Re: [gmx-users] diffusion coefficient

[Omer Markovitch]

10 ps is too short of a trajectory, even for such a large system (for pure
water it is considered large). i would guess that it is a typing-error and
you ran for 10 ns?
omer.

On Wed, Feb 10, 2010 at 11:05, Amit Choubey  wrote:

> I use a box of volume 6x6x6 nm^3 which has 7161 water molecules. I
> equilibriate the system for a ns and then run for additional 10 ps for
> analysis. Here are some of the numbers that i get
>
>
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Re: [gmx-users] trajectory info

[Omer Markovitch]

See for example eq. 19 & 20 at JCP 129, 84505 (
http://dx.doi.org/10.1063/1.2968608). Is this what you meant?
Omer.

On Mon, Dec 14, 2009 at 06:56, Mark Abraham  wrote:

> I think that the problem comes from pbc handling for molecules splited
>> across boundaries - I expect : do something before calc_xcm.
>> I could run trjconv before run tool, but I 'd like to use the original
>> trajectories and handle them correctly.
>> Any suggestion is appreciable.
>>
>
>
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Re: [gmx-users] Simulation at unrealistic temperatures

[Omer Markovitch]

Maybe the system is exploding? Have you looked at the movie?
And I agree with you that it might be unrealistic to do simulation at 600K
using a force-field which was parametrized at 300K.
Omer.

On Thu, Nov 26, 2009 at 05:56, Neha Bharat Gajaria wrote:

>
> Dear List,
>
> I m trying to run an NPT simulation at 600K which looks unrealistic. I m
> running minimization followed by anealing and then NPT simulation (mdp files
> are attached). The job keeps running but after 162 ps, the CPU usage
> gradually decreases to 26% without any further output. Your help is very
> much appreciated.
>
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Re: [gmx-users] g_msd => The MSD and periodic boundary condition

[Omer Markovitch]

On Fri, Nov 20, 2009 at 01:32, Chih-Ying Lin  wrote:

> So, how can I remove the periodic boundary condition to get the truly
> movement of the atoms between the two time steps ?
>

Removing PBC and placing atoms back into their "true" location is easy. In
general, if an atom has moved more than half of the box between two
consecutive timesteps then it has "jumped" over the box.
You can see for example eq. 19 & 20 in doi:10.1063/1.2968608 .
--Omer.
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Re: [gmx-users] Normalization in g_rdf

[Omer Markovitch]

On Tue, Nov 24, 2009 at 02:27, Ondrej Marsalek wrote:

> Dear all,
>
> I would like to understand better the way g_rdf performs
> normalization. I have two unexpected results:
>
> 1) In a simple simulation of atomic ions in water in a cubic box, I
> get RDFs that clearly reach a constant value at large enough
> distances, but that value is somewhat lower than one. The simulation
> is NpT, could that be a problem for the normalization?
>
> g(r) should fluctuate around 1 at large distances, say 9 Angstroms for pure
water.


> 2) In a simulation in a dodecahedron, I get an unexpected decrease in
> the RDF at larger distances (for free ions in solution). Is there some
> know problem with normalization in triclinic cells? Is the RDF perhaps
> not truncated "soon" enough?
>
Try calculating it for much larger distances, if you have PBC this should
not be a problem even with the current docecahedron.

--Omer.
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Re: [gmx-users] how to obtain the hydrogen bond energy?

[Omer Markovitch]

delta G = -R*T*ln(K). Now its just a matter of describing your hbond
cleavage reaction.
For water, the reaction is usualy bonded<-->nonbonded, and a geometrical
criteria is usualy applied. Take a look for example at this paper: "The
Distribution of Acceptor and Donor Hydrogen Bonds in Bulk Liquid Water"
http://www.informaworld.com/smpp/content?content=10.1080/00268970701877921 .

--Omer.

On Sun, Nov 22, 2009 at 14:35, lammps lammps  wrote:

> Hi,
>
> I used the OPLS-AA FF to simulate the PEO and water systems.  The are
> hydrogen bond between PEO and water. I want to obtain the average energy of
> these dydrogen bond. How can I do? Should I calculate the free energy?
>
> Any idea is appreciated. Thanks in advance.
>
> --
> wende
>
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Re: [gmx-users] Decreasing MSD of ligand ?

