Handling PBC for Free energy calculations in plumed patched Gromacs

[Abhinandan Panigrahi]

Dear all,

I am trying to study free energy profiles for base flipping in a DNA+Protein system via

umbrella sampling calculations on Gromacs 2016.3 patched with PLUMED 2.4.1. 

On visualizing the GRO file which comes after equilibriation (and which is used to make

the initial TPR that each window uses), I saw that part of the DNA molecule has moved out

of the PBC box. The atoms in the DNA concerning my collective variable are also coming out

of the PBC box (my system is huge, and the water box is not too big) (PFA the screenshot).

Simulations run using TPR generated from this GRO file have resulted in profiles that are

most likely, incorrect (scatter data from production runs is far from the minima obtained

in the PMF).

Q1) To make sure that the PLUMED calculations start with the entire system inside the PBC

box, should I apply the trjconv command to the equilibriation GRO file, and use `-pbc mol`

and `-pbc nojump` in succession to bring the part of the DNA that went outside the box

back inside it. This file will then be used to generate the initial tpr.

Q2) In the PLUMED config file where I apply my restraints, I use the command

`WHOLEMOLECULE ENTITY0:<range of all dna+protein atoms>`, which as per my understanding,

handles PBC for PLUMED calculations of the CVs. Does this conflict with the PBC treatment

that GROMACS uses? 

My CVs are angular in nature (bias applied over 2 dihedrals). The protocol for umbrella

sampling was as follows:

- equilibriate system well (total 5ns of nvt + npt runs)

- use the gro file generated above to make initial tpr, which is used by each umbrella

sampling window

- restraints/bias is defined in plumed data files passed to mdrun with -plumed flag

- run wham on plumed generated colvars to build pmf

[Giovanni Bussi]

Hi,

Q1: fixing the coordinates with trjconv is not necessary and probably useless. What matters are the coordinates stored during the simulation inside gromacs.

Q2: it does not interfere. However, it is usually not necessary to put all atoms in the WHOLEMOLECULES command. Always check the result using DUMPATOMS

Finally, if you use *real* torsions (not pseudotorsions) it is not even necessary that the molecule is whole for PLUMED to compute the angle correctly. TORSION by defaults uses PBCs to compute interatomic distances

Giovanni

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