On 1/07/2011 3:35 PM, sulatha M. S wrote:
Hi Tsjerk,
I installed gromacs myself. I put the modified gmx_trjconv.c code in
the /src/tools subdirectory where the source code is located and tried
the command
make trjconv
But it gives me a series of error messages, as given below.
They're all
Thanks Mark,
I will do the analysis in 4.5.4. Hope while doing the micelle clustering I
will not get into a infinite loop as in 4.0.7.
If I understand correctly, While using trjconv -pbc cluster, I should use
-e 0.002 or the frames (-dump option) in the xtc file (generated after the
micelles
Dear Users !
I have took a penta peptide and did topology generation ,
I have solvated it with water box ,
now i did a minimization with zero step , to know the energy of the initial
molecule ,
i used g_energy for the out put ,
like
$ g_energy -f em.edr
it gives as follows , i have
On 1/07/2011 4:40 PM, balaji nagarajan wrote:
Dear Users !
I have took a penta peptide and did topology generation ,
I have solvated it with water box ,
now i did a minimization with zero step , to know the energy of the
initial molecule ,
i used g_energy for the out put ,
like
$
Hello Everyone,
I am using PME(4.05) to calculate the long-rang electrostatic interaction,
but when I finished the
Simulation, I found that I can’t get the result of energy of the part of
“fourier space（long range part）”. In other word，there is only a
congregation of energy of that named Coul.
You can specify the energygrps in mdp file, grompp a new tpr file and use
-rerun
option of the mdrun to get a new edr file
Cheers
Jianguo
From: nishap.pa...@utoronto.ca nishap.pa...@utoronto.ca
To: gmx-users@gromacs.org
Sent: Tuesday, 7 December 2010
On 1/07/2011 5:51 PM, 李浩 wrote:
Hello Everyone,
I am using PME(4.05) to calculate the long-rang electrostatic
interaction, but when I finished the
Simulation, I found that I can’t get the result of energy of the part
of “fourier space（long range part）”. In other word，there is only a
Hi Everyone,
I would like to do some changes to the non bonded parameter of GROMOS force
field. Especially, I like modify the 3rd neighbor parameters. Unfortunately,
I cannot find them in the ffnonbonded.itp file. I assume that the parameter
in [ atomtypes ] block are taken from Table 7
Thank you for your reply! Now can I have your attention for another
quetsion? I'm not very experienced in Visual Studio because I do
almost all of my work under linux. But now it is necessary to compile
gromacs-gpu under windows. Could someone point me to a tutorial or
how-to about step-by-step
Hi Gromacs users,
I created a lipopeptide (lauroic acid connected to an 8-residue peptide
which starts with Valine).
· If I try to use pdb2gmx with -ter flag (Start terminus VAL-2:
None, End terminus ASP-9: COO-), everything seems to work (topology is
created.).
· But, if I
Hello,
I am trying to calculate the velocity autocorrelation function for my
system. I have a system with glucose + ionic liquids (128 emi (cations)
and 128 Cl (anions)).
I am not getting proper velocity autocorrelation function.
g_velacc -f 6.trr -s 6.tpr -n glu-emi-cl-128-no.ndx -nonormalize
Thanks for the reply !
I have tried building the topology with generating the index file
make_ndx -f *
it gave options i have selected the protein and the solvent
then i gave minimization
in the minimization file i have included
energygrps = Protein SOL ,
but the energy file
Otto Master wrote:
Hi Everyone,
I would like to do some changes to the non bonded parameter of GROMOS
force field. Especially, I like modify the 3rd neighbor parameters.
Unfortunately, I cannot find them in the ffnonbonded.itp file. I assume
that the parameter in [ atomtypes ] block are
balaji nagarajan wrote:
Thanks for the reply !
I have tried building the topology with generating the index file
make_ndx -f *
it gave options i have selected the protein and the solvent
An index file is unnecessary for default groups.
Hi Sulatha,
With my clustering algorithm there can be no infinite loop :)
By the way, sorry for the error messages you ran into with compiling
4.0.7. It had escaped me that these changes were made after that
version.
Cheers,
Tsjerk
On Fri, Jul 1, 2011 at 8:29 AM, sulatha M. S
Dear Users,
I'm wondering if it is possible to extract the long-range part of the
interactions of energy-groups. In the output I see only short-range
terms.
I am interested in the total interaction energy of an energy group. I
would guess that one should be able to get the long-range
gyorgy.han...@fc.up.pt wrote:
Dear Users,
I'm wondering if it is possible to extract the long-range part of the
interactions of energy-groups. In the output I see only short-range terms.
I am interested in the total interaction energy of an energy group. I
would guess that one should be
Dear Users !
Now i am able to do the protein solvent interaction !
thanks ! i have understood !
when i used the energygrps ,
when i used the
g_energy -f em.edr
this command it prints all terms and asks to make selection as below,
1 Bond 2 Angle3 Proper-Dih.
balaji nagarajan wrote:
Dear Users !
Now i am able to do the protein solvent interaction !
thanks ! i have understood !
when i used the energygrps ,
when i used the
g_energy -f em.edr
this command it prints all terms and asks to make selection as below,
1 Bond 2 Angle
Dear Users !
i would like to do this to a set of files !
so how to print the required values in the text mode or is there any flag for
this in
g_energy ,
thanks in advance
Date: Fri, 1 Jul 2011 13:40:28 -0400
From: jalem...@vt.edu
To: gmx-users@gromacs.org
Subject: Re:
balaji nagarajan wrote:
Dear Users !
i would like to do this to a set of files !
so how to print the required values in the text mode or is there any
flag for this in
I quoted the help description for how to do this. Is there some problem? For
instance, if you want to write the
Dear users !
thanks for the reply
I was able to do that , otherwise we can select the number of the option one by
one and enter then after that if we leave a empty line and
enter it gives all the needed energy terms !
my intension is not to do like this
is it possible to give it
balaji nagarajan wrote:
Dear users !
thanks for the reply
I was able to do that , otherwise we can select the number of the option
one by one and enter then after that if we leave a empty line and
enter it gives all the needed energy terms !
my intension is not to do like this
is it
Could someone forward the citation of how dVpot/dlambda is calculated
for a free energy run.
I am specifically interested in knowing if it is an analytic or numeric
based calculation.
--
any problemworth attack
proves its worth by fighting back
Dennis Sprous, PhD
BioLeap Inc.
Dennis Sprous, PhD wrote:
Could someone forward the citation of how dVpot/dlambda is calculated
for a free energy run.
I am specifically interested in knowing if it is an analytic or numeric
based calculation.
The equations relevant to free energy calculations are discussed in the
Please make sure to keep the discussion on the gmx-users list.
gyorgy.han...@fc.up.pt wrote:
Thank you very much for the reply.
So I guess the same holds for all Ewald-like long-corrections, right?
Sounds right.
But we don't have this problem with reaction field correction do we?
On 1/07/2011 8:35 PM, Emine Deniz Tekin wrote:
Hi Gromacs users,
I created a lipopeptide (lauroic acid connected to an 8-residue
peptide which starts with Valine).
How is the link from acid to peptide created?
·If I try to use pdb2gmx with -ter flag(Start terminus VAL-2: None,
End
27 matches
Mail list logo
