[gmx-users] LINCS Warnings in the middle of an MD run

David van der Spoel spoel at xray.bmc.uu.se
Wed Dec 26 21:27:54 CET 2001

On Wed, 26 Dec 2001, paloureiro wrote:

>I read with great interest the discussion in December 14 about LINCS warnings during an MD run. It was suggested to run trjconv so as to change the number of decimal places, introducing in this way a small round-off error.
>But I was left with some simple questions:
>1)should I expect to have my output files (.trr or .gro) with 7 decimal places? I am not able but to see 3 in the .gro and 5 in the .trr files.
>2)the small error will be introduced only in the .gro file created by trjconv?

When you do trjconv to a gro file, you get 3 decimal places, to a pdb file
you get 4, to g96 even more. You then use this gro or pdb file to start a
new (continuation) simulation. Do not forget to set the starting time
correct. When that simulation is finished you can concatenate the results
using trjcat and eneconv.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

More information about the gromacs.org_gmx-users mailing list