[gmx-users] FEP

[P]

Hi all.
I'm trying FEP In gromacs3.3.  My system (3nm; 3nm; 3nm) consists 
of one Na, Cl, DUM ion and solvent molecules. 
 During my free energy calculations I want to perturb:
1) Cl-     into a DUM atom
2) DUM    into Cl-


I'm using ffgmx.  I've added new  atom DUM into ffgmx.atp:
...
   SD  32.06000 ;     DMSO Sulphur
   OD  15.99940 ;     DMSO Oxygen
   CD  15.03500 ;     DMSO Carbon
  CHE  12.01100 ;     HEME RING CARBON
 MNH3   0       ;     Dummy mass in rigid tetraedrical NH3 group
   MW   0       ;     Dummy mass in rigid tyrosine rings
   IW   0       ;     Dummy particle in TIP4P etc.
  DUM   0       ;     moj atom
...

I've updated ffgmxnb.itp:
..
OWT3    15.99940       0.000       A   0.24889E-02   0.24352E-05
   SD    32.06000       0.000       A   0.10561E-01   0.21499E-04
   OD    15.99940       0.000       A   0.22715E-02   0.75147E-06
   CD    15.03500       0.000       A   0.90507E-02   0.21758E-04
  CHE    12.01100       0.000       A   0.23402E-02   0.33740E-05
 MNH3     0             0.000       A   0.0           0.0
   MW     0             0.000       A   0.0           0.0
  DUM     0             0.000       A   0.0           0.0
..

My dual topology for Cl and DUM atoms:

[ moleculetype ]
; molname       nrexcl
Cl              1

[ atoms ]
; id    at type res nr  residu name     at name  cg nr  charge
1       DUM      1       DUM              DUM       1      0       35.45300    Cl   -1  35.45300


. and 

[ moleculetype ]
; molname       nrexcl
ClB              1

[ atoms ]
; id    at type res nr  residu name     at name  cg nr  charge
1       Cl      1       Cl              Cl       1      -1        35.45300  DUM   0   35.45300


I did calculations for 20 lambda values 0.05,  0.10 , 0.15  ..
 0.95 and for those values delta free energy looks reasonable.
My problem is that I get error every time I try to run 
 FEP for lambda = 1 or lambnda = 0.
Am I doing something wrong.  Please give me some advice. 
 (I'm using PME,  DUM and Cl atom are restrained, step 1fs)


My ERROR message for lambda = 0  is :
.
..

 Large VCM(group Cl):    -38.08457,      8.92837,    -19.97197, ekin-cm:  6.83899e+04
Large VCM(group Na):      0.04709,     -0.21100,     -0.29647, ekin-cm:  1.54762e+00

t = 0.002 ps: Water molecule starting at atom 61 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates
Large VCM(group SOL):     -0.01922,     -0.00999,     -0.02540, ekin-cm:  8.98334e+00
Large VCM(group Cl):      4.35556,      2.33494,      5.86521, ekin-cm:  2.08547e+03
Large VCM(group Na):      0.04590,     -0.19717,     -0.27716, ekin-cm:  1.35412e+00
Large VCM(group SOL):     -0.05937,      0.00317,     -0.07617, ekin-cm:  7.52736e+01
Large VCM(group Cl):     13.48634,     -0.66233,     17.40376, ekin-cm:  1.72022e+04
Large VCM(group Na):      0.04470,     -0.18096,     -0.25439, ekin-cm:  1.14329e+00
Large VCM(group SOL):     -0.00393,     -0.03332,      0.01434, ekin-cm:  1.07341e+01
Large VCM(group Cl):      0.88076,      7.63229,     -3.18263, ekin-cm:  2.45181e+03

t = 0.003 ps: Water molecule starting at atom 631 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb
 files with previous and current coordinates
Large VCM(group Cl):      6.73354,     14.12955,    -14.62614, ekin-cm:  1.62697e+04


Thank you for your help
ALL BEST
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060330/bd44a61a/attachment.html>