[gmx-users] simulating Cellulose using GAFF force field

Vitaly V. Chaban vvchaban at gmail.com
Mon Sep 21 18:06:44 CEST 2015

Plot all energy components vs. time.

Normally, the probem is within dihedrals, e.g. not all of them defined.

On Mon, Sep 21, 2015 at 11:17 AM, Fahimeh <fahimeh.baftizadeh at gmail.com>

> Hi gromacs users,
> I am trying to melt a crystalline structure of cellulose. This structure
> contains 8mers and monomers of cellulose molecules. To start the
> simulation, I computed the resp charges of 8mers and monomers of Cellulose
> and I am using GAFF force field for simulating this structure. To test
> wether the force field is correct … I performed a simulation using only one
> 8mer molecule and I it doing well. I can bring the temperature up to 300k
> and at that point the cellulose molecule is folded and seems nothing is
> wrong … however when I start to run the simulation for the crystalline
> Cellulose the problem starts.
> First I minimized the system using steepest decent and then I perform NVT
> at low T(10k) which is followed by NPT simulation to warm the system from
> 10k to 298k. I increase the temperature every 1000ps by 10 degree which is
> very slow based on my experience … But the system explode every time the
> temperature reaches above 150 or 200k. Using dt=0.001fs and different types
> of barostate doesn’t help as well.
> I thought the problem might be the starting configuration. Therefore I
> used the relaxed 8mer that I initially simulated … and I used packmol
> program to put almost 50 of 8mers in a box based on the experimental
> density that I had. Packmol successfully pack the relaxed 8mers in the box
> and then I repeat all the steps that I explained above… but exactly the
> same problem happens.
> At this point I am not sure where the problem can be:
> 1- If the problem is force filed … .then how comes that I can run the
> simulation of one 8mer molecule without any problem
> 2- If the problem is starting configuration, then how comes that even
> using other techniques such as packing the relaxed molecules in a box …
> does not help
> It would be great to hear your ideas
> Thanks
> Fahimeh
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