Hi,
I initiated MD by heating the ligand-protein complex with no
constraints on the atoms from 0 to 300K in 10 ps.Then 100ps eqilibration
at the constant temp. 300K was performed on restrained backbone and
distance. I got crazy MD output. THe energy and temp. went to very high
and a lot of vlimit warnings. Below is the input file and part of the
output file. Please take a look for me.
Thank you very much and happy good Friday!
MDIN:
dynamics w/o belly on protein, 9.0 cut, with constraints of backbone and
distance
&cntrl
nmropt = 1,
ntx = 5, irest = 1, ntrx = 1, ntxo = 1,
ntpr = 1000, ntwx = 1000, ntwv = 0, ntwe = 0,
ntf = 1, ntb = 0,
cut = 9.0, nsnb = 10, dielc=4.0
ibelly = 0, ntr = 1,
imin = 0,
nstlim = 100000,
nscm = 0, dt = 0.001,
temp0 = 300.0, tempi = 300.0,
heat = 0.0,
ntt = 1,
tautp = 2.0,
vlimit = 20.0,
ntc = 1, tol = 0.00001,
&end
&ewald
eedmeth=5,
&end
&wt
type='END' ,
&end
LISTOUT=POUT
DISANG=RST.dist
Hold the backbone restrainted
500.0
FIND
* CT * *
* N * *
* C * *
* O * *
SEARCH
RES 1 293
END
END
OUTPUT
vlimit exceeded for step 992; vmax = 1297679.08
vlimit exceeded for step 993; vmax = 200557512.
vlimit exceeded for step 994; vmax = 86296.6221
vlimit exceeded for step 995; vmax = 530655.444
vlimit exceeded for step 996; vmax = 719129.926
vlimit exceeded for step 997; vmax = 2.54845046E+09
vlimit exceeded for step 998; vmax = 97404.1622
vlimit exceeded for step 999; vmax = 330667.274
NSTEP = 1000 TIME(PS) = 11.000 TEMP(K) =********* PRESS = 0.0
Etot = ************ EKtot = ************ EPtot =
3906732.9101
BOND = 865895.1848 ANGLE = 223527.1116 DIHED =
15612.3010
1-4 NB = 1509819.0853 1-4 EEL = 546.5250 VDWAALS =
163607.4823
EELEC = -1106.9859 EHBOND = 0.0000 RESTRAINT =
1128832.2060
EAMBER (non-restraint) = 2777900.7040
Received on Fri Apr 18 2003 - 16:53:01 PDT
