Dear Amber Users,
I am having a some kind of peculiar problem. I will really appriciate any kind of help
or clue in this matter.
I have my system with 3 components. PMMA, CCl4 and Al2O3 crystal. I am fixing
Al203 crystal by ibelly =1 option.
Here is an example of my input file
Constant Pressure Simulation
$cntrl
imin=0,
ntx=5,irest = 1,
ntb=2,
ntpr=50,ntave=50,ntwr=100,iwrap=1,ntwx=200,ntwv=200,ntwe=200,
ntf=1,ibelly=1,
nstlim=100000,
temp0=293.0,tempi=293.0,ntt=1,
ntp=2
$end
Group input for free atoms
RES 1 763
END
END
I have in total 859 residues. 1-381 are ccl4, 382 is my PMMA and 383-763 are ccl4
again. 764-859 are my crystal residues. SO I was expecting that the crystal would
remain fix. But when I look into my mdcrd file using vmd, I see a small part of the
crystal is also moving. Though most of it is fixed. I am not getting, why a small part
of the crystal is moving and is not fixed. This is at the corner of my crystal. More
specifically, the corresponding residue numbers are 764 765 and 766. I tried to
change my input file group format by atom types instead of res number, like following
but it also gave me same result.
Constant Pressure Simulation
$cntrl
imin=0,
ntx=5,irest = 1,
ntb=2,
ntpr=50,ntave=50,ntwr=100,iwrap=1,ntwx=200,ntwv=200,ntwe=200,
ntf=1,ibelly=1,
nstlim=50000,
temp0=293.0,tempi=293.0,ntt=1,
ntp=2
$end
Group input for free atoms
FIND
* c * *
* c3 * *
* cl * *
* h1 * *
* hc * *
* o * *
* os * *
SEARCH
RES 1 859
END
END
If any body have any clue what may be the reason for this discrepency, I would
really really appreciate his help.
Thanks,
Many regards
Vikas
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Received on Tue Oct 28 2003 - 19:53:01 PST
