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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