[gmx-users] error in md.log files

[Justin Lemkul]

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

-- 
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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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