[gmx-users] oplsaa and lincs error

[Jochen Hub]

MURAT CETINKAYA wrote:

>Hi gmx users,
>
>I am trying to perform Free Energy calculations on a non-standard residue using
>oplsaa force field. Two problems arise:
>
>1) When I try to minimize in vacuo, atoms split apart and molecule is destroyed.
>This is independent of the algorithm. I tried with and witohut constraints on
>the system. This is the input file for in vacuo:
>
>
>  
>
...

>2)If I solvate the system with tip4p, I can do minimization (although ending
>very early) and I can perform POSRE NVT equilibration. When I switch to NVT w/o
>restrains on the peptide, system gives out LINCS errors (relative constraint
>deviation) although I dont use any constraints. I also turned off PME. 
>  
>
When doing EM with water, what is your final force? It should be around 
1+e04.

Probably your structure contains some atom clashes, which cause the EM 
to fail and cause the LINCS warnings. Maybe you want to try this this 
em.mdp, if it does not work, your structure has a problem...

; VARIOUS PREPROCESSING OPTIONS =
title                    =
cpp                      = /lib/cpp
include                  =
; define                   = -DFLEXIBLE
; warnings               = 10

; RUN CONTROL PARAMETERS =
integrator               = steep
; start time and timestep in ps =
tinit                    = 0
dt                       = 0.0001
nsteps                   = 50

; ENERGY MINIMIZATION OPTIONS =
emtol                    = 0.00001
emstep                   = 0.001
nstcgsteep               = 1000

lincs_iter               = 4


Good luck,
Jochen

>I saw some emails talking about tip4p constraints. But I am clueless about in
>vacuo.
>any help appreciated.
>Murat CETINKAYA, M.Sc.
>BioNanoMaterials Group,
>Dept. of Engr. Science and Mechanics,
>The Pennsylvania State University,
>University Park, PA 16802
>office: (814) 863 9967
>web: www.personal.psu.edu/muc176
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>  
>


-- 
************************************************
Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
************************************************