[Omer Markovitch]

Is the decrease occurs in the long times? Omer.

On Tue, Nov 17, 2009 at 21:08, Chih-Ying Lin  wrote:

>
>
>
> HI MSD = mean square displacement diffusion coefficient = d/dt (MSD) I
> simulate the protein and ligand system and then calculate the MSD of the
> ligand. Then, i drew the plot of the time evolution of the MSD. But the the
> MSD decreases as time for some period. I see nothing about my codings. Would
> you please tell me about any possible errors i made? Thank you Lin
>
>
>
>
>
>
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Re: [gmx-users] g_rdf and number of atoms to include

[Omer Markovitch]

On Thu, Oct 22, 2009 at 05:17, Enemark Soeren  wrote:

>  Ahh, now I understand - sorry, Omer!
>
> No problem, glad to help.


>
>
> In fact, I have compared all three single hydrogen RDFs and they are
> identical and also relatively smooth. Since, however, with 3 times more data
> points (all three hydrogen atoms taken together) I get a different RDF,
> would that indicate that I do not have enough data after all?
>
See my previous answers for some checks you can do on the convergence.
You have to look at your data and decide if the differences are acceptable
by you. I could suggest, for example, RMSD between curves, focusing just on
the first peak.


>
> Are RDFs known to be slow to converge?
>
A wild answer would be no, but thats basically depends on the size of your
bin. A bin of 0.5 Angstroms would mean in each bin you'll probably have
"enough" molecules for the data of this bin to converge, but than the curve
itself wouldn't look smooth (even if it is converged). A bin size of 0.1 is
often used.

I have about 1000 water molecules and about 50+ glycine molecules, simulated
> for 10ns with 1ps sampling intervals. That should give me 500,000,000 data
> points for the distribution, right? Can I compare this number with the
> literature in which RDFs for, say, water-water interactions are reported?
>
With 50 glycines you basically average 50 curves together, but the number of
water molecules does not effect the statistics of the glycine RDF. The
number of waters does mean that you most likely have a large enough system.
As for water-water RDF, I think you should have more then enough data here.
Just make sure when comparing to similar variables with the literature
(potential, temperature, binning...). I would also worry about calculating
my water-water RDF for a water which is close to glycine if I wanted to
compare bulk water.


>
>
> One important point, which was not really clear to me before was if,
> provided that I have enough data, the RDFs should be identical no matter
> whether I use 1, 2, or 3 hydrogen atoms for generating the RDF. As far as I
> understood, both yours and Omer’s responses indicate that the RDFs should be
> identical. Did I get that correctly?
>
>From the top of my head I would say yes, you are correct. I recommend you
look at some trajectory snapshots to make sure that indeed all 3 hydrogens
have similar neighboring.

Cheers, Omer.
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Re: [gmx-users] g_rdf and number of atoms to include

[Omer Markovitch]

On Wed, Oct 21, 2009 at 07:28, Enemark Soeren  wrote:

>  Dear users,
>
> I would like to compare interactions between molecules by using RDF. I have
> tried looking at glycine and water, and compare the following two
> interactions:
>
> 1)  between the amine hydrogen atoms in glycine and the oxygen atom in
> water
>
> 2)  between the carboxyl oxygen atoms in glycine and the oxygen atom
> in water
>
> However, my result in 1) depends on how many of the 3 hydrogen atoms I
> include in the calculations. Why is that?
>
If you mean that when focusing your RDF calculations on either one of the
three hydrogens results in three different RDFs then it means that each
hydrogen feels water differently. I bet this difference is only for the
first peak of g(r) and the other peaks overlap between the three RDFs. As
for how reasonable this result, its not unlikely because glycine has atleast
2 different types of hydrogens (say, C-H vs. N-H), depending on the
protonation state. You might want to provide more details on the system you
are studying to get better answer.
I am assuming that the RDFs are converged so that including more trajectory
data and/or sampled molecules and/or changing bin size does not result in a
drastic change to the curves.


