[gmx-users] How to construct mixed lipid bilayer

2013-11-13 Thread Nikhil Agrawal 
Dear All,

can anyone tell me how to construct mixed lipid bilayer in gromacs

id possible also provide me the command to construct the mixed bilayer


Thanks in advance

Nikhil
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[gmx-users] Unstable System

2013-10-10 Thread Nikhil Agrawal 
DearAll,

when I am running NVT equilibration phase i am getting following error

Back Off! I just backed up step0c.pdb to ./#step0c.pdb.4#
Wrote pdb files with previous and current coordinates
starting mdrun 'Gromacs Runs On Most of All Computer Systems in water'
25 steps,500.0 ps.

WARNING: Listed nonbonded interaction between particles 6483 and 6507
at distance 3f which is larger than the table limit 3f nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.

if any one have solution for that. please let me know

Thanks in advance.

Best,
Nikhil


-- 
Nikhil Agrawal
Project Fellow
Institute of Genomic  Integrative Biology (IGIB)
Mathura Road
New Delhi 110020
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[gmx-users] Membrane Curvature calaculation

2013-07-31 Thread Nikhil Agrawal 
Dear All,

How to calculate membrane curvature with function of time in gromacs? what
are the parameters that define curvature?
mean angle and distance and all ? can anybody help me to solve this problem
, because I am new to gromacs..:)

Thanks in advance,

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