[gmx-users] Grompp error

[Justin Lemkul]

On 5/30/16 10:55 AM, Anurag Dobhal wrote:
> Thanks a lot for your reply.
>
> I have set tc-groups as
>
>
> tc-grps = Other   acetone ; two coupling groups - more accurate
> tau_t = 0.1  0.1           ; time constant, in ps
> ref_t = 300  300           ; reference temperature, one for each
>
>

Then you can't rely on such groups to be correct.  Other and acetone overlap. 
Define appropriate groups.

-Justin

>
>
> *Anurag Dobhal*
> *Graduate Student (Bioprocess Technology)*
> *Institute of Chemical Technology, Mumbai*
> *Contact: +91 8898486877*
>
>
> On Mon, May 30, 2016 at 8:18 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 5/30/16 10:40 AM, Anurag Dobhal wrote:
>>
>>> Dear Gromacs users
>>>
>>> I am solvating my molecule ( a ploymer chain, having 78 atoms) in
>>> Propan-2-one
>>> [ molecules] = acetone. I have already updated  [ molecules ] section in
>>> the topology file (topol.top) after the solvation step.
>>>
>>> after the sucessful energy minimization step, while runing grompp I am
>>> geting an error,
>>>
>>> " Excluding 3 bonded neighbours molecule type 'Other'
>>> turning all bonds into constraints...
>>> Excluding 3 bonded neighbours molecule type 'acetone'
>>> turning all bonds into constraints...
>>> Setting gen_seed to 3080450167
>>> Velocities were taken from a Maxwell distribution at 300 K
>>> Removing all charge groups because cutoff-scheme=Verlet
>>>
>>> Fatal error:
>>> Atom 79 in multiple T-Coupling groups (1 and 2) "
>>>
>>> The error means that T-coupling is treating both the polymer (other) and
>>> solvent (acetone) as other molecules.
>>> How can I rectify the error ?
>>>
>>>
>> You haven't shown us what you've set as tc-grps but there is clearly
>> redundancy between whatever those groups are.  If you have multiple groups,
>> you need to ensure that they are defined correctly, using index groups as
>> needed.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> 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
>>
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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

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