[gmx-users] Gromacs 4.6 crushes in PBS queue system

2013-02-16 Thread Tomek Wlodarski
Hi! I have problem in running gromacs 4.6 in PBS queue... I end up with error: [n370:03036] [[19430,0],0]-[[19430,1],8] mca_oob_tcp_msg_recv: readv failed: Connection reset by peer (104) -- mpirun noticed that process rank

Re: [gmx-users] Re: question about fftw3 in gromacs 4.6 installation

2013-02-09 Thread Tomek Wlodarski
Hi guys! Thanks for help! I have finally manage to solve this problem. Like Szilárd notice it was a problem with assembler. When I installed binutils-2.23.1 (previously I had 2.20.1) it worked :) So my combination was gcc 4.7.2 and binutils-2.23.1. All the best! tomek On Sun, Feb 3, 2013 at

Re: [gmx-users] Re: question about fftw3 in gromacs 4.6 installation

2013-02-02 Thread Tomek Wlodarski
On Sat, Feb 2, 2013 at 12:34 PM, Mark Abraham mark.j.abra...@gmail.comwrote: On Sat, Feb 2, 2013 at 1:00 AM, Justin Lemkul jalem...@vt.edu wrote: On 2/1/13 5:26 PM, didymos wrote: Hi Justin! I had the same problem and I used your advise but I am not sure if this entirely worked

Re: [gmx-users] Re: question about fftw3 in gromacs 4.6 installation

2013-02-02 Thread Tomek Wlodarski
Páll szilard.p...@cbr.su.se wrote: On Sat, Feb 2, 2013 at 2:38 PM, Tomek Wlodarski tomek.wlodar...@gmail.comwrote: On Sat, Feb 2, 2013 at 12:34 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Sat, Feb 2, 2013 at 1:00 AM, Justin Lemkul jalem...@vt.edu wrote: On 2/1/13 5

Re: [gmx-users] Re: question about fftw3 in gromacs 4.6 installation

2013-02-02 Thread Tomek Wlodarski
On Sat, Feb 2, 2013 at 10:12 PM, Mark Abraham mark.j.abra...@gmail.comwrote: On Sat, Feb 2, 2013 at 8:48 PM, Tomek Wlodarski tomek.wlodar...@gmail.comwrote: Thanks Szilárd, good idea:) I tried to build gromacs and I got errors..: /tmp/ccBvi1my.s: Assembler messages: /tmp/ccBvi1my.s

Re: [gmx-users] restart REMD

2012-05-22 Thread Tomek Wlodarski
On Sun, May 20, 2012 at 4:50 PM, Tomek Wlodarski tomek.wlodar...@gmail.com wrote: Hi Francesco, Thanks! However, it does not work with my case.. tomek On Sun, May 20, 2012 at 1:47 PM, francesco oteri francesco.ot...@gmail.com wrote: Hi, usually I use something like: mdrun_mpi -v

Re: [gmx-users] restart REMD

2012-05-20 Thread Tomek Wlodarski
that it has to load topol_1.cpt topol_2.cpt ecc.ecc Anyway, you can do a small test, i.e. using 5 replicas and stopping you simulation after a few seconds Francesco 2012/5/20 Tomek Wlodarski tomek.wlodar...@gmail.com Hi, I am running REMD simulation: mdrun_mpi -v -deffnm -s topol_

[gmx-users] REMD - low temperature ranges

2012-04-27 Thread Tomek Wlodarski
Hi, I have notice that quite often people in REMD simulation use replicas in lower than 300K temp. Using for example temperature ranges from 250 to 450K I am wondering what is the purpose of those replicas. I have limited computational resources and I am wondering if for studing 175 aa protein is

Re: [gmx-users] REMD - low temperature ranges

2012-04-27 Thread Tomek Wlodarski
better when you also include lower temperature.? best! tomek On Fri, Apr 27, 2012 at 3:40 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 27/04/2012 10:59 PM, Tomek Wlodarski wrote: Hi, I have notice that quite often people in REMD simulation use replicas in lower than 300K temp. Using

[gmx-users] protein and DMPC in Charmm36 ff

2012-04-15 Thread Tomek Wlodarski
Hi, I would like to simulate protein in DMPC bilayer in Charmm36 ff. I checked mailing list and KALP-15 tutorial, but still I have a few basic questions. 1) I have problem with DMPC bilayer... - VMD membrane builder only provides POPE and POPC lipids... - on the Peter Tieleman page there is a

Re: [gmx-users] tip3p water in gromacs_4.5.4

2011-12-16 Thread Tomek Wlodarski
Hi Shahid, Use spc216.gro file, it also works for tip3p water model. Best! tomek On Fri, Dec 16, 2011 at 11:26 AM, shahid nayeem msnay...@gmail.com wrote: Dear all I want to use tip3p water model for solvating my protein with genbox command . I couldnt find tip3p.gro file in

[gmx-users] deprotonated Cys in Zn ion binding site

2011-08-03 Thread Tomek Wlodarski
Hi all! I would like to carry out a simulation of protein with Zn ion coordinated by 2 Cys and 2 His in Gromos ff. So I would need a deprotonated Cys however I know that it is present only in Amber ff... Do any of You have some experience with deprotonated Cys in Gromos ff? especially bounded to

Re: [gmx-users] trjconv center on protein

2011-05-08 Thread Tomek Wlodarski
! Best! tomek On Fri, May 6, 2011 at 10:28 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hey :) Option -center shifts the system, which will show up as a component in the displacement. Cheers, Tsjerk On May 6, 2011 5:39 PM, Justin A. Lemkul jalem...@vt.edu wrote: Tomek Wlodarski wrote

Re: [gmx-users] trjconv center on protein

2011-05-06 Thread Tomek Wlodarski
wrote: Tomek Wlodarski wrote: Hi all! I have a trajectory of simulation (protein in box of water) and I would like to have all the time protein in the center of the water box, becasue protein is drifting to the edge during simulation and I am calculating some properties of water arround

[gmx-users] trjconv center on protein

2011-05-05 Thread Tomek Wlodarski
Hi all! I have a trajectory of simulation (protein in box of water) and I would like to have all the time protein in the center of the water box, becasue protein is drifting to the edge during simulation and I am calculating some properties of water arround the protein. I was playing with trjconv