Dear AMBER users,
I am doing simulations about protein stretching, and using a script so that
the output is fragmented in pieces. This makes a new simulation start every
few steps, using as input the output of the last. However, when I run this
script, the first step has a really high temperature (which is immediately
corrected in the next step).
I am attaching my mdin file, and the output I get, from one of the runs of
the script. This one is an example with restrained atoms, but the same
applies to atoms without constrains
I hope someone can help me find a reason as to why this might happen, since
I think it is the origin of some mistakes in my simulations.
Thank you for your attention.
Yours faithfully,
A. Gomez-Sicilia
Protein nanomechanics lab
Cajal Institute - CSIC
Avda. Doctor Arce, 32
28002 Madrid (Spain)
Phone number: (+34) 91-585.47.44
Fax number: (+34) 91-585.47.54
E-mail: agomezsicilia.cajal.csic.es
======================================================================================
================mdin====================
&cntrl
nmropt = 0, ntx = 1, irest = 0,
ntrx = 1, ntxo = 1,
ntpr = 100, ntwx = 100, ntr = 1,
ntf = 2, ntb = 0, dielc = 1.0, ntc = 2,
cut = 12, nsnb = 10, scnb = 2.0, scee = 1.2,
imin = 0, igb = 1, gbsa = 1,
nstlim = 2000, dt = 0.001,
temp0 = 300, tempi = 300, saltcon=.15,
ntt = 1, ig = -1, vlimit = 20.0,
&end
[Some constrains]
END
==============OUTPUT===================
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
| # of SOLUTE degrees of freedom (RNDFP): 17018.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 17012. NUM_NOSHAKE = 0 CORRECTED RNDFP = 17012.
| TOTAL # of degrees of freedom (RNDF) = 17012.
NSTEP = 0 TIME(PS) = 12.000 TEMP(K) = 362.67 PRESS =
0.0
Etot = -544.0153 EKtot = 6130.3019 EPtot =
-6674.3172
BOND = 1148.5589 ANGLE = 3488.7189 DIHED =
4520.2884
1-4 NB = 1479.8295 1-4 EEL = 25505.5344 VDWAALS =
-2936.0980
EELEC = -30606.4571 EGB = -9593.1313 RESTRAINT =
188.7604
ESURF= 129.6789
EAMBER (non-restraint) = -6863.0775
------------------------------------------------------------------------------
NSTEP = 100 TIME(PS) = 12.100 TEMP(K) = 290.34 PRESS =
0.0
Etot = -1571.4974 EKtot = 4907.6805 EPtot =
-6479.1779
BOND = 1240.9106 ANGLE = 3549.1990 DIHED =
4510.9609
1-4 NB = 1465.9346 1-4 EEL = 25342.3176 VDWAALS =
-2984.5638
EELEC = -30580.9585 EGB = -9498.7837 RESTRAINT =
346.4802
ESURF= 129.3252
EAMBER (non-restraint) = -6825.6581
------------------------------------------------------------------------------
NSTEP = 200 TIME(PS) = 12.200 TEMP(K) = 292.08 PRESS =
0.0
Etot = -1557.6990 EKtot = 4937.0216 EPtot =
-6494.7206
BOND = 1250.3320 ANGLE = 3482.4232 DIHED =
4514.9317
1-4 NB = 1453.3219 1-4 EEL = 25466.0571 VDWAALS =
-2987.6032
EELEC = -30938.1491 EGB = -9282.1549 RESTRAINT =
415.8525
ESURF= 130.2682
EAMBER (non-restraint) = -6910.5731
------------------------------------------------------------------------------
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Received on Thu Feb 24 2011 - 01:30:05 PST
