[gmx-users] Problem with CG in double precision

[anwar at cdfd.org.in]

Dear users,
I am getting a problem with CG minimization of protein in Double Precision. 
The error is 
###################################################################
processing topology...
Generated 279 of the 1225 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 1
Excluding 2 bonded neighbours for SOL 10511
Excluding 1 bonded neighbours for NA+ 5
processing coordinates...
double-checking input for internal consistency...
ERROR: can not do Conjugate Gradients with constraints (31533)
Fatal error: There was 1 error
##################################################################
I kept none constrains in em.mdp.
##################################################################
;
;       User spoel (236)
;       Wed Nov  3 17:12:44 1993
;       Input file
;
cpp                 =  /lib/cpp
define              =  -DFLEX_SPC
constraints         =  none
integrator          =  cg
nsteps              =  10000
;
;       Energy minimizing stuff
;
emtol               =  100
emstep              =  0.01
nstcgsteep          =  100

nstcomm             =  1
ns_type             =  grid
rlist               =  1
rcoulomb            =  1.0
rvdw                =  1.0
Tcoupl              =  no
Pcoupl              =  no
gen_vel             =  no
#################################################
I am adding NA+ ions and water in the simulation. Where could be the constrains 
as reported by the program. 
Waiting for the reply
Thanks
----------------------
Mohd Anwaruddin, M.Sc.
C/o DR.H.A.Nagarajaram,
Lab of Computational Biology and Bioinformatics
Center for DNA Fingerprinting and Diagnostics(CDFD),
Nacharam,
Hyderabad-500 076, INDIA.
Tel : +91-40-27151344 ext 1207,1208.
anwar_m1 at rediffmail.com
-----------------------


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Date:Sat Jul 24 18:00:08 CST 2004
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Today's Topics:

   1. On isotropic pressure coupling (xzp02 at mails.tsinghua.edu.cn)
   2. box type (sadhna)


---------------------------------------------------------------------- 

Message: 1
Date: Sat, 24 Jul 2004 14:40:44 +0800
From: "" <xzp02 at mails.tsinghua.edu.cn>
Subject: [gmx-users] On isotropic pressure coupling
To: gmx-users at gromacs.org
Message-ID: <290651244.27018 at mails.tsinghua.edu.cn>
Content-Type: text/plain

Dear all:
During simulate a polymer PBC system, I use Berendsen pressure coupling 
method 
to get a configuration, while in the result file I found the Pressure is 
quite 
good as I want. But Pxx, Pyy, Pzz are quite different.
--------------------------------------------------------------
Box_a     Box_b     Box_c
5.97400   5.18700   4.92600
Pressure    Pxx          Pyy         Pzz
-17.807373  1600.537476  505.298706  -2159.258301
--------------------------------------------------------------
Is it physically resonable? Or I should use the anistropic pressure coupling 
to get a pressure tensor as:
[ P/3  0   0 ]
[  0  P/3  0 ]
[  0   0  P/3]
?

   Thanks.


Best,
ZP
---------------------------------------------
Xu ZhiPing
Ph.D Candidate
Office: 3-405
Tel    : +86-10-627-83814
Department of Enginnering Mechanics
Tsinghua University
Beijing, CHINA, 100084
---------------------------------------------  




------------------------------

Message: 2
Date: Sat, 24 Jul 2004 12:31:07 +0530 (IST)
From: sadhna <sadhana at che.iitb.ac.in>
Subject: [gmx-users] box type
To: gmx-users at gromacs.org
Message-ID: <Pine.LNX.4.58.0407241230220.17170 at mercury.che.iitb.ac.in> 
Content-Type: TEXT/PLAIN; charset=US-ASCII

hi,
   Is truncated octahedron box type implemented in GROMACS 3.1

thanks
sadhna

Sadhna Joshi
Research Scholar
Dept of Chemical Engg
Indian Institute of Technology,Powai
Mumbai-400076
India



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