchange simulations on one node work fine. I've reproduced

Re: [gmx-users] gromacs 4.6.7 plumed -Segmentation fault

On Wed, 2015-10-21 at 10:20 -0500, Ana Marija wrote: > Hi, > > I installed gromacs 4.6.7 with plumed like this: > module swap PrgEnv-cray PrgEnv-gnu > module load fftw/3.3.4.0 > module load cray-mpich/7.0.5 > module load gsl/1.15 > module load cmake > #in /lustre/beagle2/ams/new/gromacs make

Re: [gmx-users] Gromacs and Gcc5.2

On Fri, 2015-10-02 at 09:57 +0200, Nicolas Cheron wrote: > Dear all, > > I am wondering if there is an official statement regarding compiling > Gromacs with gcc5.2.0 (or any gcc from the 5.x branch). Is it recommended > or not? Should we expect improvements? I don't think there is an official

Re: [gmx-users] GMXLIB does not induce residuetype.dat

On Thu, 2015-10-01 at 20:21 +, Ebert Maximilian wrote: > Dear list, > > I have my own force field working folder so I cloned the entire top folder to > no mess with the original files. I added residues to the residue type file to > add my residues to the protein group. My FF is included due

Re: [gmx-users] GROMACS OPLS-AA question

On Thu, 2015-09-10 at 11:32 -0600, Eric Smoll wrote: > Hello GROMACS users, > > I am interested in using the OPLS-AA as implemented in GROMACS. > The OPLS-AA forcefield omits all nonbonded (Coulomb and LJ) > interactions 1 > and 2 bonds away. Nonbonded interactions 3 bonds are away are scaled >

Re: [gmx-users] How to create a spherocylindrical wall

On Fri, 2015-09-11 at 11:57 +0530, Jagannath Mondal wrote: > Hi > I would like to perform a simulation ( without any periodic > boundary > condition) where I need to have a wall of spherocylindrical geometry. > In > other words the particles will be confined inside a spherocylinder. > > Is

Re: [gmx-users] Pull parameters to Restrain motion along the Z Axis

to allow my protein only move in x, y direction. I am restricting it so It can't move be in Z direction. There might be other ways to do that with restraints, but this may give you the result you want, too. On Wed, Aug 26, 2015 at 8:38 PM, Barnett, James W jbarn...@tulane.edu wrote

Re: [gmx-users] what's the easiest way to generate a md trajectory for ligand flying into/being pulled out of the pocket?

Look into the pull code. You'll want to choose two groups (one for the ligand, one for the binding site), and one coordinate with those groups where the pull rate is not zero (negative rate to bring them together, positive rate to pull them apart). -- James “Wes” Barnett, Ph.D. Candidate

Re: [gmx-users] Pull parameters to Restrain motion along the Z Axis

pull_start = yes means COM distance is added to the pull_init value. So whatever distance your two pull groups starts out at plus pull_init is the window where it will sample. pull_start = no means just the pull_init value is used as the reference distance. If you have pull_init set to 1.0

Re: [gmx-users] Free energy calculations (FEP) and soft core potential 1-1-48

-48 It just crashes... Without any error message. I am now re-running the simulations with fewer lambda points and for 5ns. Let's see what comes up. 2015-07-15 18:12 GMT+02:00 Barnett, James W jbarn...@tulane.edu: Do you get any output with the crash? Or is it just a segmentation fault

Re: [gmx-users] Free energy calculations (FEP) and soft core potential 1-1-48

Do you get any output with the crash? Or is it just a segmentation fault? -- James “Wes”​ Barnett Ph.D. Candidate Chemical and Biomolecular Engineering Tulane University Boggs Center for Energy and Biotechnology, Room 341-B New Orleans, Louisiana 70118 jbarn...@tulane.edu​ LinkedIn​​

Re: [gmx-users] solvation by ethanol

This was a different force field, but the idea remains the same: http://statthermo.blogspot.com/2015/06/using-another-solvent-besides-water-in.html -- James “Wes”​ Barnett Ph.D. Candidate Chemical and Biomolecular Engineering Tulane University Boggs Center for Energy and Biotechnology, Room

Re: [gmx-users] Atomtype OW not found

What does your topology (.top) file look like? And what's the exact command you are using for grompp? -- James “Wes”​ Barnett Ph.D. Candidate Chemical and Biomolecular Engineering Tulane University Boggs Center for Energy and Biotechnology, Room 341-B New Orleans, Louisiana 70118

Re: [gmx-users] User directive for non-bonded interactions

Just to weigh in, I think the unclear part is that the section itself is in the printed manual (pdf file). The online manual is copied verbatim into the printed manual as section 7, so statements like that remain. -- James “Wes”​ Barnett Ph.D. Candidate Chemical and Biomolecular Engineering

Re: [gmx-users] how to assign options of the same type?

