On 5/3/17 8:04 AM, B Prakash wrote:
On Wed, May 3, 2017 at 5:22 PM, Mark Abraham <[email protected]>
wrote:
Hi,
The number inserted depend on clashes with the input coordinates, so if you
change those, don't be surprised if the output changes :-)
Hi Mark,
surprisingly, there were no changes in neither the pdb file nor the input
commands. However genbox accomodated 13 more methanol molecules in the same
space. The only reason for it I could imagine is minor changes in protein
orientation.
If there are "minor changes in protein orientation" then you cannot say there
are no changes in the PDB file. If the coordinates are in any way different,
then the overlap with the solvent will be different and you will get a different
outcome, as Mark has said. Do a diff on the input coordinate files to make sure
you're doing what you think you are doing.
-Justin
Mark
On Wed, 3 May 2017 13:29 B Prakash <[email protected]> wrote:
On Wed, May 3, 2017 at 3:53 PM, Mark Abraham <[email protected]>
wrote:
Hi,
On Wed, May 3, 2017 at 11:24 AM B Prakash <[email protected]> wrote:
Dear all,
am trying to do a simulation of a protein in methanol. Am using
gromacs
4.6.1.
Do yourself a favour and for new work, install a version that isn't
four
years old, has extra bugs for free, and is unsupported ;-)
Dear Mark,
thank you. I will do so. However, I was curious about the difference in
the
number of methanol molecules added when all other parameters are same.
Am using the methanol box supplied in gromacs. In some of the
simulations, the box took nearly 10K (10040) methanol molecules. But
in
others the number varied a little (10053). In editconf command, I
tried
to
center the protein in the simulation box. Is the variation in
methanol
molecules due to minor changes in orientation of protein by editconf
and
genbox. Please correct.
Yes. There's an option to choose the maximum number of molecules added,
if
you want a little more control.
Mark
Regards,
Prakash.
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==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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