Dear users,
Before energy minimization step , I performed the preprosessing step using
grompp .
However, there are two note that :
*NOTE 1 [file topol.top, line 52]:*
System has non-zero total charge: -1.50e+01
*NOTE 2 [file topol.top]:*
The largest charge group contains 11 atoms.
Hi Ahmet,
As suggested, it's better to break up your molecule into smaller
charge groups. Note that charge groups don't need to have zero charge,
nor integer charge. In your case, I'd suggest two COH groups for EDO,
which will have zero net charge each, and for TRS I'd take the COH
groups as
On 31/03/2011 5:18 PM, ahmet y?ld?r?m wrote:
Dear users,
Before energy minimization step , I performed the preprosessing step
using grompp .
However, there are two note that :
*_NOTE 1 [file topol.top, line 52]:_*
System has non-zero total charge: -1.50e+01
This is an integer. See
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Dear Tsjerk,
I will ask you one thing but please do not get angry (I know you are not a
private tutor but I need your helps).
How do I apply on the files (EDO.itp and TRS.itp) that you said? (or can you
suggest a tutorial?)
Thanks
2011/3/31 Mark Abraham mark.abra...@anu.edu.au
On 31/03/2011
On Wed, 2011-03-30 at 20:23 +0200, David van der Spoel wrote:
On 2011-03-30 20.16, Nilesh Dhumal wrote:
Thanks.
How can I take average.
summing up and dividing by the number of sims.
How much long I should run the simulation.
until the average converges.
Nilesh
On Wed, March
On 31/03/2011 6:17 PM, ahmet yıldırım wrote:
Dear Tsjerk,
I will ask you one thing but please do not get angry (I know you are
not a private tutor but I need your helps).
How do I apply on the files (EDO.itp and TRS.itp) that you said? (or
can you suggest a tutorial?)
You'll need to
in advance
--
Ahmet YILDIRIM
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On 2011-03-31 09.25, Dommert Florian wrote:
On Wed, 2011-03-30 at 20:23 +0200, David van der Spoel wrote:
On 2011-03-30 20.16, Nilesh Dhumal wrote:
Thanks.
How can I take average.
summing up and dividing by the number of sims.
How much long I should run the simulation.
until the average
Hi Ahmet,
Why would I get angry? :) Sending a reply to the list will not usually
be taken as asking for private tutoring...
As Mark pointed out, you need to get familiar with the format of the
files. That's the first thing you should do if you get to the point of
needing to use non standard
On Thu, 2011-03-31 at 10:39 +0200, David van der Spoel wrote:
On 2011-03-31 09.25, Dommert Florian wrote:
On Wed, 2011-03-30 at 20:23 +0200, David van der Spoel wrote:
On 2011-03-30 20.16, Nilesh Dhumal wrote:
Thanks.
How can I take average.
summing up and dividing by the number of
Hi All
I have generated several PMF curves for the one system using umbrella
sampling. In the first part of the curve (barrier region) I use a high
force constant with small intervals between the windows. The latter part
of the curve I use a lower force constant with larger window spacing.
Anyway
On Mar 31, 2011, at 11:53 AM, Gavin Melaugh wrote:
Hi All
I have generated several PMF curves for the one system using umbrella
sampling. In the first part of the curve (barrier region) I use a high
force constant with small intervals between the windows. The latter
part
of the curve I use
Dear all,
I intend to run a simulation for a membrane protein. As per a tutorial, i
require a lipid bilayer and some (.itp) files for editing manually a toplogy
file for the lipid bilayer. Question is how do I choose the appropriate
lipid bilayer and its subsequent (.itp) file? Also, what are the
Hi Xavier
Thanks for the reply. With respect to your answer of my first query.
What if you had two windows practically on top of each other, but one
was not supposed to be there. e.g A window with r0 of 0.80 nm and
centred at 0.78 nm and a window with r0 of 0.78 nm centred at 0.78nm.
