On 6/11/13 1:25 PM, Neha wrote:
Hi everybody,
Thank you so much for taking the time to read this.
I thought ref_p would need to be 0.0 and 0.0 if I wanted zero surface
tension. How else could I get a tensionless membrane?
As far as I understand, surface tension is only applied when using "pcoupl =
surface-tension" and then ref_p specifies the value of surface tension in
bar-nm. Normally, ref_p specifies the reference pressure for an NPT ensemble.
As for the generating velocities, I completely forgot that would ruin the
equilibrium. Would you recommend saying gen_vel = no or simply raising the
gen_temp closer to the required value? If the second how close do you think
I should keep it? Sorry for bombarding you guys with so many questions!
gen_temp is irrelevant when gen_vel is set to "no."
Also no one has commented on this so I'm guessing using the structure file
from the Berendsen run is an okay way to do what I want?
The configuration alone is insufficient. You should preserve the previous
ensemble by passing the final .cpt file to grompp -t.
-Justin
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
