[gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

[Anurag Dobhal]

how will I get to know that the system have shrunken enough, and which file
I need to solvate.



On Thu, Oct 2, 2014 at 9:16 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/2/14 8:50 AM, Anurag Dobhal wrote:
>
>> Thanks Justin
>>
>> I m running the command
>>
>>   " mdrun -s em.tpr  " and I did get the confout.gro file as output.
>>
>> after that I am running the command
>>
>> " perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5
>> area_shrink1.dat "
>> and then again the energy minimization command.
>>
>> " mdrun -s em.tpr"
>>
>> After that  I am solvating the system.
>> I did put a local copy of vdwradii.dat in my working directorie  and
>> change
>> the value of C from 0.15 to 0.375.
>>
>>
>>   I am solvating my system by the command
>>
>> " genbox -cp system_shrink1.gro -cs spc216.gro -o system_solv.gro -p
>> topol.top "
>>
>> after that I am adding the ions in the system by the command
>>
>> " grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr"
>>
>> But now I am getting an error
>>
>> number of coordinates in coordinate file (system_solv.gro, 8218)
>>      does not match topology (topol.top, 1956)
>>
>>
>> can you please help what caused this error.
>>
>>
> Don't solvate the intermediate steps.  It makes no physical sense.  Only
> solvate when you have shrunk the system to an appropriate size based on
> APL. Regardless, the number of atoms in the system is way too small to be
> correct for the tutorial system.
>
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> 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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