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I tried to a perform constant volume (few tortional restraint ) MD from the restart file generated again from contant volume minimization with few tortional restraints. (FOr testing recently installed amber8 in Opteron)
For minimization
&cntrl
imin=1, maxcyc=2000, ncyc=1000, nmropt=1,
cut=6.0,
ipol=1,
ntpr=10, ntb=1,
&wt type='END' /
LISTOUT=POUT_dmso_min
DISANG=RST_Tri_cons
Upto here no problem . Then for the constant volume MD
&cntrl
imin=0, irest=0, ntx=1, tempi=0.0, cut=11.0,
ntt=1, temp0=300.0, tautp=2.0, nmropt=1,
ntp=0, nrespa=1, ipol=1,
ntb=1, ntc=1, ntf=1,
nstlim=100000, dt=0.001,
ntwe=200, ntwx=200, ntpr=200,
&wt type='END' /
LISTOUT=POUT_dmso_cv
DISANG=RST_Tri_cons
--- I find in the output file that
Here is the input file:
&cntrl
imin=0, irest=0, ntx=1, tempi=0.0, cut=11.0,
ntt=1, temp0=300.0, tautp=2.0, nmropt=1,
ntp=0, nrespa=1, ipol=1,
ntb=1, ntc=1, ntf=1,
nstlim=100000, dt=0.001,
ntwe=200, ntwx=200, ntpr=200,
&wt type='END' /
LISTOUT=POUT_dmso_cv
DISANG=RST_Tri_cons
Could not find cntrl namelist
I check each of the cntrl keys in amber8 manual. Each of them are there as well. I am wondering where could be the error.
With regards,
Jiten
----- Original Message -----
From: Carlos Simmerling
To: amber.scripps.edu
Sent: Wednesday, July 14, 2004 10:39 PM
Subject: Re: AMBER: Angle restraint during MD
sorry, that was a typo. check page 119.
----- Original Message -----
From: Jiten
To: amber.scripps.edu
Sent: Wednesday, July 14, 2004 1:51 AM
Subject: Re: AMBER: Angle restraint during MD
Hello Dr. Carlos,
In page 199 is about the analysis (ptraj). Also I do not want to use ntr (cartitian restraint) because it will forbid the translational and rotational motion of the ion.
Regards,
jiten
----- Original Message -----
From: Carlos Simmerling
To: amber.scripps.edu
Sent: Wednesday, July 14, 2004 2:47 AM
Subject: Re: AMBER: Angle restraint during MD
try reading the section starting at page 199 too, it tells you
there how to use the iat() values for angle restraints.
----- Original Message -----
From: Jiten
To: amber.scripps.edu
Sent: Tuesday, July 13, 2004 12:21 PM
Subject: Re: AMBER: Angle restraint during MD
Hello Dr. Carlos,
What I can see in the amber8 manual (5.20.3 - page 162) about the makeANG_RST is about defining only the tortional restraints. So, it seems to me that for the angle restraint between three atoms (A-B-C) - I should rather define the distance restraint between A and C. Am I right? If not how can what could be the format of contraint and constraint_library ?
I tried to a perform constant volume (few tortional restraint ) MD from the restart file generated again from contant volume minimization with few tortional restraints. (FOr testing recently installed amber8 in Opteron)
For minimization
&cntrl
imin=1, maxcyc=2000, ncyc=1000, nmropt=1,
cut=6.0,
ipol=1,
ntpr=10, ntb=1,
&wt type='END' /
LISTOUT=POUT_dmso_min
DISANG=RST_Tri_cons
Upto here no problem . Then for the constant volume MD
&cntrl
imin=0, irest=0, ntx=1, tempi=0.0, cut=11.0,
ntt=1, temp0=300.0, tautp=2.0, nmropt=1,
ntp=0, nrespa=1, ipol=1,
ntb=1, ntc=1, ntf=1,
nstlim=100000, dt=0.001,
ntwe=200, ntwx=200, ntpr=200,
&wt type='END' /
LISTOUT=POUT_dmso_cv
DISANG=RST_Tri_cons
--- I find in the output file that
Here is the input file:
&cntrl
imin=0, irest=0, ntx=1, tempi=0.0, cut=11.0,
ntt=1, temp0=300.0, tautp=2.0, nmropt=1,
ntp=0, nrespa=1, ipol=1,
ntb=1, ntc=1, ntf=1,
nstlim=100000, dt=0.001,
ntwe=200, ntwx=200, ntpr=200,
&wt type='END' /
LISTOUT=POUT_dmso_cv
DISANG=RST_Tri_cons
Could not find cntrl namelist
I check each of the cntrl keys in amber8 manual. Each of them are there as well. I am wondering where could be the error.
With regards,
Jiten
----- Original Message -----
From: Carlos Simmerling
To: amber.scripps.edu
Sent: Tuesday, July 13, 2004 9:00 PM
Subject: Re: AMBER: Angle restraint during MD
ok, I didn't understand the last mail well. you can
definitely do angle restraints using the NMR restraint
option. check the manual carefully, and if it is not clear,
please let us know which part you do not understand.
----- Original Message -----
From: Jiten
To: amber.scripps.edu
Sent: Tuesday, July 13, 2004 5:28 AM
Subject: AMBER: Angle restraint during MD
Hello all,
Sorry for the previous mail without subject.
Sander does no more support the restrainXYZ in the parmtop file. But using the NMR restraint I could do only distance and torsional angle restraint. I wish to put a small ion (having 3 atoms) under angle restraint during MD. I am wondering how can I solve this probelm
Any suggestions will be highly appreciated.
Thanks inadvance,
N. Jiten Singh
C/O Prof. Kwang S. Kim
Department of Chemistry
Pohang University of Science and Technology
San 31, Hyojadong, Namgu
Pohang 790-784, Korea
Phone : 82-54-279-5853 ( Lab ) / 279-4138 ( Appt )
Fax : 82-54-279-8137 (or +82-54-279-3399)
Web : http://csm.postech.ac.kr/ and http://www.postech.ac.kr/e
Home Page : http://www.geocities.com/njs_19
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Received on Wed Jul 14 2004 - 17:53:01 PDT