Gavin
Raghuvir R S Pissurlenkar wrote:
Dear Justin
I removed the constrain on the DPPC molecules, however I find still
LINCS errors are prominent
Any alterative can I try
Reduce the pull_rate. If you pull too fast, your system cannot adapt properly
to the collisions that are induced by the
On 31/03/11, Nishith Saurav Topno nto...@bicpu.edu.in wrote:
Dear all,
I intend to run a simulation for a membrane protein. As per a tutorial, i
require a lipid bilayer and some (.itp) files for editing manually a toplogy
file for the lipid bilayer. Question is how do I choose the
Dear all,
I am trying to do a QM/MM calculation with gromacs/CPMD. When I try to use a
parallel version of mdrun and CPMD I get a segmentation fault.
I have seen in the examples that LAM is used in runcpmd. It is mandatory for
parallel runs?
I do not have this problem when I run just CPMD in
You can present the data differently:
you have two windows at 0.78 nm giving different distribution.
That indicates these windows are not converged. Does not mean
that the others (0.80 nm) are converged :))
On Mar 31, 2011, at 12:20 PM, Gavin Melaugh wrote:
Hi Xavier
Thanks for the reply.
On 31/03/11, Elena Formoso elena.form...@phys.chem.ethz.ch wrote:
Dear all,
I am trying to do a QM/MM calculation with gromacs/CPMD. When I
try to use a parallel version of mdrun and CPMD I get a segmentation fault.
I have seen in the examples that LAM is used in runcpmd. It is mandatory
Sorry I am not sure that I follow. Will the window with r0 =0.80 giving
the distribution centred around 0.78nm not drive my free energy profile
up. If I remove this window prior to running g_wham the free energy goes
down. Should I increase the force constant so that the mean of the
window is
Hi Elena,
if you use GMX/CPMD in parallel, you can use any mpi implementation, but
you should start GMX on a single core and CPMD in parallel (via
runcpmd). You can not run both in parallel.
Greets,
Christian
On Thu, 2011-03-31 at 13:05 +0200, Elena Formoso wrote:
Dear all,
I am trying to do
Thanks Christian
That is why it was not working. It is not possible to run both in parallel
Cheers
Elena
On Thu, Mar 31, 2011 at 1:14 PM, Christian Seifert
cseif...@bph.ruhr-uni-bochum.de wrote:
Hi Elena,
if you use GMX/CPMD in parallel, you can use any mpi implementation, but
you
Gavin Melaugh wrote:
Sorry I am not sure that I follow. Will the window with r0 =0.80 giving
the distribution centred around 0.78nm not drive my free energy profile
up. If I remove this window prior to running g_wham the free energy goes
down. Should I increase the force constant so that the
Dear All,
I am running MD simulations of an Alcohol Dehydrogenase ( a tetramer) with
the bound NADPH in explicit solvent. I am employing GROMOS96 43a1 force
field for the simulations. I need a clarification on the CUT-OFFs applicable
for this force field. I have seen many people using *rvdw = 1.4*
Thanks Justin for the reply
Gavin
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
Sorry I am not sure that I follow. Will the window with r0 =0.80 giving
the distribution centred around 0.78nm not drive my free energy profile
up. If I remove this window prior to running g_wham the free energy
Kishore wrote:
Dear All,
I am running MD simulations of an Alcohol Dehydrogenase ( a tetramer)
with the bound NADPH in explicit solvent. I am employing GROMOS96 43a1
force field for the simulations. I need a clarification on the CUT-OFFs
applicable for this force field. I have seen many
My bad, I red to quick and though you had three windows ...
you should follow Justin's advice.
On Mar 31, 2011, at 2:20 PM, Gavin Melaugh wrote:
Thanks Justin for the reply
Gavin
Justin A. Lemkul wrote:
Gavin Melaugh wrote:
Sorry I am not sure that I follow. Will the window with r0 =0.80
Thanks Flo for detail reply.
