Thank you Justine
I have another question. I run my simulation for 5ns and when i just
check the density of my solvent, the density did not look right. I
used the N-H and P-R for the thermostat and barostat. Both shows the
correct temperature and pressure (300K and 1bar). when I use the
g_density to check only the density of my solvent (in this case
Toluene), it shows 0.933g/ml, but the actual density according to
literature is 0.866g/ml. I have no idea what the problem is.
Can you please give me some suggestions.
Robel
Quoting "Justin A. Lemkul" <[email protected]>:
[email protected] wrote:
Dear Gromacs users,
I am using gromacs 3.3.3 for my simulation.
I run my project for 5ns and want to extend to 10 ns. Can any body
tell me if this is the right way to do.
tpbconv -s previous.tpr -f previous.trr -e previous.edr -o next.tpr
-extend timetoextend
Being that you've copied the entry from here:
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
...I would guess that it's correct :)
The previous.tpr means for the 5ns MD run.
The next.tpr is for the 10ns.
what does the -extend means?
Per tpbconv -h:
"Extend runtime by this amount (ps)"
-Justin
what does timetoextend means ( in my case is timetoextend is 5ns)
Please give me some suggestions.
Rob
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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