Thank you for responce and explanation!
So is it a good alghorithm to use gromacs genrestr command and then
include this posre.itp file into topology (without any changes) after
insertion of a ligand.itp?
Thank you in advance
On 4/2/13 6:07 AM, alex rayevsky wrote:
Dear All!
I have a doubt
On Wed, Apr 3, 2013 at 4:56 AM, Elisabeth katesed...@gmail.com wrote:
Hi Vitaly,
I realize that when one extends the Z direction the resulting interface is
liquid-vacuum, but I see that even at T below boiling point some molecules
still leave the interface and enter the empty zone and are
Dear gmx,
I have tried in both (32 and 64 bit cygwin) format in my win7 -64 bit system
but both gave me the compiler gcc-broken as follows :
-- Check for working C compiler: /usr/bin/gcc-4.exe -- broken (32 bit)
-- Check for working C compiler: /usr/bin/gcc.exe -- broken (64 bit)
--
Yes.
On 3 Apr 2013, at 04:07, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote:
Hello,
I am calculating the hydrogen bond life time for my system.
Do program consider the hydrogen bond criteria for calculation of
autocorrelation function?
Nilesh
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Dear users,
I will run MD simulations of all water models in Gromacs. I need spce.gro
and tip3p.gro files. How can I find them?
Thanks in advance
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Ahmet Yıldırım
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On 4/3/13 2:36 AM, alex rayevsky wrote:
Thank you for responce and explanation!
So is it a good alghorithm to use gromacs genrestr command and then
include this posre.itp file into topology (without any changes) after
insertion of a ligand.itp?
As long as you use a suitable input file for
On 4/3/13 6:26 AM, Ahmet yıldırım wrote:
Dear users,
I will run MD simulations of all water models in Gromacs. I need spce.gro
and tip3p.gro files. How can I find them?
These don't exist within Gromacs. Since SPC, SPC/E, and TIP3P are all 3-point
water molecules, just use spc216.gro and
After reading the manual and trying to find more information on the mailing
list. I'm still not sure about this 1-4 interactions, when I want to calculate
the energy between two groups (lets say one residue and the rest of the
protein) should I sum everything (including the 1-4 interactions) or
On 4/3/13 7:16 AM, Liron Cohen wrote:
After reading the manual and trying to find more information on the mailing
list. I'm still not sure about this 1-4 interactions, when I want to calculate
the energy between two groups (lets say one residue and the rest of the
protein) should I sum
I am using PME, can you elaborate about the decomposing you mentioned?
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin Lemkul [jalem...@vt.edu]
Sent: Wednesday, April 03, 2013 2:32 PM
To: Discussion list for GROMACS
On 4/3/13 7:49 AM, Liron Cohen wrote:
I am using PME, can you elaborate about the decomposing you mentioned?
The mesh term includes all long-range interactions and is not broken down, even
in the presence of energygrps in the .mdp file. Some time ago, someone posted a
method of several
Dear Gromacs users!
I want to simulate Cytochrome C in complex with HEM using NMR full-atom
structure of that protein as the starting conformation and charm36 force
field's parameters.
in the charm36 ff I've found parameters for HEM but I have not found params
for the hydrogens (in the
On Wed, Apr 3, 2013 at 8:24 AM, James Starlight jmsstarli...@gmail.comwrote:
Dear Gromacs users!
I want to simulate Cytochrome C in complex with HEM using NMR full-atom
structure of that protein as the starting conformation and charm36 force
field's parameters.
in the charm36 ff I've
hmm
I've done parametrization of the hem using standart charmm36 parameters but
indeed there is some confusing with the hydrogens
for example my pdb (obtained from NMR structure) consist of 2 extra
hydrogens (which both parts of the methyl groups) which are not present in
the rtp parameters. So
Does other compiling with these compilers work?
Mark
On Wed, Apr 3, 2013 at 10:12 AM, 라지브간디 ra...@kaist.ac.kr wrote:
Dear gmx,
I have tried in both (32 and 64 bit cygwin) format in my win7 -64 bit
system but both gave me the compiler gcc-broken as follows :
-- Check for working C
http://www.satoriholistichealth.com/uws/wd.fto?ntw
Wholly Peach
4/3/2013 2:39:18 PM
rl
4/3/2013 2:39:18 PM
Wholly Peach
--
sorry it was mistake :)
assuming that heme is covalently bonded to the cytochrome by means of 2
cysteines how should I define such bindings (assuming that heme is part of
my protein) based onb the charmm parameters ?
its not clear for me why such connection is absent in the residue.dat
(having
I've successfully parametrize cytochrome-HEME complex by means pdb2gmx but
after processing that structure to grompp I've obtained errors like
ERROR 1 [file topol.top, line 2106]:
No default Bond types
ERROR 2 [file topol.top, line 2144]:
No default Bond types
ERROR 3 [file topol.top,
On Wed, Apr 3, 2013 at 10:27 AM, James Starlight jmsstarli...@gmail.comwrote:
I've successfully parametrize cytochrome-HEME complex by means pdb2gmx but
after processing that structure to grompp I've obtained errors like
ERROR 1 [file topol.top, line 2106]:
No default Bond types
ERROR 2
Hi,
I have a polymer box on which I wish to apply energy minimization. However,
when I do energy minimization runs to polymer chain unravels and goes out
of the box. I guess this is because periodic conditions are not applied.
