On 5/17/13 10:08 PM, Shima Arasteh wrote:
Hi,
I am simulating a system composed if POPC , peptide, waters and ions.
I used the InflateGRO methodology to construct the system.
There
are 2 Tryptophan residues in my peptide. Each Tryptophan has 2rings
connected from one side. After inflategro one of the Tryptophan rings is
normal, but the other is not because What I see them in vmd, there are
2rings remain close to eachother but the expected bonds between them are
not visible.
The top file shows the correct bonds and angles and ... .
I ran EM, NVT, NPT, and thought this problem would be solved but it is still as
well as before.
The EM was also ok and did not show high enegy or crash.
Does this problem relate to the vmd and its algorithms? Or there is a problem
with my system.
http://www.gromacs.org/Downloads/Related_Software/Visualization_Software#Topology_bonds_vs_Rendered_bonds
The topology is definitive. VMD is not.
How would the rings look usual? How could I solve it?
Run EM. InflateGRO should not have messed with the coordinates though. If the
bad geometry is a result of EM, that means you have really nasty forces
somewhere in the system.
-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 [email protected]
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 [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
