Re: [gmx-users] Error in gmx trjcat

>> Hey Mark, >> >> Still the same problem persists. >> >> >> > Hi, > > That looks like a broken build of GROMACS, rather than a bug in the code or > a broken file. Can you try those gmx check commands on another installation > somewhere else? (Also gmx check -m doesn't do anything useful any more,

[gmx-users] Length of a constrained bond

Hello Gromacs Users, When setting "constraints=h-bonds" in an mdp file, what sets the constrained bond length? Is it the equilibrium bond length in the topology, the bond length deduced from the initial coordinates, or something else. Best, Eric -- Gromacs Users mailing list * Please search

[gmx-users] simulation crash

Hi there, I am running several independent replica of similar system but in different pose of protein-peptide. I am in NVT ensemble and the length of the simulation is 125ns (dt=2fs). Few of them are crashing with the classic error: "1 particles communicated to PME node 8 are more than 2/3

[gmx-users] 3dc warning

Hello Gromacs users, I am using version 2018.1. I have a system in an infinite slab configuration (periodic in the x and y dimensions; in the z dimension, the atoms are permanently confined to 1/3 of the unit cell length with the remainder vacuum). I am interested in simulating the system with

Re: [gmx-users] trjconv ndec not working

Paul and Mark, Thanks for the reply! Good to know I wasn't doing anything wrong. Best, Eric On Tue, Apr 17, 2018 at 10:08 AM, Mark Abraham wrote: > Hi, > > What Paul said agrees with my memory, but I'd not found time to check that > yet. We should indeed fix the

Re: [gmx-users] trjconv ndec not working

Hi, What Paul said agrees with my memory, but I'd not found time to check that yet. We should indeed fix the docs. Mark On Tue, Apr 17, 2018, 16:42 Paul Bauer wrote: > Hello Eric, > > I had a look at the code for writing gro files and it looks to me that > it is only

Re: [gmx-users] trjconv ndec not working

Hello Eric, I had a look at the code for writing gro files and it looks to me that it is only able to write three decimal places there. There is a comment in the code that mentions that writing other precisions has been removed. This means that we need to update the man page text to not be

Re: [gmx-users] CGenff parameters in gromacs but missing in charmm package

On 4/17/18 11:24 AM, Fabian Keller wrote: Dear Justin, On 4/17/18 3:34 AM, Fabian Keller wrote: Dear all, I am using the CGenFF/paramchem framework for a new molecule (an imidazolium cation derivative with methyl groups on both N atoms). I faced a known problem going from CHARMM package to

Re: [gmx-users] CGenff parameters in gromacs but missing in charmm package

Dear Justin, > On 4/17/18 3:34 AM, Fabian Keller wrote: >> Dear all, >> I am using the CGenFF/paramchem framework for a new molecule (an imidazolium >> cation derivative with methyl groups on both N atoms). >> I faced a known problem going from CHARMM package to Gromacs with parameters >>

Re: [gmx-users] Error in gmx trjcat

On Tue, Apr 17, 2018 at 3:32 PM Syed Azeem wrote: > Hey Mark, > > Still the same problem persists. > > > Hi, That looks like a broken build of GROMACS, rather than a bug in the code or a broken file. Can you try those gmx check commands on another installation

Re: [gmx-users] Error in gmx trjcat

Hey Mark, Still the same problem persists. GROMACS: gmx check, VERSION 5.1.4 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Command line: gmx check -f new2.xtc -m report.tex Checking file new2.xtc Reading frame 0 time 10.000 # Atoms 10174 Precision

Re: [gmx-users] CGenff parameters in gromacs but missing in charmm package

On 4/17/18 3:34 AM, Fabian Keller wrote: Dear all, I am using the CGenFF/paramchem framework for a new molecule (an imidazolium cation derivative with methyl groups on both N atoms). I faced a known problem going from CHARMM package to Gromacs with parameters already existing in CHARMM for

Re: [gmx-users] Error in gmx trjcat

Hi, I meant to run gmx check -f 100cat.xtc gmx check -f new2.xtc on the separate files, to find out e.g. whether they are trajectories that have matching numbers of particles, etc. Mark On Tue, Apr 17, 2018 at 1:13 PM Syed Azeem wrote: > > Hi, > > > > What does

[gmx-users] Issues using Implicit Solvent with Charmm 27

Hi there, I am trying to simulate a protein using a GBSA (implicit solvent) approach, and first I've been googling a bit in order to set the parameters of the simulation (mdp file) as better as possible. I am using the following mdp options for the minimization step (the parameters of the

Re: [gmx-users] Error in gmx trjcat

> Hi, > > What does gmx check report on the two input .xtc files? Hey Mark, Thanks for the reply. I did gmx check on both the .xtc files. Now, even this command is yielding the same error. My command: gmx check -f 100cat.xtc -f2 new2.xtc -m report.tex error: x[10172] ( 2.76900e+00