> Does that mean that I cannot directly compare the strengths (RDF peak
> height) of the two interactions as they are not based on the same number of
> atoms? Does it also mean that I must always calculate RDFs by using 1 atom
> on each of the particles/groups that I am comparing?
>
I am not sure how good it is to use the first peak of g(r) to analyze
strengths, but you should also consider the width and area under peak. This
peak is an average on all nearest neighbours, bonded or not, so it might not
give you a good estimate of the hydrogen bond, for example.
If you are unsure of your g(r) calc it just for water (that is - only
oxygen-oxygen of water-water). At long distances (~10 Angstroms) it should
fluctuate around 1.

Bests, Omer Markovitch.
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Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

[Omer Markovitch]

What I do is visualize as trace. Than all the coarse-grained sphere
are connected. Hope it helps. Omer.

Koby Levy research group,
Weizmann Institute of Science.
FAX: 972-77-444-7905
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Fri, Oct 16, 2009 at 11:24, Thomas Schmidt wrote:

> Dear all,
>
> is there any possibility to give the bond information out of GROMACS
> files to VMD? Especially for coarse-grained models (using the MARTINI
> FF) this would be a nice feature for visualization.
>
> But in that case the distance analysis doesn't work, because we will
> always have too high distances between two particles (CG scale). If I
> use "Dynamic Bonds" (as described in this thread:
> http://oldwww.gromacs.org/pipermail/gmx-users/2008-September/036124.html)
> VMD draws bonds also between non-bonded particles.
>
> I know that there is no official solutions for this
> (http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD), but maybe
> anybody of you has a script to convert *.top/*.itp/*.rtp files with a
> corresponding *.gro file into the PDB format with connectivity section
> or into the (NAMD) *.psf format. (?)
> The solution that I've found (top2psd.pl) is not smart enough because
> it's a simple 1-to-1 conversion of GROMACS topology files and has not
> the ability to replicate (and renumber) the topological data of single
> molecules (http://baaden.free.fr/soft/compchem.html).
>
> Thanks for your help...
> Thomas
>
> --
> Thomas H. Schmidt, PhD student
> Computational Structural Biology
> Chair of Life Science Informatics, B-IT
> LIMES-Institute, University of Bonn
> Dahlmannstrasse 2, D-53113 Bonn, Germany
>
> Phone: +49-(0)228-2699 323
> Fax: +49-(0)228-2699 341
> http://www.csb.bit.uni-bonn.de
>
>
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Re: [gmx-users] reduced units

[Omer Markovitch]

On Sat, Oct 17, 2009 at 06:10, lammps lammps  wrote:

> Dear,
>
> I want to do stochastic simulations in the framework of Langevin dynamics
> using Gromacs with the reduced units.  The questions are:
>
> 1. How to turn on the reduced units? Is there any parameters for setting?
>
> I am not sure I understand. For Langevin dynamcis/thermostat use:
"integrator = SD" & "bd-fric=0"; Read the manual about the relations between
dt & tau-t, I use 5e-4 & 2, respectively.

Hope I helped. Omer.
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Re: [gmx-users] Making Commands Non-Interactive

[Omer Markovitch]

Have you tried:
echo 0 > zero
trjconv bla bla bla < zero
You could put more arguments in the file, for example - use the "-center"
option, and then echo another 0 into the zero file.
--Omer.

On Sun, Oct 4, 2009 at 18:22, ABEL Stephane 175950 wrote:

> Dear GMX Users,
>
> echo 0 | /usr/pbs/bin/mpiexec /scratch/name/gromacs-4.0.5/bin/trjconv_mpi
> -s Peptide_43A1_topol.tpr -f ./XTC/Whole_Traj_43A1.xtc -o
> ./XTC/Whole_Traj_43A1noPBC.xtc -pbc mol -ur compact. With the selection 0
> ("System")
>
>
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Re: [gmx-users] option for finding forces between two groups

[Omer Markovitch]

Work with groups and an index file, and define energy_groups in the mdp file
also.
For indices, check make_ndx utility.
Omer.

