Re: [gmx-users] concatenating 2 xtc files

2013-08-02 Thread Kavyashree M
Sir, But if something went wrong, then "over" is rather irrelevant, isn't it? Yes. I am planning to rerun ifI dont get any solution. > So your simulation started from some previous point and re-ran? I don't > see how this would be possible given what you have been posting. The overlap was

Re: [gmx-users] concatenating 2 xtc files

2013-08-01 Thread Justin Lemkul
On 8/1/13 11:44 AM, Kavyashree M wrote: Sir, Thank you for the suggestion.. I will make use of it in future runs. but now the simulation is over. But if something went wrong, then "over" is rather irrelevant, isn't it? There was some overlap of few ns in 8core machine. so while checking t

Re: [gmx-users] concatenating 2 xtc files

2013-08-01 Thread Kavyashree M
Sir, Thank you for the suggestion.. I will make use of it in future runs. but now the simulation is over. There was some overlap of few ns in 8core machine. so while checking the rmsd plot there was a significant difference in rmsd between 8 core and 64 core overlapped region of simulation. 1 mo

Re: [gmx-users] concatenating 2 xtc files

2013-08-01 Thread Justin Lemkul
On 8/1/13 3:42 AM, Kavyashree M wrote: Dear Sir, First trajectory - traj1.xtc (0 to 5... ns) Second trajectory - traj2.xtc (5... to 25ns) But there is no gap in between. for concatenating - $ trjcat -f traj1.xtc traj2.xtc -o trajf.xtc For nujump - $ trjconv -f trajf.xtc -s md.tpr -pbc nojum

Re: [gmx-users] concatenating 2 xtc files

2013-08-01 Thread Kavyashree M
Dear Sir, First trajectory - traj1.xtc (0 to 5... ns) Second trajectory - traj2.xtc (5... to 25ns) But there is no gap in between. for concatenating - $ trjcat -f traj1.xtc traj2.xtc -o trajf.xtc For nujump - $ trjconv -f trajf.xtc -s md.tpr -pbc nojump -o trajf.xtc I also have a case where I

Re: [gmx-users] concatenating 2 xtc files

2013-07-31 Thread Tsjerk Wassenaar
Hi Kavya, That shouldn be a problem. Please post your sequence of commands for concatenating and further processing of the trajectory. Cheers, Tsjerk On Thu, Aug 1, 2013 at 8:12 AM, Kavyashree M wrote: > Dear users, > > I ran a simulation for 25ns. First 5ns in 8 core machine > and late part

[gmx-users] concatenating 2 xtc files

2013-07-31 Thread Kavyashree M
Dear users, I ran a simulation for 25ns. First 5ns in 8 core machine and late part in 64 cores. It ran without any problem. The trajectories were concatenated, jumps are removed and rmsd was calculated. But there was sudden jump in the rmsd curve. Is it wrong to run simulations in different cores