Re: [gmx-users] installion of gromacs 5.07

Hi, No, CUDA is a toolkit for compiling and running on GPUs. A compiler is a program for turning source code into something a computer can run. Your OS seems quite old, so the default compiler is too old to be useful for compiling GROMACS. How to decide what to do to get an updated compiler is

Re: [gmx-users] installion of gromacs 5.07

Thank you so much for your quick reply. "you will need to use a more recent compiler" for my installation error i did not understand about "CUDA". Did i need to install cuda to overcome the error. On 4/17/18, Mark Abraham wrote: > Hi, > > Please consider installing a

Re: [gmx-users] Error in gmx trjcat

Hi, What does gmx check report on the two input .xtc files? Mark On Tue, Apr 17, 2018 at 12:06 PM Syed Azeem wrote: > Hey all, > > I'm experiencing an error while using trjcat command. Initially, I ran > a simulation for 50 ns and then extended till 100ns. After

Re: [gmx-users] installion of gromacs 5.07

Hi, Please consider installing a recent version of GROMACS, which is not only easier to use and install but is still supported and will have fewer bugs, too. Either way, you will need to use a more recent compiler than you seem to have available on your system. Mark On Tue, Apr 17, 2018 at

[gmx-users] Fwd: installion of gromacs 5.07

-- Forwarded message -- From: SHAHEE ISLAM Date: Tue, 17 Apr 2018 16:16:41 +0530 Subject: installion of gromacs 5.07 To: gromacs.org_gmx-users@maillist.sys.kth.se hi, i am just new of gromacs.I want to install the gromacs 5.07.I am following this tutorial

[gmx-users] Error in gmx trjcat

Hey all, I'm experiencing an error while using trjcat command. Initially, I ran a simulation for 50 ns and then extended till 100ns. After extension, I concatenated the trajectories of both the runs using gmx trjcat. Then, again I extended the run from 100 ns to 500 ns. Finally, I tried to

Re: [gmx-users] Error in full MD

here is my log and mdp file. On Tue, Apr 17, 2018 at 3:22 PM, RAHUL SURESH wrote: > Hi > > Please add your log file as well as your mdp settings. > > On Tue, Apr 17, 2018 at 3:10 PM, ISHRAT JAHAN wrote: > > > Dear all, > > I am trying to do md

[gmx-users] installion of gromacs 5.07

hi, i am just new of gromacs.I want to install the gromacs 5.07.I am following this tutorial http://www.gromacs.org/Documentation/Installation_Instructions_5.0 at first i have install cmake3.2.0.then follow this tar xfz gromacs-5.0.7.tar.gz cd gromacs-5.0.7 mkdir build cd build cmake ..

Re: [gmx-users] Error in full MD

Hi Please add your log file as well as your mdp settings. On Tue, Apr 17, 2018 at 3:10 PM, ISHRAT JAHAN wrote: > Dear all, > I am trying to do md simulation of protein in osmolyte. When I run the full > md, the simulation stops after 9 ps with lots of step.pdb file. No

[gmx-users] Error in full MD

Dear all, I am trying to do md simulation of protein in osmolyte. When I run the full md, the simulation stops after 9 ps with lots of step.pdb file. No error appears in .log file but simulation stop. will anyone please tell me what should I do as I am unable to understand the error. Also no

[gmx-users] Installation of g_mmpbsa with Gromacs 2016.3

Dear Gromacs-Users, I know that g_mmpbsa is not a Gromacs tool but I guess there are some people here who installed / used it. I want to install g_mmpbsa using my current 2016.3 gromacs gmx_mpi installation and my already installed apbs 1.4.1. First of all, in the installation instruction of

[gmx-users] CGenff parameters in gromacs but missing in charmm package

Dear all, I am using the CGenFF/paramchem framework for a new molecule (an imidazolium cation derivative with methyl groups on both N atoms). I faced a known problem going from CHARMM package to Gromacs with parameters already existing in CHARMM for Gromacs. I assume that this is due to

[gmx-users] CGenff parameters in gromacs but missing in charmm package

Dear all, I am using the CGenFF/paramchem framework for a new molecule (an imidazolium cation derivative with methyl groups on both N atoms). I faced a known problem going from CHARMM package to Gromacs with parameters already existing in CHARMM for Gromacs. I assume that this is due to

Re: [gmx-users] REMD Simulation

Hi, On Mon, Apr 16, 2018 at 10:21 AM ISHRAT JAHAN wrote: > Dear all, > I am trying to do REMD simulation in different cosolvents. I have generated > temperatures using temperature genrating tools but it gives different > number of temperatures in different solvents with

[gmx-users] Fwd: REMD Simulation

Dear all, I am trying to do REMD simulation in different cosolvents. I have generated temperatures using temperature genrating tools but it gives different number of temperatures in different solvents with exchange probability of 0.25. Is it fair to do remd with different replicas? In what way it