- Original Message -
From: "Justin A. Lemkul"
Date: Friday, June 18, 2010 23:55
Subject: Re: [gmx-users] Plotting Energies versus time
To: Discussion list for GROMACS users
>
>
> Rabab Toubar wrote:
> >Hi,
> >
> >I want to extract the values for potential E, kinetic E, total
> E, an
Lennart Nilsson wrote:
Hi Justin,
In brief:
In practice there is only one CHARMM forcefield - all components work
together; the components happen to have numbers corresponding to the
most recent version of CHARMM at the time this particular component was
produced. The lipid and sugar
Moeed wrote:
for PE. or maybe this dies not affect the results since charges and mass
are the same..?!
You can set the charges to whatever you want them to be, so this is no issue at
all.
Also: can opls_157 be used for both CH3 & CH2,on PE chain? what is the
suitable atom type for car
Dear experts,
For hexane molecule I used atom types
opls_157 12.01100 ; all-atom C: CH3 & CH2, alcohols
opls_158 12.01100 ; all-atom C: CH, alcohols
in residue file:
[ HEX ]
[ atoms ]
C1 opls_157-0.180 1
H11 opls_140 0.060 1
H12 opls_140 0.060 1
On 2010-06-18 20.22, Sikandar Mashayak wrote:
I am concerned about the number density of water. At T = 300 K and P = 1
atm, SPC/E water has certain number density (no. of molecules/nm^3).
With genbox I get .gro file with 34.04 molecules/nm^3 number density,
which will remain constant even if I do
Sai Pooja wrote:
Hi,
I need to use charmm22 all atom force field with gromacs. What would be
the best way to do this?
a) Use perl scripts
If you want CHARMM22, you'll have to implement it yourself. This may require
the use of the Perl scripts that are somewhere on the Gromacs site, but
I am concerned about the number density of water. At T = 300 K and P = 1
atm, SPC/E water has certain number density (no. of molecules/nm^3). With
genbox I get .gro file with 34.04 molecules/nm^3 number density, which will
remain constant even if I do equilibration in NVT simulation set up. So does
Hi,
I need to use charmm22 all atom force field with gromacs. What would be the
best way to do this?
a) Use perl scripts
b) Use a git version in which charmm is implemented
Pooja
--
Quaerendo Invenietis-Seek and you shall discover.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists
On 2010-06-18 18.24, Sikandar Mashayak wrote:
Hi
When a bulk SPC/E water box(.gro) is created using the command "genbox
-cs spc216.gro -box 4.0 4.0 4.0", what is the thermodynamic condition of
water?
Is it 300K at 1atm?
thanks
sikandar
No. You have to equilibrate because the box is not compl
I will re-ask my question as it didn't come out right in previous
mail. Read below.
On Wed, Jun 16, 2010 at 6:11 PM, Mark Abraham wrote:
>
>
> - Original Message -
> From: Gaurav Goel
> Date: Thursday, June 17, 2010 5:21
> Subject: [gmx-users] how small rcoulomb can be
> To: Discussion l
Hi,
There seem to be a problem with pdb2gmx's way of handling c-terminal oxygen
atoms. As far as I understand in the case of G53a6 force field there are two
(excluding [None]) choices:
[ COO- ] with oxygen atoms named 'O1' and 'O2'
[ COOH ] with oxygen atoms named 'O' and 'OT' (and hydrogen atom
Hi
When a bulk SPC/E water box(.gro) is created using the command "genbox -cs
spc216.gro -box 4.0 4.0 4.0", what is the thermodynamic condition of water?
Is it 300K at 1atm?
thanks
sikandar
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Pl
Rabab Toubar wrote:
Hi,
I want to extract the values for potential E, kinetic E, total E, and
temperature from the log file so as to plot them versus time. In NAMD it is
easy to do that using cat |grep, is there a similar way to do it in GMX
That's what g_energy is for.
-Justin
Thanks
Hi,
I need to use charmm22 all atom force field with gromacs. What would be the
best way to do this?
a) Use perl scripts
b) Use a git version in which charmm is implemented
Pooja
--
Quaerendo Invenietis-Seek and you shall discover.
