Dear All,
i've been trying to use AMBER to simulate DNA with some free
metal-containing ligands.
The ligands have been parametrized and simulations show that they are
stable.
When running DNA with these ligands however, many of the simulations break.
Looking at the trajectories it seems that most of the simulations break
when the ligands approaches the edges of the box.
Also, the simulations appear to be even less stable when increasing the
time-step. I'm using between 1 and 1.6fs.
Even more unusual, in a couple of simulations (where it broke) i've reduced
NTPR to 5 (to have a look at the system and see if i can understand what's
happening) and sure enough the simulation ran without any problems!!
Does anyone have any idea what could be wrong?
I'm sending below 2 outputs that have failed... (the second one simply
fails with no messages). As well as the beginning of an output file.
Thank you very much in advance!
kind regards,
fatima
NSTEP = 25235000 TIME(PS) = 41476.000 TEMP(K) = 300.72 PRESS =
-0.6
Etot = -78590.1859 EKtot = 17016.3867 EPtot =
-95606.5726
BOND = 213.3783 ANGLE = 418.6505 DIHED =
543.7025
1-4 NB = 194.1447 1-4 EEL = -3731.9950 VDWAALS =
12615.5121
EELEC = -105859.9656 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 8171.2402 VIRIAL = 8174.9510 VOLUME =
284395.0370
Density =
1.0090
------------------------------------------------------------------------------
check COM velocity, temp: 0.000048 0.00(Removed)
check COM velocity, temp: 0.000036 0.00(Removed)
check COM velocity, temp: NaN NaN(Removed)
check COM velocity, temp: NaN NaN(Removed)
check COM velocity, temp: NaN NaN(Removed)
NSTEP = 25240000 TIME(PS) = 41484.000 TEMP(K) = NaN PRESS =
6859.8
Etot = NaN EKtot = NaN EPtot =
**************
BOND = ************** ANGLE = 111746.1954 DIHED =
0.0000
1-4 NB = ************** 1-4 EEL = ************** VDWAALS =
-808.1573
EELEC = ************** EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = ************** VOLUME =
**************
Density =
0.0000
------------------------------------------------------------------------------
------------------------------------------------------------------------------
NSTEP = 295000 TIME(PS) = 1395.000 TEMP(K) = 301.12 PRESS =
17.8
Etot = -83684.4292 EKtot = 18182.6523 EPtot =
-101867.0815
BOND = 189.2779 ANGLE = 382.4836 DIHED =
544.3077
1-4 NB = 205.8781 1-4 EEL = -3546.3340 VDWAALS =
13389.9438
EELEC = -113032.6385 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 8879.3139 VIRIAL = 8763.1238 VOLUME =
302886.8889
Density =
1.0105
------------------------------------------------------------------------------
check COM velocity, temp: 0.000012 0.00(Removed)
check COM velocity, temp: 0.000003 0.00(Removed)
check COM velocity, temp: 0.000008 0.00(Removed)
check COM velocity, temp: 0.000003 0.00(Removed)
-------------------------------------------------------------------------------------
-------------------------------------------------------
Amber 11 SANDER 2010
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 11
| Run on 03/15/2012 at 11:34:12
[-O]verwriting output
File Assignments:
| MDIN: npt.in
| MDOUT: prod1.out
| INPCRD: md19.rst
| PARM: start.top
| RESTRT: prod1.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: prod1.ene
| MDCRD: prod1.x
| MDINFO: prod1.inf
|LOGFILE: logfile
Here is the input file:
1ns input file for extending
&cntrl
ntx=7, irest=1,
ntwr=1000,
ntf=2, ntb=2,
ntr=0,
nstlim=30000000, dt=0.001,
ntwx=5000, ntwe=5000, ntpr=5000,
temp0=300, ntt=1,
ntp=1, cut=9,
ntc=2,
&end
|--------------------- INFORMATION ----------------------
| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
| Version 2.3
|
| 12/14/2011
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Received on Thu Mar 15 2012 - 05:30:05 PDT
