AMBER Archive (2004)

Subject: AMBER: Sander : Vrand flag

From: sachin patil (sachin_ppatil_at_yahoo.com)
Date: Mon Aug 23 2004 - 12:59:30 CDT

Dear Amber Users,
In the MD simulations I am curently running, the system was constanly exploding and I could see few water molecules out of the systems. And was getting an error in the MDOUT file as-
The system has extended beyond the extent of the virtual box..................
.....restarting shold resolve the error.
And the tempratures were constantly getiing higher and higher.
 
But when I set vrand=100 the simulation went throught just fine. But now my problem is, the temperature of the system is too cold after every 100 steps.
 
I dont know the implications of this on my system.And I am not sure what effect this has on the final results.
So any experiences on similar problems, answers, suggestions or comments are wel-comed.
 
Thank You,
 
Sachin Patil,
============
Graduate student,
Dept. of Medicinal & Biological Chemistry
College of Pharmacy
University of Toledo,
Toledo, Ohio 43606
 
Follwing is the sample out put-
 
 =======================================================
 
Setting new random velocities at step 8500
 NSTEP = 8500 TIME(PS) = 218.500 TEMP(K) = 149.65 PRESS = 0.0 Etot = -17275.3978 EKtot = 3503.8761 EPtot = -20779.2738 BOND = 1126.2674 ANGLE = 3085.7870 DIHED = 3889.4866 1-4 NB = 1416.2147 1-4 EEL = 13519.4021 VDWAALS= -1183.8538 EELEC = -43371.0430 EHBOND = 0.0000 RESTRAINT = 738.4651 EAMBER (non-restraint) = -21517.7389
------------------------------------------------------------------------------ ------------------------------------------------------------------------------
 NSTEP = 8550 TIME(PS) = 218.550 TEMP(K) = 300.98 PRESS = 0.0 Etot = -11965.3497 EKtot = 7046.9539 EPtot = -19012.3036 BOND = 1099.3445 ANGLE = 3024.5770 DIHED = 3922.5966 1-4 NB = 1448.0821 1-4 EEL = 13583.3557 VDWAALS= -1153.0540 EELEC = -41662.9215 EHBOND = 0.0000 RESTRAINT = 725.7160 EAMBER (non-restraint) = -19738.0196
-------------------------------------------------------------------------- -------------------------------------------------------------------------
 
 Here is the input file:
 
 &cntrl nstlim=190000,dt=0.001,
cut=12,ntb=0,nscm=1000, temp0=298,
tempi=298, vrand=100,ntt=1,
irest=1,ntx=5,nmropt=1, ntr=1,tautp=2.0,
fcap=.5, ntf=2, ntc=2,
ivcap=1,ntwe=500, ntwx=500, ntpr=50,
ntwr=5000, nrespa=1,matcap=6178, &end
&wt type='END'
&end
DISANG=./distfinal.rst
LISTOUT=POUT
group input for restrained atoms
2.0
RES 1 375
END
END

                
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