[gmx-users] regarding GROMACS Tutorial KALP15 in DPPC

[Justin Lemkul]

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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