AMBER Archive (2003)

Subject: AMBER: ibelly problem

From: Vikas Varshney (vikas_var_at_rediffmail.com)
Date: Tue Oct 28 2003 - 13:34:00 CST

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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