Dear Amber users,
If I notice asteriosk or stars marks in my output file and restart file
what does this imply. I had this job run in sander without any issues and
noticed some error in pmemd cuda. I tried to rectify this by using iwrap 1
and still notice similar result.
I used mpi run and also single processor run.
Can you tell me if the issue is with my input files or my starting
structure. Minimization run was preformed on the solvent with restraint on
solute before this step.
My input file
Minimization:
&cntrl
imin=1, ntx=1,
dielc=1.0,ntmin=2,
ntrx=1, ntxo=1,
ntb=1,ioutfm=1,
irest=0, cut=10.0,
ntpr=1,
maxcyc=10000,
ntt=0, ntr=1,
&end
Hold the PRO fixed
40.0
RES 1 300
END
END
Second step which give me the error
&cntrl
imin=0,ntx=1,
cut=10.0,tempi=0.0,
ntpr=100,ntwx=100,ntwe=100,
nstlim=1000000,temp0=100.0,
dt=0.001,
ntc=2, ntf=2,
irest=0,tautp=4.0,
ntb=1,iwrap=1,
ntt=3,gamma_ln=5.0,ntr=1,
&end
Hold surface fixed
40.0
RES 1 300
END
END
NSTEP = 100 TIME(PS) = 0.100 TEMP(K) =********* PRESS =
0.0
Etot = ************** EKtot = ************** EPtot =
**************
BOND = -0.0000 ANGLE = 1580104.7120 DIHED =
12738.0737
1-4 NB = 0.0000 1-4 EEL = -19.0698 VDWAALS =
**************
EELEC = -308.1300 EHBOND = 0.0000 RESTRAINT =
**************
EAMBER (non-restraint) = **************
mden file
L0 Nsteps time(ps) Etot EKinetic
L1 Temp T_solute T_solv Pres_scal_solu
L2 Pres_scal_solv BoxX BoxY BoxZ
L3 volume pres_X pres_Y pres_Z
L4 Pressure EKCoM_x EKCoM_y EKCoM_z
L5 EKComTot VIRIAL_x VIRIAL_y VIRIAL_z
L6 VIRIAL_tot E_pot E_vdw E_el
L7 E_hbon E_bon E_angle E_dih
L8 E_14vdw E_14el E_const E_pol
L9 AV_permMoment AV_indMoment AV_totMoment Density
dV/dlambda
L0 100 0.1000000000E+00 0.2542518727E+16 0.2542508165E+16
L1 0.3949644593E+14 0.3949644593E+14 0.2525519783E+22 0.1000000000E+01
L2 0.1000000000E+01 0.1015340000E+03 0.1656810000E+03 0.3714600000E+02
L3 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
L4 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
L5 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
L6 0.0000000000E+00 0.1056199933E+11 0.1970472220E+10 -.3081299803E+03
L7 0.0000000000E+00 -.1024454832E-07 0.1580104712E+07 0.1273807373E+05
L8 0.0000000000E+00 -.1906978498E+02 0.8589934592E+10 0.0000000000E+00
L9 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
0.0000000000E+00
Can you help me with this.
Thanks
Kirtana
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 23 2014 - 09:00:03 PDT
