[gmx-users] g_msd problem

2013-05-18 Thread Yutian Yang 
Dear all,

I am using g_msd to calculate diffusion coefficient of the centre of mass of 
single polymer chain with the following command:
g_msd_mpi -f 1.trr -s eqm.tpr -n run.ndx -rmcomm -beginfit 5 -endfit 40

However, it often get killed for number of beads larger than 37, as shown below:

Reading file eqm.tpr, VERSION 4.0.3 (single precision)
Reading file eqm.tpr, VERSION 4.0.3 (single precision)

Select a group to calculate mean squared displacement for:
Group 0 ( System) has 13042 elements
Group 1 (PEO) has37 elements
Group 2 ( WF) has  1301 elements
Group 3 (  W) has 11704 elements
Group 4 (   WF_W) has 13005 elements
Select a group: 1
Selected 1: 'PEO'

Now select a group for center of mass removal:
Group 0 ( System) has 13042 elements
Group 1 (PEO) has37 elements
Group 2 ( WF) has  1301 elements
Group 3 (  W) has 11704 elements
Group 4 (   WF_W) has 13005 elements
Select a group: 1
Selected 1: 'PEO'
trn version: GMX_trn_file (single precision)
Reading frame   24000 time 24.000   Killed.

Is it also a bug in the program or have I done something wrong on the command?

Thank you!

Best Regards
Yutian Yang



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Re: [gmx-users] g_msd problem

2013-05-18 Thread rajat desikan 
I have experienced something similar with large trajectories.

This command got killed by 42 ns, with the same error. It is a 60 ns
trajectory of a large membrane-protein system (approx 45 particles,
Gromos 54A7 ff) with data stored every ps.

g_msd -f analysis_60ns_pbcnojump.xtc -s analysis.tpr -o
msd_popc_overall.xvg -lateral z -n index.ndx


On Sun, May 19, 2013 at 1:57 AM, Yutian Yang yyan...@syr.edu wrote:

 Dear all,

 I am using g_msd to calculate diffusion coefficient of the centre of mass
 of single polymer chain with the following command:
 g_msd_mpi -f 1.trr -s eqm.tpr -n run.ndx -rmcomm -beginfit 5 -endfit
 40

 However, it often get killed for number of beads larger than 37, as shown
 below:

 Reading file eqm.tpr, VERSION 4.0.3 (single precision)
 Reading file eqm.tpr, VERSION 4.0.3 (single precision)

 Select a group to calculate mean squared displacement for:
 Group 0 ( System) has 13042 elements
 Group 1 (PEO) has37 elements
 Group 2 ( WF) has  1301 elements
 Group 3 (  W) has 11704 elements
 Group 4 (   WF_W) has 13005 elements
 Select a group: 1
 Selected 1: 'PEO'

 Now select a group for center of mass removal:
 Group 0 ( System) has 13042 elements
 Group 1 (PEO) has37 elements
 Group 2 ( WF) has  1301 elements
 Group 3 (  W) has 11704 elements
 Group 4 (   WF_W) has 13005 elements
 Select a group: 1
 Selected 1: 'PEO'
 trn version: GMX_trn_file (single precision)
 Reading frame   24000 time 24.000   Killed.

 Is it also a bug in the program or have I done something wrong on the
 command?

 Thank you!

 Best Regards
 Yutian Yang



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-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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Re: [gmx-users] g_msd problem

2013-05-18 Thread Justin Lemkul 



On 5/18/13 4:32 PM, rajat desikan wrote:

I have experienced something similar with large trajectories.

This command got killed by 42 ns, with the same error. It is a 60 ns
trajectory of a large membrane-protein system (approx 45 particles,
Gromos 54A7 ff) with data stored every ps.

g_msd -f analysis_60ns_pbcnojump.xtc -s analysis.tpr -o
msd_popc_overall.xvg -lateral z -n index.ndx




Both issues sound like memory problems.  See 
http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume 
for advice.  If reducing the number of frames allows the program to run 
successfully, you have your answer.


In the OP's case, I would advise upgrading from version 4.0.3, which is ancient. 
 At the very least, try 4.0.7, which is the terminal version in the 4.0.x 
series.  Development is fluid and small bugs get fixed all the time, so using a 
version that is more than 4 years old may be asking for trouble.


-Justin


On Sun, May 19, 2013 at 1:57 AM, Yutian Yang yyan...@syr.edu wrote:


Dear all,

I am using g_msd to calculate diffusion coefficient of the centre of mass
of single polymer chain with the following command:
g_msd_mpi -f 1.trr -s eqm.tpr -n run.ndx -rmcomm -beginfit 5 -endfit
40

However, it often get killed for number of beads larger than 37, as shown
below:

Reading file eqm.tpr, VERSION 4.0.3 (single precision)
Reading file eqm.tpr, VERSION 4.0.3 (single precision)

Select a group to calculate mean squared displacement for:
Group 0 ( System) has 13042 elements
Group 1 (PEO) has37 elements
Group 2 ( WF) has  1301 elements
Group 3 (  W) has 11704 elements
Group 4 (   WF_W) has 13005 elements
Select a group: 1
Selected 1: 'PEO'

Now select a group for center of mass removal:
Group 0 ( System) has 13042 elements
Group 1 (PEO) has37 elements
Group 2 ( WF) has  1301 elements
Group 3 (  W) has 11704 elements
Group 4 (   WF_W) has 13005 elements
Select a group: 1
Selected 1: 'PEO'
trn version: GMX_trn_file (single precision)
Reading frame   24000 time 24.000   Killed.

Is it also a bug in the program or have I done something wrong on the
command?

Thank you!

Best Regards
Yutian Yang



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--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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