Re: [gmx-users] mpi segmentation error in continuation of REMD simulation with gromacs 4.5.5

in the latest > releases. > > Mark > > > Hi, I installed different versions of gromacs with the same MPI library. Surprisingly, the problem doesn't occur in gromacs-4.5.1.. but still in the gromacs-4.6.3... The MPI version is MVAPICH2-1.9a for infinite band. Best, Qin

[gmx-users] mpi segmentation error in continuation of REMD simulation with gromacs 4.5.5

Dear all, I'm trying to continue a REMD simulation using gromacs4.5.5 under NPT ensemble, and I got the following errors when I tried to use 2 cores per replica: "[node-ib-4.local:mpi_rank_25][error_sighandler] Caught error: Segmentation fault (signal 11) [node-ib-13.local:mpi_rank_63][error_sigh

Re: [gmx-users] Error in Installing gromacs4.6.3 with mpi

On Wed, Sep 11, 2013 at 3:08 PM, Mark Abraham wrote: > No idea if it's causing your problem, but you need all the Ds in > -DBUILD_SHARED_LIBS=no > > Mark > > On Wed, Sep 11, 2013 at 6:15 AM, Qin Qiao wrote: > > Dear all, > > > > I'm trying to inst

[gmx-users] Error in Installing gromacs4.6.3 with mpi

Dear all, I'm trying to install gromacs4.6.3 with mvapich2-1.9a on a local cluster and got the following error in step 'make': "/usr/bin/ld: /usr/local/mvapich2-1.9a-gcc/lib/libmpich.a(mvapich_malloc.o): relocation R_X86_64_32 against `.bss' can not be used when making a shared object; recompile

[gmx-users] Re: Install gromacs4.6.3 with mpi

On Sat, Sep 7, 2013 at 4:55 PM, Qin Qiao wrote: > Dear all, > > I'm trying to install gromacs4.6.3 with mvapich2-1.9a on a local cluster > and got the following error in step 'make': > > "/usr/bin/ld: > /usr/local/mvapich2-1.9a-gcc/lib/libmpich.a(mv

[gmx-users] Install gromacs4.6.3 with mpi

Dear all, I'm trying to install gromacs4.6.3 with mvapich2-1.9a on a local cluster and got the following error in step 'make': "/usr/bin/ld: /usr/local/mvapich2-1.9a-gcc/lib/libmpich.a(mvapich_malloc.o): relocation R_X86_64_32 against `.bss' can not be used when making a shared object; recompile

[gmx-users] error while loading shared libraries: libgmx.so.6

Dear all, I'm using a c++ code to handle the xtc file with 'xtcio.h', but get the error when executing it. the command I use: g++ test.cpp -o test -I/usr/local/gromacs/include/gromacs -L/usr/local/gromacs/lib -lgmx ./test Error: ./test: error while loading shared libraries: libgmx.so.6

Re: [gmx-users] How to install a new Forcefield in Gromacs 4.5.3

2011/1/21 Justin A. Lemkul > > > Qin Qiao wrote: > >> >> >> 2011/1/21 Justin A. Lemkul mailto:jalem...@vt.edu>> >> >> >> >> >>Qin Qiao wrote: >> >> >> >>2011/1/20 Justin A. Lemkul &

Re: [gmx-users] How to install a new Forcefield in Gromacs 4.5.3

2011/1/21 Justin A. Lemkul > > > Qin Qiao wrote: > >> >> >> 2011/1/20 Justin A. Lemkul mailto:jalem...@vt.edu>> >> >> >> >>Qin Qiao wrote: >> >> >> >>2011/1/20 Justin A. Lemkul >

Re: [gmx-users] How to install a new Forcefield in Gromacs 4.5.3

2011/1/20 Justin A. Lemkul > > > Qin Qiao wrote: > >> >> >> 2011/1/20 Justin A. Lemkul mailto:jalem...@vt.edu>> >> >> >> >>Qin Qiao wrote: >> >> >> >>2011/1/20 Justin A. Lemkul >

Re: [gmx-users] How to install a new Forcefield in Gromacs 4.5.3

2011/1/20 Justin A. Lemkul > > > Qin Qiao wrote: > >> >> >> 2011/1/20 Justin A. Lemkul mailto:jalem...@vt.edu>> >> >> >> >> >>Qin Qiao wrote: >> >>Dear all, >> >>I would like to try a n

Re: [gmx-users] How to install a new Forcefield in Gromacs 4.5.3

2011/1/20 Justin A. Lemkul > > > Qin Qiao wrote: > >> Dear all, >> >> I would like to try a new forcefield in Gromacs 4.5.3. What should I do >> after I copied the ff to /share/gromacs/top directory? It seems the original >> FF.dat doesn'