Koby Levy research group,
Weizmann Institute of Science.
FAX: 972-77-444-7905
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Fri, Oct 2, 2009 at 20:31, Pradip Biswas  wrote:

> Hi,
> Anyone can please tell me whether there is any option in GROMACS to find
> forces between two groups (say for example, between two residues in a
> protein or between a peptide and a residue in a Protein for Protein-peptide
> interaction) or one need to workaround with the code to get that?
>
> Thanks in advance.
> Biswas.
>
>
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Re: [gmx-users] problem in loading xtc in VMD

[Omer Markovitch]

For VMD you first load a GRO (or pdb) file, and then XTC.
The XTC file should contain _exactly_ the same number of atoms as the GRO
file. Did you save the entire system in the XTC, or just a specific part of
it?
Omer.

Koby Levy research group,
Weizmann Institute of Science.
FAX: 972-77-444-7905
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Fri, Oct 2, 2009 at 20:39, Paymon Pirzadeh  wrote:

> Hello,
> I ran an NVT simulation from a minimized configuration. The simulation
> ended normally and I have a final configuration as well. But, when I
> load the initial coordinates and then I want to add data, which is the
> xtc file, nothing happens! no frames are loaded. This is while the xtc
> file has a reasonable size and when I load it individually in VMD, it
> loads the exact number of frames it should (300 frames). Is something
> wrong with my outputs or is there something with VMD. This is the second
> system I have such a problem.
> Regards,
>
> Payman
>
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Re: [gmx-users] Parameter to for randomizing simulation

[Omer Markovitch]

If you are performing LD then setting ldseef=-1 does the trick. For MD, try
genseed as suggested. I believe the manual explains all, including the
"range" issue.
Omer.

Koby Levy research group,
Weizmann Institute of Science.
FAX: 972-77-444-7905
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Tue, Sep 29, 2009 at 19:31, Jack Shultz wrote:

> I thought there was a way to introduce the random number generator via
> the application
> I was trying to use this parameter
> Id_seed=-1
> but it failed :-(
>
> I suppose I can insert a random number to gen_seed every time I
> submit. is there a range of numbers for gen_seed?
>
>
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Re: [gmx-users] question about energy minimization

[Omer Markovitch]

Trj "trjconv -pbc nojump", or "trjconv -h" and read the short help printed.
Omer.


>
> I actually didnt realize this until i did a long simulation after which the
> trajectories of some of the atoms looked way out of the box dimensions. The
> co-ordinates of many atoms didnt lie in the box range. Although the output
> file contained the same box dimensions as I started with. Could someone help
> me in understanding what happened?
>
>
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Re: [gmx-users] Trajectory files in vmd

[Omer Markovitch]

How do you run vmd?
The first argument should be a GRO or PDB file, and the second argument is
the TRR or XTC trajectory.
Alternatively, you can open a new molecule in vmd and than load data into
that molecule.
--Omer.

On Thu, Sep 24, 2009 at 08:21, Aditi Borkar  wrote:

> Dear All,
>
> When I am loading the GROMACS trajectory in VMD, I cannot the
> evolution of the protein structure with time.
>
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Re: [gmx-users] 1-4 interaction between atoms in PBC mode

[Omer Markovitch]

>
>
> I assume that atoms from opposite ends of the simulation box are being seen
> by GROMACS as being 1-4 neighbors as a result of the PBC,

Are you sure? have you looked at the last "good" frame before this message?
GMX treats PBC as it should during MD neighbour search, so maybe this is a
pair that was initially close and interacting, but later moved away from
each other.


> but the shortest distance between the atoms is not being observed. Is this
> the problem? Is this problem resulting in the system exploding? And, how do
> I resolve this problem?
>
If you are sure that everything else is ok, then extend the table extension.
Two other things to work around this are either reduce timestep or check
that your definition of the box is as it should.
--Omer.
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Re: [gmx-users] Large fluctuation of protein temperature with nose hoover thermostat

[Omer Markovitch]

The group PROTEIN isn't very large as the group NONPROTEIN, therefore its
total kinetic energy fluctuates more.
--Omer.

