On 2/12/13 10:29 AM, vidhya sankar wrote:
Dear Justin Thank you for your reply,
I have set the Restraint Along the Z Axis . as follows
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
i funct fcx fcy fcz
1 1 0 0 1000000
#endif
Are you using the correct define statement in the .mdp file, and is your #ifdef
in the correct location in the topology ?
As you have Asked above in previous mail i have used the
define = -DPOSRES -DPOSRES_WATER in my .mdp file My question is
1) Should i use -DPOSRES_WATER statement or Not in .mdp file ?
If you want the restraint, then yes. This seems correct.
Also I have used the #ifdef statement in the correct location in the topology
as follows
.
; Include water topology
#include "gromos53a6_lipid.ff/spc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 0 0 100000
#endif
; Include topology for ions
#include "gromos53a6_lipid.ff/ions.itp"
2) in My md.log files I have got following Lines At The end of Every 100
steps While it runs Smoothly Without Any Error .
Large VCM(group NA): -0.01457, -0.01793, -0.03262, Temp-cm:
inf
Large VCM(group NA): -0.00894, -0.07417, -0.08968, Temp-cm:
inf
Large VCM(group NA): 0.00260, -0.05862, -0.10835, Temp-cm:
inf
Large VCM(group NA): 0.02240, 0.06127, -0.08617, Temp-cm:
inf
Large VCM(group NA): 0.11406, 0.11506, -0.07386, Temp-cm:
inf
Large VCM(group NA): 0.16859, 0.05669, -0.03958, Temp-cm:
inf
Large VCM(group NA): 0.07832, -0.04243, -0.02288, Temp-cm:
inf
Large VCM(group NA): -0.05293, -0.02293, -0.03210, Temp-cm:
inf
Large VCM(group NA): 0.01289, 0.09823, -0.02071, Temp-cm:
inf
Large VCM(group NA): 0.09863, 0.18033, 0.03704, Temp-cm:
inf
Large VCM(group NA): 0.01632, 0.22306, 0.04888, Temp-cm:
inf
Large VCM(group NA): -0.04317, 0.22376, -0.02476, Temp-cm:
inf
Large VCM(group NA): 0.08154, 0.19584, -0.06280, Temp-cm:
inf
Large VCM(group NA): 0.23298, 0.14145, 0.00921, Temp-cm:
inf
Large VCM(group NA): 0.22764, 0.09442, 0.07858, Temp-cm:
inf
Large VCM(group NA): 0.09441, 0.07206, 0.02138, Temp-cm:
inf
Large VCM(group NA): 0.00187, 0.04563, -0.03987, Temp-cm:
inf
Large VCM(group NA): 0.05896, 0.00550, 0.02418, Temp-cm:
inf
Large VCM(group NA): 0.11112, 0.04126, 0.11459, Temp-cm:
inf
DD step 5199 vol min/aver 0.821 load imb.: force 1.3%
How to Eliminate The Above error ?
"Group NA" seems to imply that you are coupling solvent and ions to separate
thermostats, which is a terrible idea. The ions are moving separately from
water and they are crashing into one another. You may have to restrain the ions
in some way if you are also restraining water to prevent such collisions.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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