[gmx-users] Grompp error

[Anurag Dobhal]

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




*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
>
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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