On Wed, Sep 16, 2009 at 12:10, Stephane Abel  wrote:

> tc-grps = Protein Non-Protein ; two coupling groups - more accurate
> tau_t = 0.4 0.4 ; time constant, in ps
> ref_t = 310 310 ; reference temperature, one for each group, in K

Energy Average RMSD Fluct. Drift Tot-Drift
>
> ---
> Temperature 310 2.46886 2.46886 6.12135e-07 0.0171398
> T-Protein 310 32.1134 32.1117 -4.10352e-05 -1.14898
> T-Non-Protein 310 2.47549 2.47548 8.55869e-07 0.0239643
>
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Re: [gmx-users] table extension

[Omer Markovitch]

But what if the gmx code did notice it?

Koby Levy research group,
Weizmann Institute of Science.
FAX: 972-77-444-7905
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Thu, Aug 27, 2009 at 16:21, Mark Abraham  wrote:

> It would look up a non-random energy and force. If the code never noticed
> the distance was out-of-range, it won't notice it come back into range
> either.
>
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Re: [gmx-users] table extension

[Omer Markovitch]

Thanks.
And what happens if later on it comes back to the cut-off + table-extension
range?

Koby Levy research group,
Weizmann Institute of Science.
FAX: 972-77-444-7905
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Thu, Aug 27, 2009 at 11:13, Berk Hess  wrote:

> A interaction beyond the cut-off + table-extension will get a random energy
> and force
> depending on what is stored in the memory of your computer beyond the table
>
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Re: [gmx-users] table extension

[Omer Markovitch]

Thanks Mark.
I am simulating a dimer in vacuum, and it is my understanding that once a
non-bonded interaction has exceeded the table-extension cutoff this
interaction will NOT be included in the potential for the remaining
simulation, even if it will later come back to a distance within the
table-extension.
Your answer helped me.
It is now a matter of choosing the box dimensions & table extension that
will be reasonable yet not increase the computation time too much.
--Omer.

Koby Levy research group,
Weizmann Institute of Science.
FAX: 972-77-444-7905
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Wed, Aug 26, 2009 at 16:03, Mark Abraham  wrote:

> Probably not... if you're asking this question because you suspect
> something's not working properly, you might get enlightenment/a fix quicker
> if you're more explicit :-)
>
> Mark
>
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[gmx-users] table extension

[Omer Markovitch]

Dear GMXs,
I would like to clear something out, for myself:
The table extension given in MDP file applies to "nonbond_params" & "pairs"
interactions which are specified in the TOP file (and also electrostatics)?
Is there an interaction which does not use the table extension (other then
bonds, angles & dihdrals)?
I have read the manual.
Thanks, Omer.
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Re: [gmx-users] Periodic Boundary Condition Issues

[Omer Markovitch]

Try combining indices with that, use "make_ndx -h". --Omer.

Koby Levy research group,
Weizmann Institute of Science.
FAX: 972-77-444-7905
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Wed, Jul 22, 2009 at 18:27, Justin A. Lemkul  wrote:

> The trjconv -pbc options were designed to fix this sort of issue.
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Re: [gmx-users] Protein going out of the box

[Omer Markovitch]

Try using trjconv. Look at the -pbc options and also maybe -center options.
--Omer.

Koby Levy research group,
Weizmann Institute of Science.
FAX: 972-77-444-7905
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Wed, Jul 15, 2009 at 10:09, nikhil damle  wrote:

> but peptide remains inside the box while protein is seen outside.
>
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Re: [gmx-users] non squares box

[Omer Markovitch]

I prefer to keep discussions professional, Mark and Tsjerk.

Anyway, I am doing MD with PBC. I have a surface which sits on the XY axes,
the surface is not a square and my question is how do I tell gromacs that I
have a non standard box. Please see my original post for more details:

++
I would like to ask your help on the following - I want my simulation to
include a surface, and have PBC.
The surface I chose is aligned on the XY plane. However, the surface is not
a square.
The surface dimensions are a=b=169.2 & c=6.9 Angstroms, the angles are:
bc=ac=90 & ab=120 degrees.

