Dear friends,
I am trying to simulate folic acid using gaff force field with resp
charges.
I added hydrogen to crystal structure with "reduce" tool in amber utility
. After this, I optimized the structure with gaussian. I got the prepin and
frcmod files using ANTECHAMBER and parmchk.
I solvated the structure with TIP3P water box and ff10 parm in xleap
followed by minimizing and heating the structure up to 300K with Berendsen
thermostat (NTT=1 and NMR restraints). Beyond this, as I am trying to
equilibrate with removing the restraints from the structure, it is giving
me the "VLIMIT" error. The structure is also drastically changing its shape.
I went through this amber mailing list to short out this but couldn't find
anything to get over this error. Have any one done the simulation with
Folic acid ? I will be grateful for any suggestion from the AMBER
community.
I am attaching the topology file for the structure and the output error is
mentioned below,
Here is the error :
vlimit exceeded for step 40667; vmax = 31.4742
vlimit exceeded for step 40668; vmax = 152.9706
vlimit exceeded for step 40673; vmax = 22.8923
vlimit exceeded for step 40675; vmax = 20.7989
NSTEP = 40700 TIME(PS) = 80.700 TEMP(K) = 640.76 PRESS =
1004.4
Etot = -5311.2956 EKtot = 3781.0917 EPtot =
-9092.3873
BOND = 77.5008 ANGLE = 225.2068 DIHED =
44.1200
1-4 NB = 83.6848 1-4 EEL = -262.0259 VDWAALS =
1428.1702
EELEC = -10689.0440 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 1152.0380 VIRIAL = 507.6180 VOLUME =
29715.8201
Density =
0.9992
Ewald error estimate: 0.4139E-04
Here is the input file for equilibration.
Equilibration w/ no restraints on FOLIC, 8.0 cut
&cntrl
nmropt = 0,
ntx = 7, irest = 1, ntrx = 1, ntxo = 1,
ntpr = 100, ntwx = 500, ntwv = 0, ntwe = 0,
ntwprt = 0, ntwr = 500, ioutfm = 0,
ntf = 2, ntb = 2, dielc = 1.0,
cut = 8.0, nsnb = 10,
ipol = 0,
ibelly = 0, ntr = 0,
nstlim = 50000,
nscm = 1000,
t = 0.0, dt = 0.001,
temp0 = 300.0,
ig = 71277, heat = 0.0,
ntt = 1, dtemp = 0.0,
tautp = 0.5,
ntp = 1, pres0 = 1.0, comp = 44.6,
taup = 0.5,
ntc = 2, tol = 0.0005,
&end
&ewald
&end
--
*With Regards,
HIMANSHU JOSHI
Graduate Scholar, Center for Condense Matter Theory
Department of Physics IISc.,Bangalore India 560012*
ॐ सर्वे भवन्तु सुखिनः सर्वे सन्तु निरामयः।
सर्वे भद्रणिपश्यन्तु मा कश्चिद्दुःख भाग भवेत्॥
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Received on Wed Mar 06 2013 - 21:30:02 PST
