[gmx-users] MD simulation using TFE

Bikash Ranjan Sahoo bikash.bioinformatics at gmail.com
Tue Aug 11 04:25:42 CEST 2015

Dear All,

I want to simulate my protein in 85 and 15 % water and TFE, respectively.

Kindly guide me how to setup this system for a successful MD run.

I have used the following commands.

pdb2gmx_d -f test.pdb -o 1st.pdb -water spc -ignh -missing

editconf_d -f 1st.pdb -o 2nd.pdb -bt cubic -c -d 0.9

genbox_d -cp 2nd.pdb -cs spc216.gro -ci tfe.gro -nmol 2000 -o 3rd_b4ion.pdb
-p topol.top

grompp_d -f em.mdp -c 3rd_b4ion.pdb -p topol.top -o ion.tpr
genion_d -s ion.tpr -o 3rd_b4ion.pdb -neutral -conc 0.10 -p topol.top -g

grompp_d -f em.mdp -c 3rd_b4ion.pdb -p topol.top -o em.tpr
mdrun_d  -v -s em.tpr -o em.trr -c em.gro -g em.log -e em.edr -nt 20

The system minimization is not converged (emtol=1000). I tried to minimize
further by decreasing the emtol=100 followed by NVT run.

The NVT run is giving too many LINCS warnings followed by fatal error.

Please help me in this regard for which I shall remain ever grateful to you.

Thanking you in anticipation of a positive response
Yours sincerely

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