My em.mdp file is:
;
cpp = /usr/bin/cpp
define
I want to use both steepest descent and conjugate gradient in my energy
minimization. I need the system to use steepest descent for a given number
of steps and then switch over to conjugate gradient. Can anyone please
suggest how I can do this? How should I make the em.mdp file
Thanks in
On Wed, Apr 3, 2013 at 11:07 AM, Abhinav Agrawal abhv.a...@gmail.comwrote:
I want to use both steepest descent and conjugate gradient in my energy
minimization. I need the system to use steepest descent for a given number
of steps and then switch over to conjugate gradient. Can anyone please
On Wed, Apr 3, 2013 at 10:51 AM, Abhinav Agrawal abhv.a...@gmail.comwrote:
Hi,
I have a polymer box on which I wish to apply energy minimization. However,
when I do energy minimization runs to polymer chain unravels and goes out
of the box. I guess this is because periodic conditions are not
Dear Gromacs users,
can you help me please with next issue:
I'm analysing solvation shell of water molecules around a protein.
I use g_select to select different layers of water based on distance
criteria.
The output index file contains all the atoms which satisfy the specified
criteria.
For
There is no outside of the box.
Tsjerk
On Wed, Apr 3, 2013 at 4:51 PM, Abhinav Agrawal abhv.a...@gmail.com wrote:
Hi,
I have a polymer box on which I wish to apply energy minimization. However,
when I do energy minimization runs to polymer chain unravels and goes out
of the box. I guess
Dear users,
This is regarding an observation while calculating the
salt bridge (sb) using g_saltbr.
I used g_saltbr and g_hbond (with contact option) with
a cut of of 4Ang, for calculating sb in the whole protein
at a single frame.
I made sure that I considered sb between same set of
residues
On Wed, Apr 3, 2013 at 12:50 PM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
This is regarding an observation while calculating the
salt bridge (sb) using g_saltbr.
I used g_saltbr and g_hbond (with contact option) with
a cut of of 4Ang, for calculating sb in the whole protein
at a
Hello GMX users, I just wanted to share a python library I made that may be
of help to someone. It includes a molecular viewer and native parsing of
xtc and edr files.
Go check it out! http://chemlab.github.com/chemlab
Thank you
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On 4/3/13 11:13 AM, Oleksandr Sushko wrote:
Dear Gromacs users,
can you help me please with next issue:
I'm analysing solvation shell of water molecules around a protein.
I use g_select to select different layers of water based on distance criteria.
The output index file contains all the atoms
Dear GMX users,
I am not sure if someone has similar problems before. I cannot read half of
the frames from trr file after md simulation, and I believe my simulation
has already completed.
I have finished simulations A and B with both gmx4.5.4 and gmx4.5.5. the
only difference between A and B is
Sorry for the typo, the last evidence4) I also compared the generated
files' sizes, A = B in trr, edr , gro, cpt, if B crashes before reaching
100ns, the size would **NOT*** be the same as A.
On Wed, Apr 3, 2013 at 7:25 PM, mu xiaojia muxiaojia2...@gmail.com wrote:
Dear GMX users,
I am not
On 4/3/13 8:42 PM, mu xiaojia wrote:
Sorry for the typo, the last evidence4) I also compared the generated
files' sizes, A = B in trr, edr , gro, cpt, if B crashes before reaching
100ns, the size would **NOT*** be the same as A.
You probably have a corrupted frame. The simulation continued
Hi,
I have a polymer box on which I wish to apply energy minimization.
However,
when I do energy minimization runs to polymer chain unravels and goes out
of the box. I guess this is because periodic conditions are not applied.
My em.mdp file is:
;
cpp =
Hello all,
Does anyone know how one can study the effect of pressure on surface
tension of pure liquids?
Thanks,
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Sir,
That is true, previously you had explained regarding this.
Calculation using g_saltbr
1. For g_saltbr I included the following residues -
ASP, HIS, ARG, LYS, GLU. A trajectory and tpr was generated
which contained only these residues. sb was calculated using -
g_saltbr -f
It was strange for me the big number of such errors :)
May the construction of new scheme for the hydrogens in the .hdb file
partly solve my problem ? ( as I've mentioned previously i had mismatch in
2 hydrogens ( in comparison to the NMR-like structure).
Should also HEME be added in the
i followed the following steps to install gromacs :
1. Download cygwin from http://www.cygwin.com/ .Installed packages including
gdb, make and tcsh
NOTE : i was not able to find package gdn
2. Downloaded GROMACS (gromacs-4.0.7) source code.
3. Downloaded fftw-3.2.1.tar.gz
4. Extracted to
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