Question: The System Is Not Getting Well Minimized - Gromacs
1
gravatar for Lavanya
6.8 years ago by
Lavanya10
Lavanya10 wrote:

I am trying to simulate a membrane protein in GROMACS. But the system is not getting well minimised. Only if system gets minimized I can do the equilibration step. can anyone help with suggestion?

simulation protein • 2.2k views
ADD COMMENTlink modified 6.8 years ago by Keith Callenberg880 • written 6.8 years ago by Lavanya10
1

Hello lavanya, can you please explain your question better? How do you know that the system is not getting well minimized? Which solutions have you tried so far?

ADD REPLYlink written 6.8 years ago by Giovanni M Dall'Olio26k
2
gravatar for dimkal
6.8 years ago by
dimkal730
United States
dimkal730 wrote:

Probably there's a stearic clash or some other overlap between a protein and the membrane that the minimizer cannot resolve or untangle.

Try Desmond to run your your membrane-bound protein MD. They have an automatic membrane-specific system builder facility, so getting a simulation going, including minimization and lipid equilibration, is really easy.

ADD COMMENTlink modified 6.8 years ago • written 6.8 years ago by dimkal730
2

I strongly disagree. The solution doesn't pass through "try different software". If the system is not getting minimized, for whatever reason, the researcher should stop and think about the why. Therefore, a better explanation is required for good suggestions.

ADD REPLYlink written 6.8 years ago by João Rodrigues2.4k

Agreed. however my suggestion merely reflects the user's knowledge about setting up a membrane systems... based on how the question was asked -- clearly not much. I think there's a benefit for this particular user to skip the details of setting up simulations and just focus on simulation themselves.

ADD REPLYlink written 6.8 years ago by dimkal730

I completely understood why you mentioned this, and I agree as well that the question is badly formulated, but if you don't know what you are doing, you shouldn't be doing MD in the first place. Not focusing on the setup is a gross mistake since the setup is what determines what your simulation is going to be.

ADD REPLYlink written 6.8 years ago by João Rodrigues2.4k
1
gravatar for Keith Callenberg
6.8 years ago by
Pittsburgh, PA
Keith Callenberg880 wrote:

Membrane protein insertion can be very tricky. I would suggest following a tutorial like this one for system setup with a membrane protein. The g_membed tool might also be helpful.

ADD COMMENTlink written 6.8 years ago by Keith Callenberg880
0
gravatar for Ataly
6.8 years ago by
Ataly20
Ataly20 wrote:

Their ca be many reasons. those mentioned above are first to be looked at. adjusting the lipids is always tricky. you should have a look at your starting structure. if nothing is obvious consider also that membrane systems are usualy large and may simply need more time to get minimized.

ADD COMMENTlink written 6.8 years ago by Ataly20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1146 users visited in the last hour