[gmx-users] Distorted protein structure after MD simulation

prajwal nandekar prajwal.pharm07 at gmail.com
Wed Mar 31 10:09:45 CEST 2010

Dear Sonali,
The problem may happen with you, because you had not given the proper
pressure constraint to protein while running MD simulations. Please again
check your Parameter file once.

On Wed, Mar 31, 2010 at 1:24 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> On 31/03/2010 5:48 PM, sonali dhindwal wrote:
>> Hello All,
>> I have done one MD similation for 1 ns for my protein, having two
>> ligands and one metal ion with GROMOS96 43a1 force field and
>> dodecahedron box as tge unit cell.
>> After simulation when i checked RMSD, it is increasing till 1ns and
>> observing the .gro file in VMD, I have seen that, my protein structre is
>> very much distorted, intialy it had tim barell topolgy with 8 beeta
>> sheets and 8 alpha sheets,,now only 7 sheets are remaing,one became
>> coiled strucutre. What could b the possible reason ?
> There are many possible reasons, chief among them an inappropriate model
> physics. With no idea what your metal ion is, how you've built your topology
> and what ensemble you've used, we can't have any better ideas for you. :-)
> Mark
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Prajwal Nandekar
M.S.(Pharm) Pharmacoinformatics
Department of Pharmacoinformatics
NIPER Mohali
Mob. 09780741228
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