[gmx-users] Magic Number Error in XTC file (read 0, should be 1995)

Justin Lemkul jalemkul at vt.edu
Sun Aug 13 19:12:53 CEST 2017

On 8/13/17 12:47 PM, ZHANG Cheng wrote:
> Hi Justin,
> Thank you for explaining that.
> You said "a more reliable system", what does this mean? It is my first time adding glycines to my protein using OPLS-AA/L force field. Do you think this might be the reason, and should I switch to another force field?

I'm talking about hardware.  Failure to write a valid frame is usually due to a 
filesystem problem (i.e. hard disk).  It doesn't matter what your force field is 
or what your system contents are.

> My procedure is as follows:
> 1) I get the glycine and protein pdb, convert them to .gro files using
> gmx pdb2gmx -f glycine/protein.pdb -o glycine/protein.gro -water spce -inter
> 2) then I add the protein.gro into a box, get the protein_newbox.gro:
> gmx editconf -f protein.gro -o protein_newbox.gro -c -d 1.0 -bt cubic
> 3) then I add glycines to this box:
> gmx insert-molecules -ci glycine.gro -nmol 203 -f protein_newbox.gro -o protein_203_glycine.gro
> 4) then I do the exactly the same thing according to your tutorial, i.e. solvent with water, add ions, energy minimization, NVT, NPT, and finally the MD.
> Can I ask if the procedure is correct? Would you please recommend some tutorial for prepare a system with protein and excipients (e.g. glycine, sorbitol, etc)?

It's fine.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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