Is it possible to put PBC off during calculation of dipole moment
autocorrelation function.
I will run the simulation for 50ns ans try to save trajectroy of 0.02ps.
Thanks
NIlesh
Nilesh
On Thu, March 31, 2011 5:38 am, Dommert Florian wrote:
On Thu, 2011-03-31 at
On Thu, 2011-03-31 at 08:53 -0400, Nilesh Dhumal wrote:
Thanks Flo for detail reply.
Is it possible to put PBC off during calculation of dipole moment
autocorrelation function.
No, thats the problem, because the volume of the system will increase
and dipole density will decrease, this not
Hi there,
Since ILDN dihedrals has some parameters with up to periodicity 6, I was
wondering if it's possible to convert it in RB with 6 coefficients. If so,
what would be the formula? For example, for converting the usual Amber99SB
to RB I have:
if phase in [0, 180]:
Dear all,
I tryed to use couple-moltype=Protein Ligand directive
to annihilate both protein and ligand molecules using free energy method.
I realized that couple-moltype key works for only one molecule type.
Is it right?
To perform the same annihilation I used
couple-moltype=Protein to
Dear all,
I tryed to use couple-moltype=Protein Ligand directive
to annihilate both protein and ligand molecules using free energy method.
I realized that couple-moltype key works for only one molecule type.
Is it right?
To perform the same annihilation I used
couple-moltype=Protein to
Dear all,
I tryed to use couple-moltype=Protein Ligand directive
to annihilate both protein and ligand molecules using free energy method.
I realized that couple-moltype key works for only one molecule type.
Is it right?
To perform the same annihilation I used
couple-moltype=Protein to
I know it's supported.
I was just investigating the possibility since I build acpype to create
topologies for gromacs, but also it converts from amber to gromacs (like
amb2gmx.pl), and so I was wondering about RB with 6 coefficients since
multiple proper dihedrals is only supported for gmx 4.5
On 2011-03-31 17.19, Alan Wilter Sousa da Silva wrote:
I know it's supported.
I was just investigating the possibility since I build acpype to create
topologies for gromacs, but also it converts from amber to gromacs (like
amb2gmx.pl http://amb2gmx.pl), and so I was wondering about RB with 6
can you show us your mdp and the pmf and the histograms for the data
that you put into wham? It's a lot easier to diagnose with the real
data.
In the general case where umbrellas are spaced equally along your
reaction coordinate, sampling overlap between umbrellas will always
decrease
Hi Chris many thanks again for the advise. I have, or at least I thought
have sampled my barrier region to death, but as I say some histograms
may not be centred around r0. I will proceed with what you suggest.
Please find attached a picture of the histograms, the corresponding
profile, and a
Here is also the sample .mdp file
chris.ne...@utoronto.ca wrote:
can you show us your mdp and the pmf and the histograms for the data
that you put into wham? It's a lot easier to diagnose with the real data.
In the general case where umbrellas are spaced equally along your
reaction
.
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in your mail:
On 30 March 2011 15:30, Justin A. Lemkul jalem...@vt.edu wrote:
Elisabeth wrote:
Dear all,
I intend to obtain vaporization heat per volume for a /pure alkane
system/. Here is the steps I am taking. Please correct me.
1- Obtain total energy of system (kinetic+potential)
Elisabeth wrote:
in your mail:
On 30 March 2011 15:30, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Elisabeth wrote:
Dear all,
I intend to obtain vaporization heat per volume for a /pure
alkane system/. Here is the steps I am taking.
