i had followed the instructions in themnaual for ninbonded interactions adn
had created two tables one for nacl adn other table for water ion
interations...i wanted some information on how to use these tables for
starting thee simulation
On Mon, May 9, 2011 at 11:20 AM, Mark Abraham
On 9/05/2011 4:01 PM, sreelakshmi ramesh wrote:
i had followed the instructions in themnaual for ninbonded
interactions adn had created two tables one for nacl adn other table
for water ion interations...
That's not I really don't have any idea on how to do this. Please ask
the question you
Hi:
I have a carbon nanotube (CNT) and several carbonly groups (C=O). Meanwhile the
carbonly carbon atoms are part of the CNT. That is to say an oxygen atom is
attached to one carbon atom of the CNT to form a carbonyl group. All the carbon
atoms are supposed to be fixed, while carbonyl carbon
shivangi nangia wrote:
Hi Justin,
I used 15 nm cubic box and 6 nm shell.
I again tried to insert only 1 histidine molecule in the sphere. I get
the same error
Fatal error:
One of the box vectors has become shorter than twice the cut-off length
or box_yy-|box_zy| or box_zz has become
rashi parihar wrote:
Hi all.
I am doing dynamics studies of protein-ligand dynamics.When I am running
grompp command error is coming atomtype SDMSO NOT FOUND . I checked in
drg.itp file
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 OM 1 LIG OXT 1 -0.758 15.9994
2 C 1 LIG C 1 0.362
toby1024 wrote:
Hi:
I have a carbon nanotube (CNT) and several carbonly groups (C=O).
Meanwhile the carbonly carbon atoms are part of the CNT. That is to say
an oxygen atom is attached to one carbon atom of the CNT to form a
carbonyl group. All the carbon atoms are supposed to be
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dear gmx users,
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Maria Hamilton wrote:
Hi Prof. Mark Abraham
I recived a tutorial from you that in the tutorial 3th molecule was one
and there is not some of the 3th molecules that distributed randomly.
I will be very thankful if you introduce to me a tutorial about my work.
Tutorials are not written to
Nilesh Dhumal wrote:
Hello Justin,
In the J. Chem. Phys. paper author have run the simulation 6.5 ns. So
I run the simulation 6.5 ns for collecting data and I have total 256 water
molecules.
I also asked how you calculated the dielectric constant.
When trying to replicate others' work, it
Hi,
The git server may be temporarily offline today for maintenance.
Cheers,
Rossen
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On 9/05/2011 5:23 PM, toby1024 wrote:
Hi:
I have a carbon nanotube (CNT) and several carbonly groups (C=O).
Meanwhile the carbonly carbon atoms are part of the CNT. That is to
say an oxygen atom is attached to one carbon atom of the CNT to form a
carbonyl group. All the carbon atoms are
I mean all the positions of the carbon atoms are invariant during mdrun. In the
.gro file, carbonyl carbon and oxygen atoms are defined as group 'Carbonyl' and
the rest every single carbon atom is defined as 'CNT'. For the use of 'freeze
groups', the group 'CNT' should be freezed. But for group
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On 9/05/2011 10:43 PM, toby1024 wrote:
Please use a useful subject line when replying to a digest.
I mean all the positions of the carbon atoms are invariant during
mdrun. In the .gro file, carbonyl carbon and oxygen atoms are defined
as group 'Carbonyl' and the rest every single carbon
Sajad Ahrari wrote:
dear users
is it rational to do a simulation on a structure witch is not complete?
i mean pdb structure doesn't cover whole of the protein but it's active
core domain.
may be i should be asking this question somewhere else, but i thought
some of you may have concerned
Hi dear user's
I want to calculate total force acting on one certain atom or group.
gromacs dose not have tools for force analysis, and FDA only give pair
forces between one group of atoms
how can i do this?
thanks
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Nilesh Dhumal wrote:
I used g_dipoles to calculate dielectric constant.
g_dipoles -f water.trr -s water.tpr -eps
Group 0 ( System) has 768 elements
Group 1 ( Protein) has 768 elements
Group 2 ( Protein-H) has 256 elements
Group 3 ( C-alpha) has 0
Hi,
The git server, git.gromacs.org, was moved to a new machine:
tcbs03.theophys.kth.se, 130.237.25.132. It may take some time for the
DNS to propagate.
