AMBER Archive (2004)

Subject: RE: AMBER: Sander : Vrand flag

From: Ross Walker (
Date: Mon Aug 23 2004 - 13:20:15 CDT

Dear Sachin
By setting vrand=100 you are randomising the velocities every 100 steps.
This is probably not a good idea for the problem you are trying to solve.
The fact that your system is exploding suggests that something is wrong with
it. How did you create it? You probably have some very close contacts
You also appear to be running a vacuum simulation but you talk about waters?
How did you solvate your system? Did you add a solvent cap and a restraint
force on the cap? If not then your system is likely to just boil off into
space. Ideally if you want to run a solvated system you should use periodic
I would try running extensive minimisation of your system first. Then try
heating it slowly (possibly with a time step as short as 0.5fs if you have
to) from 0 to 100K or so over 20ps at constant volume, assuming you can run
periodic boundaries. If it is stable here then try slowly increasing the
temperature over another 20ps or so to 300K. Then equilibrate for a while at
300K before switching to constant pressure.
If you still have problems please post details about your system as well as
the input and output files.
All the best
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |


From: [] On Behalf Of
sachin patil
Sent: 23 August 2004 11:00
Subject: AMBER: Sander : Vrand flag

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
.....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
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' 
group input for restrained atoms 
RES 1 375 


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