[gmx-users] g_chi and J coupling

Hi, I wanted to check how I can calculate J couplings with gromacs. And as a test I have choosen NMR ensemble of ubiquitin from this paper: "Simultaneous determination of protein structure and dynamics" Lindorff-Larsen, Nature2005 I used g_chi: g_chi -f 1XQQ.pdb -s 1XQQ.gro -g And I always end u

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

Hi, Thanks All for help. Now is working! Best! tomek On Tue, Feb 19, 2013 at 2:38 PM, Mark Abraham wrote: > but this I got also with gromacs 4.5.5 which is running ok so I think this > > > is not a problem in my case. > > > > Like Alexey notice the problem is that my nodes have different > >

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

l, 48 bits virtual power management: ts ttp tm stc 100mhzsteps hwpstate Thanks a lot! Best! tomek On Sun, Feb 17, 2013 at 2:37 PM, Alexey Shvetsov wrote: > Hi! > > В письме от 16 февраля 2013 23:27:45 пользователь Tomek Wlodarski написал: > > Hi! > > > > I have

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

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 1

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

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 12:

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

On Sat, Feb 2, 2013 at 10:12 PM, Mark Abraham wrote: > On Sat, Feb 2, 2013 at 8:48 PM, Tomek Wlodarski > wrote: > > > Thanks Szilárd, good idea:) > > I tried to build gromacs and I got errors..: > > > > /tmp/ccBvi1my.s: Assembler messages: > > /tmp/ccB

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

M, Szilárd Páll wrote: > On Sat, Feb 2, 2013 at 2:38 PM, Tomek Wlodarski > wrote: > > > On Sat, Feb 2, 2013 at 12:34 PM, Mark Abraham > >wrote: > > > > > On Sat, Feb 2, 2013 at 1:00 AM, Justin Lemkul wrote: > > > > > > > > >

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

On Sat, Feb 2, 2013 at 12:34 PM, Mark Abraham wrote: > On Sat, Feb 2, 2013 at 1:00 AM, Justin Lemkul 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 for me... > >> > >

Re: [gmx-users] restart REMD

n, 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 < &g

Re: [gmx-users] restart REMD

rstand 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 > >> Hi, >> >> I am running REMD

[gmx-users] restart REMD

Hi, I am running REMD simulation: mdrun_mpi -v -deffnm -s topol_ -multi 72 -replex 1000 I am getting files with name like -s* (for example -s1.trr) How now I could restart this simulation? I know that for regular MD simulation only I need -cpi cpt_file_name --append to add, but what with REMD s

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

better when you also include lower temperature.? best! tomek On Fri, Apr 27, 2012 at 3:40 PM, Mark Abraham wrote: > 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 3

[gmx-users] REMD - low temperature ranges

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

[gmx-users] protein and DMPC in Charmm36 ff

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 p

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

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 wrote: > Dear all > I want to use tip3p water model for solvating my protein with genbox command > . I couldnt find tip3p.gro file in Gromacs/share/top folder . pleas

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

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 Z

Re: [gmx-users] trjconv center on protein

more clear ;) Thanks! Best! tomek On Fri, May 6, 2011 at 10:28 PM, Tsjerk Wassenaar 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. Lem

Re: [gmx-users] trjconv center on protein

n A. Lemkul 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 simu

[gmx-users] trjconv center on protein

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