On 2011-03-31 18.52, Elisabeth wrote:
in your mail:
On 30 March 2011 15:30, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Elisabeth wrote:
Dear all,
I intend to obtain vaporization heat per volume for a /pure
alkane system/. Here is the steps
Hi folks,
I have a problem with a strange residue into a PDB file. It is a
cysteinesulfonic acid, in which the -SH moiety of the Cys residue is
replaced by -SO3. This modified residue is essential for the activity of
this protein, therefore I must keep it into the protein. So, I'm trying to
add
On 31 March 2011 12:58, Justin A. Lemkul jalem...@vt.edu wrote:
Elisabeth wrote:
in your mail:
On 30 March 2011 15:30, Justin A. Lemkul jalem...@vt.edu mailto:
jalem...@vt.edu wrote:
Elisabeth wrote:
Dear all,
I intend to obtain vaporization heat per volume for
Dear all,
When GMX is builded with cmake, how to compile the template.c? I used
to make the template.c by the command make -f MakefileXXX, but it
can not work in version 4.5. Thanks for your suggestions.
Best regards,
Bert
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Elisabeth wrote:
On 31 March 2011 12:58, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Elisabeth wrote:
in your mail:
On 30 March 2011 15:30, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu mailto:jalem...@vt.edu
On 2011-03-31 19.11, Elisabeth wrote:
On 31 March 2011 12:58, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
Elisabeth wrote:
in your mail:
On 30 March 2011 15:30, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu mailto:jalem...@vt.edu
your comment:
which should be centred around 0.80nm
is flawed, as i mentioned earlier. also, it is not g_wham that is
sensitive but the convergence and sampling of phase space that is
sensitive. don`t remove any data. do evaluate your convergence.
without convergence measures, a pmf is
Hi,
It would probably be easier, faster, and more accurate to just use most of
the parameters for Cys rather than try to have PRODRG re-create a
(potentially flawed) model of your compound. The only new parameters are
related to SO3, so the rest should be identical to the Cys residue.
Tsjerk Wassenaar wrote:
Hi,
It would probably be easier, faster, and more accurate to just use most of
the parameters for Cys rather than try to have PRODRG re-create a
(potentially flawed) model of your compound. The only new parameters are
related to SO3, so the rest should be identical
I ran into some issues with the Gromacs web site:
1. I tried to register an account on the bug tracker
(http://redmine.gromacs.org/account/register). Upon entering my
information, I get the odd error message Email notifications is not
included in the list. Perhaps this is related to
Hi,
I have been tracking the code for implicit solvent,
i.e. src/mdlib/genborn.c
According to the gromacs paper on implicit solvent, J Comp Chem 31:2593,
2010, the GB force is tabulated in the X = Rij Ci Cj dimension.
However, the tabulated function, which I think is stored in fr-gbtab, is
only
Hello,
Is there a way we can apply a spatially varying external force in
GROMACS. I went through the manual if anything like this is possible
but couldn't find anything.
Any help is appreciated.
Apoorv
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Hi!
The tabulated function is applied to all interactions, both bonded and
non-bonded. The function is initialized in make_gb_table(), and accessed in the
non-bonded kernels the same way as other tabulated functions are accessed. See
GBtab[nnn] in the kernels for more details.
In
Dear all,
I tried to use couple-moltype=Protein Ligand directive
to annihilate both protein and ligand molecules using free energy method.
I realized that couple-moltype key works for only one molecule type.
Is it right?
To perform the same annihilation I used
couple-moltype=Protein to
Hi Lutz,
On 3/31/11 9:06 PM, Lutz Maibaum wrote:
I ran into some issues with the Gromacs web site:
1. I tried to register an account on the bug tracker
(http://redmine.gromacs.org/account/register). Upon entering my
information, I get the odd error message Email notifications is not
included
Hi
I want to test two test potentials compared to reference potential.
I have md trajectories from reference potential. So I do mdrun -rerun with
two different test potentials and get two separate trajectory files. Now I
want to compute difference between forces acting on each atom in each frame
Sikandar Mashayak wrote:
Hi
I want to test two test potentials compared to reference potential.
I have md trajectories from reference potential. So I do mdrun -rerun
with two different test potentials and get two separate trajectory
files. Now I want to compute difference between forces
hey thanks for the explanation..
for some constraints I need to have the difference of forces in the .trr
format so that I have position,velocity and force error values in one single
.trr file. , I dont think g_traj would help me getting that.. is there any
other option?
