[gmx-users] Re: Segmentation Fault using g_cluster

You also need to make a new index file that corresponds to the new , reduced .tpr file Cheers E Enjoy Ausserberg From: "Tsjerk Wassenaar [via GROMACS]" mailto:ml-node+s5086n5011009...@n6.nabble.com>> Date: Fri, 6 Sep 2013 02:12:25 -0700 To: Evelyne Deplazes mailto:e.de

[gmx-users] Re: Segmentation Fault using g_cluster

You're a genious. It works! Thanks a lot From: "Tsjerk Wassenaar [via GROMACS]" mailto:ml-node+s5086n5011009...@n6.nabble.com>> Date: Fri, 6 Sep 2013 02:12:25 -0700 To: Evelyne Deplazes mailto:e.depla...@uq.edu.au>> Subject: Re: Segmentation Fault using g_cluster H

[gmx-users] Re: Segmentation Fault using g_cluster

Hi guys do you have an idea what is causing the segmentation fault with g_cluster? I do the following 1 . I combine trr files from different simulations using trjcat and select backbone atoms only trjcat -f ../../*C/runs/*/*trr -cat -n index.ndx -o trajout_combined.xtc 2. I make a new .tp

[gmx-users] Re: Segmentation Fault using g_cluster

Hi guys do you have an idea what is causing the segmentation fault with g_cluster? I do the following 1 . I combine trr files from different simulations using trjcat and select backbone atoms only trjcat -f ../../*C/runs/*/*trr -cat -n index.ndx -o trajout_combined.xtc 2. I make a new .tp

[gmx-users] Re: Segmentation Fault using g_cluster

Hi guys do you have an idea what is causing the segmentation fault with g_cluster? I do the following 1 . I combine trr files from different simulations using trjcat and select backbone atoms only trjcat -f ../../*C/runs/*/*trr -cat -n index.ndx -o trajout_combined.xtc 2. I make a new .tp

[gmx-users] Re: Segmentation Fault using g_cluster

Hi guys do you have an idea what is causing the segmentation fault with g_cluster? I do the following 1 . I combine trr files from different simulations using trjcat and select backbone atoms only trjcat -f ../../*C/runs/*/*trr -cat -n index.ndx -o trajout_combined.xtc 2. I make a new .tp

[gmx-users] Re: removing rotational and translational motion (holonomic contraint)

LDFLAGS="-L/ivec/devel/intel/12.1/fftw/3.3.3/lib" export CPPFLAGS="-I/ivec/devel/intel/12.1/fftw/3.3.3/include" cd /home/deplazes/gromacs-3.3.1-rtc ./configure --prefix=/home/deplazes/gromacs-3.3.1-rtc --with-fft=fftw3 make -j4 make install I get an error message when running ma

[gmx-users] removing rotational and translational motion (holonomic contraint)

Hi guys I am running a set of umbrella sampling simulations using gromacs 333 and the "pull" code. The idea is to apply an umbrella potential to restrain the distance between a protein and a ligand in the x direction. Unfortunately, the rotational and translational movement of the protein durin

[gmx-users] Re: gmx-users Digest, Vol 82, Issue 150

ntents of gmx-users digest..." > > Today's Topics: > > 1. Re: g_covar to calculate correlation of motion (Tsjerk Wassenaar) > 2. Re: g_covar to calculate correlation of motion (bipin singh) > 3. removing pbc jumps from trajectory (Evelyne Deplazes) > 4. R

[gmx-users] removing pbc jumps from trajectory

cs.org/Documentation/Terminology/Periodic_Boundary_Conditions I also other combinations of -whole, -center and -pbc nojump of trjconv, without any luck. Can anyone suggest how I can re-center the protein and remove the pb jump ie make the protein "whole" Thanks Evelyne -- Evelyne Deplazes PhD

[gmx-users] fep: continuation of run after lambda = 1

e remaining 100 ns. But that crashed as well with similar LINCS warnings. Has anyone else ever had a similar problem? I have already spent a fair bit of time on trying to fix it and also talked to people from the Martini group who are experiences gromacs user. any ideas are appreciated Thank

[gmx-users] gromos ffG653a6 parameters for MTSET

molecule seems to be commonly used by experimentalists but I can only find a single reference of simulation studies. Does anyone know of some simulation studies or even has force field parameters for MTSET (or any of the methanethiosulfonate reagents) ? thanks -- Evelyne Deplazes PhD student

[gmx-users] energy minimization - infinite force on atom

f the restraints or removing the restraints but still get the same output. I also tried adding -DFLEXIBLE since I am using the spc model, but still the same output. can anyone tell me what that message actually means and what is wrong with my system? thanks -- Evelyne Deplazes PhD student