Hi all,
I would like to see the cis-trans isomerisation of a proline dipeptide
(with non-proteinic caps). For this I am trying to use scaled MD in
Amber14. I first ran a simulation without the scaledMD flag in the
input file:
&cntrl
iwrap = 1
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 10.0, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 5000000, dt = 0.002,
ntpr = 100, ntwx = 500, ntwr = 1000
ioutfm = 1
/
This simulation ran without any errors, but no isomerisation is
present. Next, I added the scaledMD (with lamba = 0.7). At first, this
simulation also runs without any problems. However, after a variable
number of frames (I retried a few times), the molecule seems to
"disappear" when viewed with vmd. The last meaningfull entry in the
scaledMD.log file is:
500 354500 -9646.920713734136 0.700000000000
-6752.844499613895 2894.076214120241
500 355000 NaN 0.700000000000
NaN NaN
Similarly, this MDoutput file says:
NSTEP = 354800 TIME(PS) = 729.600 TEMP(K) = 423.76 PRESS
= 432.6
Etot = -4282.2994 EKtot = 2627.3184 EPtot =
-6909.6177
BOND = 18.9484 ANGLE = 52.2623 DIHED =
53.2375
1-4 NB = 8.8145 1-4 EEL = 280.3660 VDWAALS =
1338.0893
EELEC = -11622.6005 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 1489.3212 VIRIAL = 1196.8884 VOLUME =
31310.6309
Density =
0.9927
------------------------------------------------------------------------------
NSTEP = 354900 TIME(PS) = 729.800 TEMP(K) = NaN PRESS
= NaN
Etot = NaN EKtot = NaN EPtot =
NaN
BOND = ************** ANGLE = 8471.6843 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
NaN
EELEC = NaN EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 12582912.0000 VIRIAL = NaN VOLUME =
NaN
Density =
NaN
------------------------------------------------------------------------------
However, the simulation continues until the end.
When I save the last frame (with an invisible molecule) as a pbd with
vmd, several molecules appear to be present..
Can anyone help with this issue?
Kind regards
Niels
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Received on Thu Jul 17 2014 - 23:30:01 PDT