On Thu, Mar 31, 2011 at
Sikandar Mashayak wrote:
hey thanks for the explanation..
for some constraints I need to have the difference of forces in the
.trr format so that I have position,velocity and force error values in
one single .trr file. , I dont think g_traj would help me getting that..
is there any other
Greetings,
I am trying to do Martini Forcefield + Implicit solvation model for a
large system and I need to supply parameters for the
[ implicit_genborn_params ]
section. Which I have not found.
The syntax is
Atomtype sar st pi gbr hct
Can anybody provide me a clue about where I can find these
On 1/04/2011 9:29 AM, emen...@ucalgary.ca wrote:
Greetings,
I am trying to do Martini Forcefield + Implicit solvation model for a
large system and I need to supply parameters for the
[ implicit_genborn_params ]
section. Which I have not found.
The syntax is
Atomtype sar st pi gbr hct
Can
Thanks for your promt reply Mark.
Of course I know what is the format, that is implied in my question
what I would like to know is if anybody has the specific parameters for
the amber forcefield. I will try using the gbr parameters from the sigma
in the LJ potentials, but I am not sure about
Hi...
I am try to istalling gromacs -4.5.3 on AMD phenom II.
I am following the installtions protocols, 1 St i have installed the fftw3.2.2,
./configure --enable-threads --enables-floats --enables-sse
make
make install
then I am doing the cmake.
cd gromacs-4.5.3
mkdir exec
cd exec
cmake ../
I meant to say, the MARTINI parameters,
regards
E
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Hi,
this question has been answered often. Please check the archive before
posting.
Roland
On Thu, Mar 31, 2011 at 8:01 PM, parichita parichita
parichitamajum...@yahoo.co.in wrote:
Hi...
I am try to istalling gromacs -4.5.3 on AMD phenom II.
I am following the installtions protocols, 1 St
Hi,
I have a long-chain peptide which has a net charge of +5 . I was wondering
whether the g_dipole will give any reasonable dipole moment for a molecule with
a net charge. Is there any suggestion I should follow regarding calculation of
dipole-moment of a charged molecule .
I found that
Hi,
This is regarding the energygroups that one can use in the mdp file for
tracking energy. Are these the groups defined in the index file?
I want to know if I can define a subset of atoms in the index file and track
its energy.
Pooja
--
Quaerendo Invenietis-Seek and you shall discover.
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On 1/04/2011 11:01 AM, parichita parichita wrote:
Hi...
I am try to istalling gromacs -4.5.3 on AMD phenom II.
I am following the installtions protocols, 1 St i have installed the
fftw3.2.2,
./configure --enable-threads --enables-floats --enables-sse
That's not how you successfully
On 1/04/2011 1:30 PM, Sai Pooja wrote:
Hi,
This is regarding the energygroups that one can use in the mdp file
for tracking energy. Are these the groups defined in the index file?
Yes, the groups are defined there (or created by default if an index
file is not supplied) and specified as
On 1/04/2011 10:57 AM, emen...@ucalgary.ca wrote:
Thanks for your promt reply Mark.
Of course I know what is the format, that is implied in my question
Leaving things to implication is risky. People do misunderstand,
unfortunately. Fault in such cases varies :-) If what you actually want
On Thu, Mar 31, 2011 at 10:41 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 1/04/2011 1:30 PM, Sai Pooja wrote:
Hi,
This is regarding the energygroups that one can use in the mdp file for
tracking energy. Are these the groups defined in the index file?
Yes, the groups are defined
On 1/04/2011 2:06 PM, Sai Pooja wrote:
On Thu, Mar 31, 2011 at 10:41 PM, Mark Abraham
mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote:
On 1/04/2011 1:30 PM, Sai Pooja wrote:
Hi,
This is regarding the energygroups that one can use in the mdp
file for
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