Ok so to fix the adding ions error:
number of coordinates in coordinate file (model1_solv.gro, 12266)
does not match topology (topol.top, 11116)
I am redoing the shrinking steps:
perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5
area_shrink1.dat
Follow this up by another round of EM. During the "shrinking" steps, be sure to
change the cutoff value to 0, or else you will continue to delete lipids! After
26 iterations of scaling down by 0.95, I reached an area per lipid of ~71 Å2,
above the experimental value of ~62 Å2. Since the script tends to overestimate
the area per lipid, this value is good enough to continue to equilibration.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
Here is one iteration of the 26 shrinking steps:
/usr/local/gromacs/bin/gmx grompp -f minim.mdp -c system_shrink1.gro -p
topol.top -o em.tpr
/usr/local/gromacs/bin/gmx mdrun -s em.tpr -v
perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
Is that correct? Do I just copy and paste it into the command line 26 times to
iterate it 26 times?
Thank you so much I have come so far this weekend on this part of my senior
project.
Sincerely,
Thomas
On Sunday, November 9, 2014 6:21 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 11/9/14 5:09 PM, Thomas Lipscomb wrote:
> 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
> -------------------------------------------------------
>
This is a common error resulting from incorrect bookkeeping. The addition of
solvent and ions doesn't happen until after lipid compaction, so I don't know
why you're doing this.
>
>
> Maybe I should modify this so it is topol.top instead of topol_dppc.top?:
>
As I said before, topol_dppc.top is specific to the DPPC bilayer and is only
ever used to account for DPPC periodicity. Do not use it for anything else.
> /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?:
>
No, this approach is incorrect because the intervening minimization steps is
never actually utilized. Explained:
> /usr/local/gromacs/bin/gmx grompp -f minim.mdp -c system_shrink1.gro -p
> topol.top -o em1.tpr
This is correct.
> /usr/local/gromacs/bin/gmx mdrun -s em1.tpr -v
I would recommend avoiding the use of default names. I would suggest you use
-deffnm to name everything "em1" so you know exactly what you're dealing with.
> perl inflategro.pl system_shrink1.gro 0.95 DPPC 0 system_shrink2.gro 5
> area_shrink2.dat
>
Here, you've basically ignored the previous mdrun. The file system_shrink1.gro
is the un-minimized output of InflateGRO. This is not what you want. The
input
coordinate file at this step should be the output of energy minimization, viz.
confout.gro if you're using default names or em1.gro if you use my -deffnm
approach.
-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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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