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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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