--
gmx-users mailing listgmx-users@gromacs.org
http://list
Hi,
I want to extract the values for potential E, kinetic E, total E, and
temperature from the log file so as to plot them versus time. In NAMD it is
easy to do that using cat |grep, is there a similar way to do it in GMX
Thanks
Rabab Toubar
--
gmx-users mailing listgmx-users@gr
you zou wrote:
Hi again,
Thank you, I added missing atoms with emacs, but my question is this ring
doesn't have to be complete and if I add missing atoms with HIS680's name, I
change its structure. Is it true?
All structures have to be complete in order for pdb2gmx to process them. The
on
Hi again,Thank you, I added missing atoms with emacs, but my question is this
ring doesn't have to be complete and if I add missing atoms with HIS680's name,
I change its structure. Is it true?
> Hi Users,
>
> I have a .pdb file, in this file when I want to use pdb2gmx command
> there is this er
Thanks for your reply Mark.
On Wed, Jun 16, 2010 at 6:11 PM, Mark Abraham wrote:
>
>
> - Original Message -
> From: Gaurav Goel
> Date: Thursday, June 17, 2010 5:21
> Subject: [gmx-users] how small rcoulomb can be
> To: Discussion list for GROMACS users
>
>> For my NPT/NVT simulations I
- Original Message -
From: oguz gurbulak
Date: Friday, June 18, 2010 21:36
Subject: [gmx-users] a query about analysis
To: gmx-users@gromacs.org
---
| - - - > Dear All,
I study on molecular dynamics simulations of or
There are many programs you could use for large data sets, although
I'm not sure how many of them belong to the "excel-like" category.
Personally, I'm quite happy with Matlab and its free-counterpart,
Octave. Both of them can quite easily be made to read matrices and
xvg-files. They are muc
oguz gurbulak skrev:
Dear All,
I study on molecular dynamics simulations of organic molecules. I want
to learn that Is there an excel-like program that accepts more data
set ( for instance output info for 5000 records ) in order to make
analysis ? Could you please give me some suggestions
Dear All,
I study on molecular dynamics simulations of organic molecules. I want to
learn that Is there an
excel-like program that accepts more data set ( for instance output info for
5000
records ) in order to make analysis ? Could you please give me some suggestions
about this issue ?
Tsjerk Wassenaar wrote:
There are no protons in crystal structures.
http://www.rcsb.org/pdb/explore/explore.do?structureId=2VB1
I stand corrected :) In general, though, most crystal structures do not have
resolution sufficient enough to assign hydrogen positions. This one is
especially
Thanasis Koukoulas skrev:
Hello
[ atomtypes ]
; type mass charge ptype c6 c12
CH3 15.035 0.000 A 9.0638e-3 2.5206e-5
CH2 14.027 0.000 A 5.8108e-3 2.2071e-5
CS2 14.027 0.000 A 5.8108e-3 2.2071e-5
OS 15.999 0.000 A 8.8147e-4 4.2477e-7
OA 15.999 0.000 A 2.3465e-3 1.7802e-6
HO 1.008 0.000 A 0.e0
- Original Message -
From: Thanasis Koukoulas
Date: Friday, June 18, 2010 19:55
Subject: [gmx-users] Question about topologies
To: gmx-users@gromacs.org
---
| > Hello
> [ atomtypes ]> ; type masschargeptype c6
Hello
[ atomtypes ]; type mass charge ptype c6 c12
CH3 15.035 0.000 A 9.0638e-3 2.5206e-5 CH2 14.027
0.000 A 5.8108e-3 2.2071e-5 CS2 14.027 0.000 A
5.8108e-3 2.2071e-5 OS 15.999 0
Hi,
shake_tol sets the relative tolerance of the constraint lengths.
This means that the constraints should not differ more than +-shake_tol
after constraining: for example a constraint of length 0.1 nm with
shake_tol=1e-4
should be between 0.0 and 0.10001 nm.
Note that the settings in your
Hi Abdul,
please keep Gromacs-related questions on the list. The error
is exactly as printed: You have more than 128 backups of md.log
in your directory, at this point mdrun does not make more backups
of md.log any more. You have to delete the #md.log.*# files.
Carsten
On Jun 18, 2010, at 7:24
I don't who does not get it right. My constraints work and
it does change when I comment out the constraints. I put
the constraints right there they write it in the
Documentation. I do not even include water.itp. My question
is how I can constrain the bonds more rigid. And for this I
would like to
> There are no protons in crystal structures.
http://www.rcsb.org/pdb/explore/explore.do?structureId=2VB1
--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands
--
g
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