[gmx-users] (no subject)

[Thomas Lipscomb]

Ok I got it to work but then I got an error during this:
/usr/local/gromacs/bin/gmx grompp -f ions.mdp -c model1_solv.gro -p topol.top -o ions.tpr


-------------------------------------------------------
Program gmx, VERSION 5.0.1
Source code file: /home/tlipscomb/gromacs-5.0.1/src/gromacs/gmxpreprocess/grompp.c, line: 603

Fatal error:
number of coordinates in coordinate file (model1_solv.gro, 12266)
             does not match topology (topol.top, 11116)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------



Maybe I should modify this so it is topol.top instead of topol_dppc.top?:

/usr/local/gromacs/bin/gmx grompp -f minim.mdp -c system_shrink1.gro -p topol_dppc.top -o em1.tpr
/usr/local/gromacs/bin/gmx mdrun -s em1.tpr -v
perl inflategro.pl system_shrink1.gro 0.95 DPPC 0 system_shrink2.gro 5 area_shrink2.dat

/usr/local/gromacs/bin/gmx grompp -f minim.mdp -c system_shrink2.gro -p topol_dppc.top -o em2.tpr
/usr/local/gromacs/bin/gmx mdrun -s em2.tpr -v
perl inflategro.pl system_shrink2.gro 0.95 DPPC 0 system_shrink3.gro 5 area_shrink3.dat

etc.

FIXED?:

/usr/local/gromacs/bin/gmx grompp -f minim.mdp -c system_shrink1.gro -p topol.top -o em1.tpr
/usr/local/gromacs/bin/gmx mdrun -s em1.tpr -v
perl inflategro.pl system_shrink1.gro 0.95 DPPC 0 system_shrink2.gro 5 area_shrink2.dat

/usr/local/gromacs/bin/gmx grompp -f minim.mdp -c system_shrink2.gro -p topol.top -o em2.tpr
/usr/local/gromacs/bin/gmx mdrun -s em2.tpr -v
perl inflategro.pl system_shrink2.gro 0.95 DPPC 0 system_shrink3.gro 5 area_shrink3.dat


On Sunday, November 9, 2014 3:22 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
 




On 11/9/14 2:20 PM, Thomas Lipscomb wrote:
> Ok I figured out half of it:
>
> perl inflategro.pl system_shrink1.gro 0.95 DPPC 0 system_shrink2.gro 5 area_shrink2.dat
> perl inflategro.pl system_shrink2.gro 0.95 DPPC 0 system_shrink3.gro 5 area_shrink3.dat
> etc
>
> But if I have to minimize inbetween those steps I am not clear how to connect mdrun minimization with inflategrow:
>
> perl inflategro.pl system_shrink1.gro 0.95 DPPC 0 system_shrink2.gro 5 area_shrink2.dat
> mdrun -s topol.tpr -v
>
> perl inflategro.pl system_shrink2.gro 0.95 DPPC 0 system_shrink3.gro 5 area_shrink3.dat
> mdrun -s topol.tpr -v
>

Well, you have to run grompp in between to generate a .tpr with the new 
coordinates.  Your topology is always the same, the .mdp file is always the 
same, the only thing you're changing are the coordinates, which need to be 
minimized at each step.

If these concepts aren't clear, back up and do some more basic tutorial(s) 
before doing something complex.  Learn to walk before you try to run.


-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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