[gmx-users] error in md.log files

[vidhya sankar]

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  ?


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 ?

Thanks In Advance