[gmx-users] MD simulation using TFE

Bikash Ranjan Sahoo bikash.bioinformatics at gmail.com
Thu Aug 13 16:05:49 CEST 2015


Dear Dr. Justin,

Thank you so much for your time and kind reply.

I have used maxwarn as there is fatal error due to large rlist.
*The sum of the two largest charge group radii (23.903836) is larger than*
*  rlist (1.000000)*

I do not exactly understand this point.
*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.*

Kindly guide me how to generate the initial box.

Please help in finding the exact command in genbox to create the initial
Water+TFE complex (will be grateful to you if you will write the command
here)


Thanking you in anticipation
Yours sincerely
Bikash



On Thu, Aug 13, 2015 at 8:59 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>> posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>>>
>>>
>>>
> --
> ==================================================
>
> 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
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>


More information about the gromacs.org_gmx-users mailing list