If you use -deffnm it gives the same prefix to all files that are output (and requires the same prefix on the .tpr file that is input). For example, if your tpr file is md.ttr you could do gmx mdrun -deffnm md Your checkpoint files will be named md.cpt and your trr files will be named md.trr,

Re: [gmx-users] Generate the water box

Use gmx editconf first to create the box then gmx solvate to fill it with water (omitting -box directive this time). -- James Wes Barnett Ph.D. Candidate Chemical and Biomolecular Engineering Tulane University Boggs Center for Energy and Biotechnology, Room 341-B New Orleans, Louisiana 70118

Re: [gmx-users] Editconf error

It'd be more helpful for troubleshooting your problem if you post the entire file in each case, not just parts of them. If it's a large file use Pastebin.com or something similar. -- James Wes Barnett Ph.D. Candidate Chemical and Biomolecular Engineering Tulane University Boggs Center for

Re: [gmx-users] GPU low performance

What's your exact command? Have you reviewed this page: http://www.gromacs.org/Documentation/Acceleration_and_parallelization James Wes Barnett Ph.D. Candidate Chemical and Biomolecular Engineering Tulane University Boggs Center for Energy and Biotechnology, Room 341-B

Re: [gmx-users] Can only find GPU'S on first node

Have you tried using: mpirun -np (number of mpi-processes total) -npernode (number of gpus per node) . when you execute mdrun? Not sure if it will do the trick, but it looks like it may work. What that command should do it limit the number of mpi-process to the number of gpus (so that

[gmx-users] [ constraints ] in .rtp database not recognized by pdb2gmx

I'm using fixed bond lengths from TRAPPE-UA with [ constraints ] type 1. I'm attempting to place constraints in an .rtp file for use with pdb2gmx, but it looks like GROMACS doesn't recognize the keyword in that case. It thinks it is a new residue name: Fatal error: in .rtp file in residue

[gmx-users] Comb. Rule 2 LJ Params. Being Stored in .tpr as Rule 1 and Vice Versa?

I have combination rule set as 2 in my [ defaults ] section. However, when I do gmx grompp and then gmx dump on the .tpr file, the values indicate they are being stored as combination 1. My understanding from the manual section 5.3.2 is that for combination rule 2 the last two values on an [

[gmx-users] Coul. Recip. in Logfile for Classical Ewald

I'm doing a classical Ewald simulation with GROMACS (obviously I should be using something other than Ewald in my simulations like PME, but I am just trying to understand the concept and write some analysis code.). In the logfile does Coul. Recip. include the self correction (or any other kind

Re: [gmx-users] Length of .xtc file in frames for C-Code

I have a question to all the people who are familiar with C-code. How can I read in the total number of frames in my *.xtc file? Especially when I do the analysis somewhere in the middle? Are you using the XDR library or something else? In the XDR library there is a way to get the status each

Re: [gmx-users] Fwd: sigma unit conversion

The Amber molecular dynamics program (sander) uses a different format of the van der Waals equation, so Amber force fields are designed to use different parameters than those used in Gromacs. So, it's not as simple as converting from Angstroms to nanometers. The coefficents used in the Amber

Re: [gmx-users] Amber to Gromacs conversion

On 12/03/2013 11:45 AM, Chetan Mahajan wrote: are there other tools to convert Amber input files into the ones for Gromacs? I've had success with acpype: https://code.google.com/p/acpype/ Use the amb2gmx mode: acpype -p _prmtop_ -x _inpcrd_ -- Wes Barnett | jbarn...@tulane.edu -- Gromacs

Re: [gmx-users] Amber to Gromacs conversion

-i FFF.pdb File ../acpype.py, line 1231 with open(pklFile, wb) as f: # for python 2.6 or higher ^ SyntaxError: invalid syntax Unfortunately, I do not know python. Thanks On Tue, Dec 3, 2013 at 12:01 PM, Barnett, James W. jbarn...@tulane.eduwrote: On 12/03/2013 11