[gmx-users] Restart REMD

2013-08-16 Thread minwuh081
Hi gmx-users I had an error as followed when I restart my REMD with commands: mpirun mdrun_mpi -multi 96 -deffnm prefix_ -s prefix_.tpr -cpi -noappend -replex 250 in gromacs version 4.5.5 Error: [glenn32-3.int.private:26794] *** An error occurred in MPI_Allreduce [glenn32-3.int

Re: [gmx-users] Restart REMD

2013-08-16 Thread Mark Abraham
Probably the same issue as http://redmine.gromacs.org/issues/1072, which is probably fixed if you update to 4.5.7. Mark On Fri, Aug 16, 2013 at 3:05 PM, Min Wu wrote: > Hi gmx-users > > > > I had an error as followed when I restart my REMD with commands: > > > > mpirun mdrun_mpi -multi 96 -deffn

[gmx-users] Restart REMD

2013-08-16 Thread Min Wu
Hi gmx-users I had an error as followed when I restart my REMD with commands: mpirun mdrun_mpi -multi 96 -deffnm prefix_ -s prefix_.tpr -cpi -noappend -replex 250 in gromacs version 4.5.5 Error: [glenn32-3.int.private:26794] *** An error occurred in MPI_Allreduce [glenn32-3.int.private:26

Re: [gmx-users] restart REMD

2012-05-22 Thread Mark Abraham
On 23/05/2012 1:24 AM, Tomek Wlodarski wrote: Hi, -s before -deffnm works, now after starting once more REMD from the scratch I can do restart. I use mpirun mdrun_mpi -multi $nrepls -deffnm ${name}_sim $npme -cpi ${name}_sim -append and it Just Works with 4.5.5. Mark Thanks. Best tome

Re: [gmx-users] restart REMD

2012-05-22 Thread Tomek Wlodarski
Hi, -s before -deffnm works, now after starting once more REMD from the scratch I can do restart. Thanks. Best tomek On Mon, May 21, 2012 at 2:39 AM, mu xiaojia wrote: > try put -s before -deffnm > mdrun_mpi -s -deffnm file_name -multi 120 -replex 250 -cpi -append > > > On Sun, May 20, 2012

Re: [gmx-users] restart REMD

2012-05-20 Thread mu xiaojia
try put -s before -deffnm mdrun_mpi -s -deffnm file_name -multi 120 -replex 250 -cpi -append On Sun, May 20, 2012 at 4:50 PM, Tomek Wlodarski 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

Re: [gmx-users] restart REMD

2012-05-20 Thread Tomek Wlodarski
Hi Francesco, Thanks! However, it does not work with my case.. tomek On Sun, May 20, 2012 at 1:47 PM, francesco oteri wrote: > Hi, > usually I use something like: > > mdrun_mpi -v -deffnm topol_ -multi 72 -replex 1000 *-cpt* > * > * > gromacs is smart enough to understand that it has to load

Re: [gmx-users] restart REMD

2012-05-20 Thread francesco oteri
Hi, usually I use something like: mdrun_mpi -v -deffnm topol_ -multi 72 -replex 1000 *-cpt* * * gromacs is smart enough to understand 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

[gmx-users] restart REMD

2012-05-20 Thread Tomek Wlodarski
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