Dear all,
I would like to ask whether it is possible to decompose the GB/SA
contributions of an implicit solvent md run in a per-residue/domain basis
(like the LJ and Coloubic terms)?
I haven't seen these terms decomposed in the md.edr output file.
Thank you,
Boaz
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gmx-users mailing list
Hello again
In my protein-membrane-water-ion system (inserted via g_membed) I have run
a 1ns NVT equilibration with the protein restrained and now I am trying to
equilibrate with NPT and LINCS/mdrun is crashing after about 5000 iterations.
Here is my NPT mdp file:
define
Peter C. Lai wrote:
Hello again
In my protein-membrane-water-ion system (inserted via g_membed) I have run
a 1ns NVT equilibration with the protein restrained and now I am trying to
equilibrate with NPT and LINCS/mdrun is crashing after about 5000 iterations.
Here is my NPT mdp file:
On 2011-04-08 08:02:14AM -0500, Justin A. Lemkul wrote:
Peter C. Lai wrote:
Hello again
In my protein-membrane-water-ion system (inserted via g_membed) I have run
a 1ns NVT equilibration with the protein restrained and now I am trying to
equilibrate with NPT and LINCS/mdrun is
Peter C. Lai wrote:
On 2011-04-08 08:02:14AM -0500, Justin A. Lemkul wrote:
Peter C. Lai wrote:
Hello again
In my protein-membrane-water-ion system (inserted via g_membed) I have run
a 1ns NVT equilibration with the protein restrained and now I am trying to
equilibrate with NPT and
On 2011-04-08 08:16:19AM -0500, Justin A. Lemkul wrote:
Peter C. Lai wrote:
On 2011-04-08 08:02:14AM -0500, Justin A. Lemkul wrote:
Peter C. Lai wrote:
Hello again
In my protein-membrane-water-ion system (inserted via g_membed) I have
run
a 1ns NVT equilibration with the
Peter C. Lai wrote:
On 2011-04-08 08:16:19AM -0500, Justin A. Lemkul wrote:
Peter C. Lai wrote:
On 2011-04-08 08:02:14AM -0500, Justin A. Lemkul wrote:
Peter C. Lai wrote:
Hello again
In my protein-membrane-water-ion system (inserted via g_membed) I have run
a 1ns NVT equilibration with
Hi Gromacs users,
I want to covalently link the lauroic acid to the Valine residue (it is a
peptide (amide) bond), I know that I should update the specbond.dat. But
before updating this file, I need the NH as an N terminal of the first
residue (Valine). When I used pdb2gmx with the –ter flag,
Hey
One of the developers write to me. Everyone who is using that code is having
the same problem. This is his answer:
You are right 'CPMD sleeps' expecting further communication from Gromacs.
This part was not taken care of in the current version. We are working on a
newer version with
http://jtemplin.de/limpallo.html--
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Dear All,
I am trying to simulate the interaction between DNA, and CNT. But when I try to
create the toplogy file with command
g_x2top -f ssdna.gro -o ssdna.top -ff select, I get the following error: Fatal
error: Could only find a forcefield type for 119 out of 287 atoms
I am using the
majid hasan wrote:
Dear All,
I am trying to simulate the interaction between DNA, and CNT. But when I
try to create the toplogy file with command
g_x2top -f ssdna.gro -o ssdna.top -ff select, I get the following error:
Fatal error: Could only find a forcefield type for 119 out of 287
Thanks Justin!
But with pdb2gmx, after selecting force field and water model, I get this
error:
Fatal Error: Residue 'DA3' not found in residue topology (on selecting oplsaa),
and when I selected amber99, I got following fatal error: there is a dangling
bond at at least one of the terminal
majid hasan wrote:
Thanks Justin!
But with pdb2gmx, after selecting force field and water model, I get
this error: Fatal Error: Residue 'DA3' not found in residue topology (on
selecting oplsaa), and when I selected amber99, I got following fatal
Right, there are no nucleic acids in
Okay, I'll try to create a better .pdb file, and see how it goes. So if oplsaa
doesn't have nucleic acids, then Amber is a better choice?
Thanks,
Majid
From: Justin A. Lemkul jalem...@vt.edu
To: Gromacs Users' List gmx-users@gromacs.org
Sent: Fri, April 8,
majid hasan wrote:
Okay, I'll try to create a better .pdb file, and see how it goes. So if
oplsaa doesn't have nucleic acids, then Amber is a better choice?
A force field should be chosen based on thorough study of the literature,
including the derivation of the parameter sets and their
Yes, of course. But right now I am just trying to make sure that my input files
are all correct, and then I will dig into these actual forcefields.
Thanks a lot,
Majid
From: Justin A. Lemkul jalem...@vt.edu
To: Gromacs Users' List gmx-users@gromacs.org
Sent:
Hi all,
I looked at source code in /src/mdlib/genborn.c and have two questions
regarding the Still implicit solvent model.
1. in the function calc_gb_chainrule(), only Still model have extra factor
of 2 apply on dvda, which I don't know why.
2. in calc_gb_rad_still(), does dccf miss a factor of
majid hasan wrote:
I looked at the error in more detail (output attached), and it says
that: Warning: Residue T6 in chain has different type (Other) from
starting residue A1 (RNA). I had a dna.pdb file so first but its reading
the first residue as RNA.
So to me, problem seems to be that
Dear Chi-Xheng,
We have tried GB module in gromacs, but unfortunately we found something wrong
with it.
What we found is that the results got from gromacs were quite different from
those obtained from AMBER codes.
We did not check in details why.
Yuguang
From: gmx-users-boun...@gromacs.org
Hello,
Right now I'm trying to perform a REMD simulation of a poly-alanine peptide,
using 43 replicas ranging from 300-500 K. the procedure I'm using is the
following:
1. Energy minimization of the peptide in vacuum
2. generation of the simulation box. a dodecahedron box.
3. filling the
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