[gmx-users] FEP

[paloureiro at biof.ufrj.br]

Hi,

are you using soft core portentials?
Despite the theoretical drawbacks (see the previous discussion), the
creation/annihilation of atoms was impossible (in my experience) without those
potentials.

Regards.

Pedro.


> 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
>



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