[gmx-users] How to install a new Forcefield in Gromacs 4.5.3

Dear all, I would like to try a new forcefield in Gromacs 4.5.3. What should I do after I copied the ff to /share/gromacs/top directory? It seems the original FF.dat doesn't exist in 4.5.3.. Could you give me some help? Best, Qin -- gmx-users mailing listgmx-users@gromacs.org http://lists.g

Re: [gmx-users] To make continuous trj in REMD

2011/1/7 Justin A. Lemkul > > > Qin Qiao wrote: >> >> >> 2011/1/7 Justin A. Lemkul mailto:jalem...@vt.edu>> >> >> >> >>    Qin Qiao wrote: >> >> >> >>        2011/1/7 Justin A. Lemkul >      

Re: [gmx-users] Nose-hoover T-coupling in REMD

2010/12/26 ms > On 25/12/10 02:12, Qin Qiao wrote: >>> >>> Thanks a lot! >>>> >>>> It says Nose-hoover coupling generates the correct canonical ensemble, >>>> and >>>> that's the reason why I used it. I wonder whethe

Re: [gmx-users] To make continuous trj in REMD

2011/1/7 Justin A. Lemkul > > > Qin Qiao wrote: > >> >> >> 2011/1/7 Justin A. Lemkul mailto:jalem...@vt.edu>> >> >> >> >> >>Qin Qiao wrote: >> >>Dear all, >> >>I came across a probl

Re: [gmx-users] To make continuous trj in REMD

2011/1/7 Justin A. Lemkul > > > Qin Qiao wrote: > >> Dear all, >> >> I came across a problem when I want to make the REMD trajectories >> continuous. >> >> What I did: >> >> 1. 'demux.pl <http://demux.pl> REMD_0.log'

[gmx-users] To make continuous trj in REMD

Dear all, I came across a problem when I want to make the REMD trajectories continuous. What I did: 1. 'demux.pl REMD_0.log' --to get the 'replica_index.xvg' 2. 'trjcat -f ../REMD_*.xtc -o resort.xtc -demux ../replica_index.xvg' It seems smooth. But when I check the rmsd of the output

Re: [gmx-users] Nose-hoover T-coupling in REMD

I'm not sure, since actually kinetic energy should have fluctuation, and the v-rescaling may suppress the fluctuation.. 2010/12/25 ms > On 25/12/10 02:12, Qin Qiao wrote: > >> Thanks a lot! >> >> It says Nose-hoover coupling generates the correct canonical ensemble,

Re: [gmx-users] Nose-hoover T-coupling in REMD

Thanks a lot! It says Nose-hoover coupling generates the correct canonical ensemble, and that's the reason why I used it. I wonder whether v-rescale can also get the correct ensemble. Could you tell me? I'm quite curious how to choose the frequency of the T-coupling in REMD. Though it seems the h

[gmx-users] Nose-hoover T-coupling in REMD

uld you tell me? Thanks a lot. Best, Qin 2010/12/21 Qin Qiao > Dear all, > > I wonder what will happen in Nose-hoover coupling when tau_t = dt * > nsttcouple, while nsttcouple = nstlist. (I used -maxwarn 1 to ignore the > Gromacs warning) > > I tried this setting, to find the

[gmx-users] Nose-hoover T-coupling nsttcouple

Dear all, I wonder what will happen in Nose-hoover coupling when tau_t = dt * nsttcouple, while nsttcouple = nstlist. (I used -maxwarn 1 to ignore the Gromacs warning) I tried this setting, to find the temperature is OK, but I am not sure whether it will introduce some artifacts in the simulation

Re: [gmx-users] Question about Extention simulation in REMD

Thanks! It really is. For the input cpt may have been overwritten before, when I put it in mdrun again.. 2010/12/17 Mark Abraham > > > On 12/17/10, *Qin Qiao * wrote: > > Thanks! > > But still sth strange: I found the total energy is not identical between > the last fr

Re: [gmx-users] Question about Extention simulation in REMD

whether there's some problem and what caused it.. My setting In the .mdp of the previous simulation, gen_vel was on; I didn't record the velocity by putting nstvout =0; I used xtcgrp = Protein. Best Qin 2010/12/15 Justin A. Lemkul > > > Qin Qiao wrote: > >> Dear Sir

[gmx-users] Question about Extention simulation in REMD

Dear Sir or Madam, I wonder how to continue a REMD running using .cpt file in Gromacs 4.5.1. Since I ran a REMD of 56 replicas, there are one cpt file for each replica.. I couldn't do it by tpbconv -s previous.tpr -extend timetoextendby -o next.tpr mdrun -s next.tpr -cpi previous.cpt I guess it