[gmx-users] (no subject)

[Thomas Lipscomb]

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 <jalemkul at 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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