I have used "editconf -f -box 16.92 16.92 0.69 -angles 90.0 90.0 120.0". To
test this, I have used "trjconv -pbc nojump -center yes -boxcenter zero". My
problem is that the trjconv generates a structure where some of the surface
atoms are cut and/or overlapping...
++

Thank you. Omer.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
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Re: [gmx-users] non squares box

[Omer Markovitch]

Thanks.
I am not sure how this addresses my problem. I am getting "broken" structure
at the end of the MD (in confout.gro), and want to be sure that GMX treat it
correctly during the MD.
--Omer.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Sun, Jun 21, 2009 at 13:42, Tsjerk Wassenaar  wrote:

> To check your periodicity use genconf:
>
> genconf -f in.pdb -o out.pdb -nbox 2 2 2
>
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[gmx-users] non squares box

[Omer Markovitch]

Dear All,
I would like to ask your help on the following - I want my simulation to
include a surface, and have PBC.
The surface I chose is aligned on the XY plane. However, the surface is not
a square.
The surface dimensions are a=b=169.2 & c=6.9 Angstroms, the angles are:
bc=ac=90 & ab=120 degrees.

I have used "editconf -f -box 16.92 16.92 0.69 -angles 90.0 90.0 120.0". To
test this, I have used "trjconv -pbc nojump -center yes -boxcenter zero". My
problem is that the trjconv generates a structure where some of the surface
atoms are cut and/or overlapping...

Could you please help me? Wheres the problem?
The input PDB I use is about 2 MB in size, so it can't be attached here.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
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Re: [gmx-users] PBC

[Omer Markovitch]

Remember that for PBC=xyz, the neighbor search is faster, so I suggest using
PBC with a very large box.
--Omer.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
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Re: [gmx-users] Re: Alternative TRP residue

[Omer Markovitch]

How many letters for residue name are allowed in the PDB format? Omer.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
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Re: [gmx-users] Combining LJ and buckingham potential

[Omer Markovitch]

Hello Osmair,
Perhaps you can try using the "[ nonbond_params ]" & "[ pairs ]" sections of
the TOP file?
How did you define these interactions in your TOP file?
--Omer.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Fri, Apr 17, 2009 at 22:51, osmair oliveira  wrote:

>  Hi,
> I have tried to simulate a crystal in water solvent, however I
> found the error:
>
> ERROR 0 [file "new-topol3.top", line 19]:
>   Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR)
>
> So, my question: How can I use or define  LJ potential (for water) and
> buckingham potential (for a crystal) in the same *.top, *.itp?
>
> Thanks,
>
> Osmair V. Oliveira
> Ph.D. Student
> Brazil
>
>
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Re: [gmx-users] (no subject)

[Omer Markovitch]

Hello.
What do you mean by "jump"? Perhaps the "connected MN" is a stable state?
If you'll supply more details we could try to help you better.
--Omer.

On Sat, Mar 14, 2009 at 08:15, Homa Azizian wrote:

> My ion jump out of the protein after MD.My ion (MN) has not any covalant
> bond by its neibour, just has electrostatic intraction.
> is there any line that I have to add to the itp file or top file in order
> to
> prevent this problem.
>
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Re: [gmx-users] is there a possibility to convert .gro files directly to PDB?

[Omer Markovitch]

Use: trjconv -f conf.gro -s conf.gro -o conf.pdb.
Note the use of "-s" on the same gro file.
--Omer.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
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Re: [gmx-users] initial velocities Langevin dynamics

[Omer Markovitch]

>
> Thus I am a bit confused about it!
>>
>
> I'm confused about the manual comment about only being meaningful with the
> MD integrator, but we'll have to wait until someone who knows something
> about LD can post!


