[gmx-users] MD simulation using TFE

[Mark Abraham]

On Tue, Aug 11, 2015 at 4:26 AM Bikash Ranjan Sahoo <
bikash.bioinformatics at gmail.com> wrote:

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

Start simpler. Make sure you can simulate pure water, and water-TFE mixture
first. One of your problems right now is that you don't know where your
problem is...


> 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
>

Please read the pdb2gmx -h documentation for -missing and reconsider why
you are using it.

Mark

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
> ion.log
>
> 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
> Bikash
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