Re: [gmx-users] crashed run...

2012-02-29 Thread Mark Abraham
On 1/03/2012 5:30 PM, rama david wrote: Hi GROMACS specialist, My MD run get crashed because of less memory. I given the command mdrun -s -f -e -o -g -cpi -append -v Now is my system is started from the initial time or from the time

[gmx-users] crashed run...

2012-02-29 Thread rama david
Hi GROMACS specialist, My MD run get crashed because of less memory. I given the command mdrun -s -f -e -o -g -cpi -append -v Now is my system is started from the initial time or from the time of crash?? What is the process for to start

Re: [gmx-users] crashed run

2010-12-09 Thread Justin A. Lemkul
shiva birgani wrote: Dear friends Thanks for help I did what you said. but now I have another question. why when I compute RMSD, there is a turbulence in the digits between two MD runs (MD1 & MD2)? Along 10nS RMSD values increase but after that in continued MD RMSD values start with lower d

[gmx-users] crashed run

2010-12-09 Thread shiva birgani
Dear friends Thanks for help I did what you said. but now I have another question. why when I compute RMSD, there is a turbulence in the digits between two MD runs (MD1 & MD2)? Along 10nS RMSD values increase but after that in continued MD RMSD values start with lower digits. So the obtained RMSD

RE: [gmx-users] Crashed run

2010-12-05 Thread Mark Abraham
d, or  circumvent the problem with appropriate use of mdrun -append Mark > > > > > > > > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf > Of shiva birgani [sh.birg...@gmail.com] > > Sent: Monday, December 06, 2010 3:16 PM > > To: gmx-users &

RE: [gmx-users] Crashed run

2010-12-05 Thread Shi Wenxiong (Dr)
PM To: gmx-users Subject: [gmx-users] Crashed run Dear Justin I had a crashed run and continued it by tpbconv and mdrun. After that in order to analysis the results of new MD run I used of this command trjcat -s md2.tpr -settime But when I want to compute RMSD, DSSP, ... I do not know how I can pu

[gmx-users] Crashed run

2010-12-05 Thread shiva birgani
Dear Justin I had a crashed run and continued it by tpbconv and mdrun. After that in order to analysis the results of new MD run I used of this command trjcat -s md2.tpr -settime But when I want to compute RMSD, DSSP, ... I do not know how I can put together the results of MD1 (crashed run) and MD2