Dear Amber Users,
Following is the frcmod file
MASS
H1 1.0
OH 16.
CT 12.
HO 1.
NONB
H1 1.3770 0.0150
OH 1.7210 0.2104
CT 1.9080 0.1094
HO 0.0 0.0
I am using methanol to solvate my polymer chain. I have attached the
library file used for my simulations. When I perform constant pressure
simulations of polymer in methanol box at 300K the box expands. So now I
have used only methanol in a box constructed with the following commands in
xleap using the library file.
source leaprc.ff03
loadamberparams methanol.frcmod
loadoff methanol.off
setbox a vdw 2
saveamberparm a M.prmtop M.inpcrd
The library file, prmtop and inpcrd file are attached.
My simulation run is minimization, constant volume simulations where I heat
to 300K followed with constant pressure run
cntrl
imin=1,
ntb=1,
cut=10.0,
maxcyc=10000, ncyc=1000,
ntt=0,
&end
&cntrl
imin=0,
ntxo=1, ntrx=1,
cut=12.0,tempi=0.1,
ntpr=500, ntwx=500, ntwe=500,
nstlim=300000, temp0=300.0,
dt=0.002,dielc=33,
ntc=2, ntf=2,tol=0.00001,
ntx=1, irest=0,
ntb=1,tautp=2,
ntt=1,
nmropt=1,ntr=1,
/
&wt
type='TEMP0', istep1=0, istep2=200000, value1=0.1, value2=300.0,
/
&wt
type='TEMP0', istep1=200001,istep2=300000,value1=300.0, value2=300.0,
/
&wt type='END',
/
GROUP FOR CONSTRAINTS
0.5
RES 1 1743
END
END
&cntrl
imin=0,
ntxo=1, ntrx=1,
cut=12.0,tempi=300.0,
ntpr=500, ntwx=500, ntwe=500,
nstlim=500000, temp0=300.0,
dt=0.002,dielc=33,
ntc=2, ntf=2, tol=0.00001,
ntx=5, irest=1,
ntb=1,tautp=1,
ntt=1,
/
I want to obtain the heat of vaporization using Upot from my simulations.
Please let me know where is the problem.
Thanks
Kirtana
On Fri, Jul 5, 2013 at 5:35 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Thu, Jul 04, 2013, kirtana S wrote:
> >
> > I am performing a constant pressure simulations with a methanol box . My
> > system blows up i.e during the constant pressure run the box expands.
> > Please suggest
>
> There is way too little information here for anyone on the list to be of
> much
> help. For example, we don't know which force field you used, how you
> created
> the initial coordinates, how much the box expanded, what temperature you
> used,
> and so on.
>
> ...dac
>
>
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Received on Fri Jul 05 2013 - 11:30:03 PDT
