------------------------------
Message: 3
Date: Wed, 23 Jul 2008 18:14:50 +0430
From: "shahrbanoo karbalaee" <[EMAIL PROTECTED]>
Subject: [gmx-users] Is it correct
To: gmx-users@gromacs.org
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1
Dear justin
In my work MD peptide(with 13 aa) I use this md.mdp.would ypu please
say me Is that correct.
title = cpeptide MD
cpp = /lib/cpp
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 5000 ; total 5 ps.
nstcomm = 1
nstxout = 50
nstvout = 0
nstfout = 0
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tau_t = 0.1 0.1
tc-grps = protein sol
ref_t = 300 300
; Pressure coupling is not on
Pcoupl = no
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
--
2)In the place program doesent have phrase for example PME,....does.
the gromacs use default?
3)when I use berendsen coupling is on and pcoup =yes and In my work is
effect in fluctuate?
best
sh-karbalaee
------------------------------
Message: 4
Date: Wed, 23 Jul 2008 13:54:57 +0000 (GMT)
From: Claus Valka <[EMAIL PROTECTED]>
Subject: Re : [gmx-users] switch potential function gromacs 3.3.2
To: gmx-users@gromacs.org
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset="utf-8"
Dear Sir or Madam,
For the version 3.3.2 the gromacs switch potential function is the following :
Elja1 = (4.d0*eps1*sig1**6) * &
-(1.d0/r(i)**6) * &
(1.d0 - 10.d0 * (r(i)-r1)**3 * 1.d0/(rc1-r1)**3 &
+ 15.d0 * (r(i)-r1)**4 * 1.d0/(rc1-r1)**4 &
- 6.d0 * (r(i)-r1)**5 * 1.d0/(rc1-r1)**5)
Elja2 = (4.d0*eps1*sig1**12) * &
(1.d0/r(i)**12) * &
(1.d0 - 10.d0 * (r(i)-r1)**3 * 1.d0/(rc1-r1)**3 &
+ 15.d0 * (r(i)-r1)**4 * 1.d0/(rc1-r1)**4 &
- 6.d0 * (r(i)-r1)**5 * 1.d0/(rc1-r1)**5)
Switch = Elja1 + Elja2
Remarks:
i) This is tested only when in the mdp file the vdw-type = Switch
ii) The Elja1 is the dispersion part of the potential (not the force).
iii) The Elja2 it the repulsion part of the potential (not the force).
iv) eps is the value of epsilon and sig is the value of sigma
v) r1 = rvdw-switch and rc1 = rvdw
vii) The function of the manual that sais that it applies Phi(r) both on switch
and shift option doesn't seem to apply in the switch case.
vii) Someone can find out if someone searches at :
a)/root/Desktop/software/gromacs/gromacs-3.3.2/src/mdlib/
b)The file is called tables.c
c)look under if (bSwitch), where it sais swi
d)for pow look at the beginning
e)for Vtab under the cases etabLJ6 and etabLJ12
f)for whole under if ((r_r1) && bSwitch) , that is the multiplication of the
dispersion and repulsion part with swi
g)in order to have units of energy someone must to multiply the above with
4*epsilon*sigma**6 for the dispersion part and 4*epsilon*sigma**12 for the
repulsion part
Yours Sincerely,
Nikos
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Message: 5
Date: Wed, 23 Jul 2008 09:58:14 -0400
From: "Justin A. Lemkul" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] new version of C terminus database for charmm
To: sarbani chattopadhyay <[EMAIL PROTECTED]>, Discussion
list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
sarbani chattopadhyay wrote:
Hi,
I am trying to run gromacs with charmm forcefield.
# I had run the perl program "convert_charmm_to_gromacs.pl" and put the
output files
"ffcharmmbon.itp" and "ffcharmmnb.itp" into the gromacs
share/gromacs/top directory.
# I had put all the files from the "tar" file into the share/gromacs/top
directory.
# I had updated the "FF.dat" file to include the charmm file.
# I undersatand that the format of the termini database have changed for
the 3.3.2 version.
I could make the changes in "ffcharmm-n.tdb".
Accordingly I tried to make the changes in "ffcharmm-c.tdb", but when I
give the command
pdb2gmx -f 1aoc.gro -ff charmm -ter
I get the following error
Reading Termini Database: expected 3 items of atom data in stead of 1 on
line
O OC 15.9994 -0.670
I guess the ffcharmm-c.tdb file has not been changed correctly.Has
anyone done it?
I will be grateful if someone can help me in this.
This was a strange error; I remember coming across it as well. No modification
that I could make to that line alleviated the problem, and I still don't know
why. What I ended up doing was changing the [ COO- ] section to the following:
[ COO- ]
[ replace ]
C CC 12.0110 0.340
[ add ]
2 8 O C CA N
OC 15.999 -0.670
[ delete ]
O
[ impropers ]
C CA O2 O1 improper_OB_X_X_CD_
Therefore, instead of replacing O by OC, the O is deleted, and an OC added back
in its place. I don't know why that works, and the "replace" function doesn't,
so maybe someone else has a better idea, but this is how I got around it.
-Justin
Thanks in advance
Sarbani
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 6
Date: Wed, 23 Jul 2008 10:04:36 -0400
From: "Justin A. Lemkul" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Is it correct
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
shahrbanoo karbalaee wrote:
Dear justin
In my work MD peptide(with 13 aa) I use this md.mdp.would ypu please
say me Is that correct.
The definition of "correct" is up to you. I'll give you a few pointers
(embedded below), but the leg-work of determining the validity of the parameters
is your homework, not mine (or anyone else's!)
title = cpeptide MD
cpp = /lib/cpp
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 5000 ; total 5 ps.
nstcomm = 1
nstxout = 50
nstvout = 0
Are you sure you don't want to save velocities every now and again? If your run
crashes because of a hardware problem, you may want to be able to restart it...
What about using nstxtcout? The output file will be greatly compressed relative
to the .trr. It will save a lot of disk space when running analysis.
nstfout = 0
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
All of the parameters from nstlist to rvdw have values that are generally
determined by the force field and its derivation scheme. Check the literature.
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tau_t = 0.1 0.1
tc-grps = protein sol
ref_t = 300 300
As long as you have no ions this is fine.
; Pressure coupling is not on
Pcoupl = no
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
As long as you are expecting an NVT ensemble, this is also fine.
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
Is this .mdp file for equilibration or production? You refer to it as the
md.mdp, but if you're re-generating velocities, I certainly hope this .mdp file
is for the beginning of equilibration. If you re-generate velocities
repeatedly, then you don't get a continuous trajectory.
-Justin
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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