[gmx-users] MD simulation using TFE

[Justin Lemkul]

On 8/13/15 7:51 AM, Bikash Ranjan Sahoo wrote:
> Dear Dr. Mark,
>
> Thank you so much for your kind reply.
>
> As suggested, I tried to simulate a simple Water+TFE system (without
> protein). The commands used are given below.
>
> editconf_d -f tfe.gro -o 1.gro -bt cubic  -d 5.5
>
> genbox_d -cp 1.gro -cs spc216.gro -ci tfe.gro -nmol 200 -p topol.top -o
> 2.gro
>

Don't try to simultaneously add a box of solvent and do random insertions of 
molecules.  This is one of the reasons that genbox was split into two different 
programs in recent versions; people make this mistake too often.

> grompp_d -f em.mdp -c 2.gro -p topol.top -o em.tpr -maxwarn 3
>

Any reason you're using -maxwarn?  It's very bad practice and usually  not 
(read: almost never) appropriate.

> mdrun_d -v -s em.tpr -c em.gro -nt 20
>
> (Converged to machine precision, but not to the requested precision Fmax <
> 1000)
>
>
> grompp_d -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -maxwarn 2
>
> mdrun_d -v -s nvt.tpr -c nvt.gro -nt 20
>
> Too many LINCS, ERROR.
>
>
> I am facing the same problem. I have checked the output files.
>
> The 2.gro file showing symmetric distribution of TFE in water. But, after
> EM, all TFE molecules are aggregating and migrating to the box edge.
>

EM should not allow for large-scale changes, so something doesn't add up here.

> Kindly suggest how to get rid of such problems.
>
> I have attached the tfe.gro and tfe.itp file that I have used to generate
> the initial system.
>

The list doesn't accept attachments, nor would these files be of any use.

-Justin

>
> Thanking you and in anticipation of your reply
> Yours sincerely
> Bikash
>
>
>
>
>
> On Tue, Aug 11, 2015 at 4:28 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> 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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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================