[gmx-users] Grompp error

[Anurag Dobhal]

Thanks a lot for your insight.

I will redefine them.




*Anurag Dobhal*
*Graduate Student (Bioprocess Technology)*
*Institute of Chemical Technology, Mumbai*
*Contact: +91 8898486877*


On Mon, May 30, 2016 at 8:26 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
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