[gmx-users] Problem in running Equilibration step

2012-03-24 Thread Spring buds
Hi, I am trying to run the equilibration step. I got the below error. could you explain why it happens? Thank you [ymu039-107:17471] *** Process received signal *** [ymu039-107:17471] Signal: Segmentation fault (11) [ymu039-107:17471] Signal code: Address not mapped (1) [ymu039-107:17471] Fail

Re: [gmx-users] Structure averaging problem using g_rmsf

2012-03-22 Thread Spring buds
Hi Justin, Thanks for reply. I will look into. On Fri, Mar 23, 2012 at 10:30 AM, Justin A. Lemkul wrote: > > > Spring buds wrote: > >> Hi >> >> I am trying to average the structure from the last 10ns from 100ns. So I >> used the command which is below: >

[gmx-users] Structure averaging problem using g_rmsf

2012-03-22 Thread Spring buds
Hi I am trying to average the structure from the last 10ns from 100ns. So I used the command which is below: g_rmsf –f 100.xtc –s topol.tpr –b 90001 –e 10 –ox traj_avg.pdb But I got below error: "Program g_rmsf, VERSION 4.5.4 Source code file: /root/Desktop/gromacs-4.5.4/src/gmxlib/trxio.c,

[gmx-users] Generating topology

2012-03-21 Thread Spring buds
Hi A protein sits on the top of another protein (not docking). I then used pdb2gmx command to generate the topology. Surprisingly, i got five files, as given below: I think the two proteins are not connected each other. is it possible to make it one posre and topol file. Many thanks in advance

Re: [gmx-users] Installing & uninstalling of gromacs

2012-01-28 Thread Spring buds
On Wed, Jan 25, 2012 at 7:42 PM, Mark Abraham wrote: > On 25/01/2012 12:54 AM, Spring buds wrote: > > > Removing files in /usr/local/gromacs has no bearing on the contents of >> /usr/local/bin. If you did 'make links' at the end of the installation, >> you

Re: [gmx-users] Installing & uninstalling of gromacs

2012-01-24 Thread Spring buds
lly removed or not. >> >> >> Sure. I will do now >> >> >>Which OS you are working on? >> >> >> Linux (CentOS 5.7) >> >> Thanks a lot. >> >> >> > >> > >> > On Tue, Jan 24, 2012 at

Re: [gmx-users] Installing & uninstalling of gromacs

2012-01-23 Thread Spring buds
On Tue, Jan 24, 2012 at 11:49 AM, lina wrote: > On Tue, Jan 24, 2012 at 11:42 AM, Spring buds > wrote: > > Hi lina, > > > > Thanks for reply. could you tell me how to remove completly the gromacs > > installation? > > Which commands have you issued? >

Re: [gmx-users] Installing & uninstalling of gromacs

2012-01-23 Thread Spring buds
Hi lina, Thanks for reply. could you tell me how to remove completly the gromacs installation? On Tue, Jan 24, 2012 at 2:31 AM, lina wrote: > On 24 Jan, 2012, at 1:53, Spring buds wrote: > > > Dear Gromacs users, > > > > Greetings!!! > > > > I am very

[gmx-users] Installing & uninstalling of gromacs

2012-01-23 Thread Spring buds
Dear Gromacs users, Greetings!!! I am very new users and I am trying to install grmacs 4.5.5 or 3.3.3 for past four days. But still I am not able to. So I would like to ask some questions which are below. 1.My laptop is a dual core, which means two processors?.So should I need to install MPI?