The old server is still available at git-old.gromacs.org,
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runs fine.
Hi,
I recompiled gromacs 4.5.4 and fftw3.2.2 with the newest version off the
intel compiler suit 12.0.2, still leading to segmentation faults. As
suggested, I tried lots of combinations of different forcefields, water
types and *.pdb's. Non of them was successful, so my segmentation fault
is
Dear Sir
Greetings!
I am following every gromacs applications based on your manuals. I now get
stuck in grompp -energy minimization step during generation of .tpr file for
my ligand and protein. the error which i found is the following,
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp
ITHAYARAJA wrote:
Dear Sir
Greetings!
I am following every gromacs applications based on your manuals. I now
get stuck in grompp -energy minimization step during generation of .tpr
file for my ligand and protein. the error which i found is the following,
Ignoring obsolete mdp entry
Does anybody know the reference for TIP4P water, which is supplied
in tip4p.itp in the /share folder, please?
--
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216
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On 2011-05-09 20.19, Vitaly Chaban wrote:
Does anybody know the reference for TIP4P water, which is supplied
in tip4p.itp in the /share folder, please?
--
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216
Do you think it is not the regular
Vitaly Chaban wrote:
Does anybody know the reference for TIP4P water, which is supplied
in tip4p.itp in the /share folder, please?
Reference 96 in the manual.
-Justin
--
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216
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The DNS seems to be finished updating now. Let me know if something
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Cheers,
Rossen
On 5/9/11 5:25 PM, Rossen Apostolov wrote:
Hi,
The git server, git.gromacs.org, was moved to a new machine:
tcbs03.theophys.kth.se, 130.237.25.132. It may take
On 2011-05-09 20.19, Vitaly Chaban wrote:
Does anybody know the reference for TIP4P water, which is supplied
in tip4p.itp in the /share folder, please?
--
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216
Do you think it is not
Hi,
there is no tool to do that. Trajectories assume to have the same number of
atoms per frame. What you can do is use g_order (it gives you the water
sorted by distance and the number of water within .5nm) or g_select (it can
give you an index file with the atoms within .5nm for each frame)
Ricardo O. S. Soares wrote:
Hello dear users,
I'm having a problem trying to simulate one trimer. I'm using tip4p water and
right after I fill the box with water and try to pre-process (grompp) the
resulting .gro and .top, I get the following error:
On 10/05/2011 1:38 AM, kalav...@gmx.net wrote:
Hi,
I recompiled gromacs 4.5.4 and fftw3.2.2 with the newest version off the
intel compiler suit 12.0.2, still leading to segmentation faults. As
suggested, I tried lots of combinations of different forcefields, water
types and *.pdb's. Non of them
On 10/05/2011 3:10 AM, Justin A. Lemkul wrote:
ITHAYARAJA wrote:
Dear Sir
Greetings!
I am following every gromacs applications based on your manuals. I
now get stuck in grompp -energy minimization step during generation
of .tpr file for my ligand and protein. the error which i found is
On 10/05/2011 12:50 AM, maria goranovic wrote:
Dear experts
I have a protein simulation in a water box. I now want to write a
trajectory containing only the protein, and water molecules within 5
Angstroms of the protein, with the water list being updated each time
step. How can one do this?
On 10/05/2011 12:43 AM, rasool.fakh...@ut.ac.ir wrote:
Hi dear user's
I want to calculate total force acting on one certain atom or group.
gromacs dose not have tools for force analysis, and FDA only give pair
forces between one group of atoms
how can i do this?
nstfout = xx in your .mdp file
On 10/05/2011 2:20 AM, sreelakshmi ramesh wrote:
i had three tables one for solvent na and solvent cl ions (obeying lj
potential) and na ,cl obeying my own potential.i have the following
mdp file
em.mdp
title = nacl
cpp = /usr/bin/cpp ; the c preprocessor
define= -DEFLEXIBLE
integrator = md
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