For LD, the velocities will (should) get rescaled by the random thermal
noise, that is- by the Langivin thermostat.
With MD, the thermostat works like friction (positive or negative friction).
So you see, that for LD, an initial velocity of zero should next be changed
by the thermostat, while for MD the rescaling shouldn't work for zero.

--Omer Markovitch.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
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Re: [gmx-users] Diffusion coefficients ( Exp X Simul )

[Omer Markovitch]

See also the work of Hummer (JPC-B (2004),
http://dx.doi.org/10.1021/jp0477147), dealing with box size effect on D.
Omer.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Tue, Mar 3, 2009 at 23:37, Eudes Fileti  wrote:

> Hello, someone could suggest me references
> which discusses the difficulty of obtaining
> values for diffusion coefficients in agreement
> to the experimental values?
>
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Re: [gmx-users] Turning off electrostatic or Van der Waals interactions

[Omer Markovitch]

Why not create "dummy" topologies, without charges/vdw ?
Another option, which I am not sure of its effect, is, perhaps, to take
extremely small cutoffs.
--Omer.


> Lee Soin wrote:
>
>> I'm trying to rule out the effect of electrostatic or Van der Waals
>> interactions while performing a simulation. Do you mean that I should modify
>> the code and re-compile?
>>
>>
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[gmx-users] Barostat & Density decreasing to zero

[Omer Markovitch]

Dear All,
I have simulated a protein inside a box with water and ions. I began by
minimizing my system (which has a total charge of zero), until the maximum
gradient was small enough and the potential energy become negative.
Then I heated it, slowly, to 300K at constant volume (using berendsen
thermostat and tcoupl = 1 ps).
Then I performed 500 ps NVT simulation to equilibrate the temperature, at
300K.
Then, I tried to equilibrate the pressure and run NPT simulation, using
Berendsen barostat (p=1, pcoupl=10) and Berendsen thermostat (T=300K, tcoupl
= 0.1).

My problem is, that with the barostat & thermostat both active in the same
MD run, my density drops to a very low value (at the first MD steps, the
density is 1000, dropping later to 100 kg/m^3). That is- my box dimensions
increase significantly (from around 6x6x6 to 12x12x12 nm^3. If I change the
pressure coupling constant, the speed of the expansion changes but all
simulation converged to a small density between 50-100 kg/m3.

Your help is appreciated; Probably, I am not controlling the simulation like
I should. I will appreciate any advice.
Thank you, Omer Markovitch.

I have used gromacs version 3.3.3, Here is my .MDP file for the NPT run:

integrator   = md
dt   = 0.001
nsteps   = 50
comm_grps= system
nstxout  = 500
nstvout  = 500
nstcheckpoint= 1000
nstlog   = 500
nstenergy= 500
nstlist  = 10
ns_type  = simple
pbc  = xyz
rlist= 1.0
coulombtype  = PME
rcoulomb-switch  = 0
rcoulomb = 1.0
epsilon_r= 80
epsilon_rf   = 80
vdw-type = Cut-off
rvdw-switch  = 0
rvdw = 1.0
table-extension  = 1
fourierspacing   = 0.12
pme_order= 4
ewald_rtol   = 1e-05
ewald_geometry   = 3d
optimize_fft = yes
tcoupl   = berendsen
tc-grps  = system
tau_t= 0.1
ref_t= 300
Pcoupl   = berendsen
Pcoupltype   = Isotropic
tau-p= 10
compressibility  = 4.5E-5
ref-p= 1
andersen_seed= 815131
constraints  = none
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Re: [gmx-users] RE: How to output a single index group

[Omer Markovitch]

Also check out "make_ndx -help". Omer.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Mon, Jan 19, 2009 at 18:28, Vitaly Chaban  wrote:

> > I am running a simulation of 5 time steps and am trying to avoid
> setting
> > nstxtcout = 1 or nstxout = 1.  The file size becomes unmanageable if I
> set
> > either of these two parameters to 1.  I do not need the coordinates for
> all
> > atoms in the system, just the alpha carbons, which are grouped in the
> index
> > file, but I do need coordinates for each time step.  Is there any way of
> > specifying in the parameter file to only output the coordinates for the
> alpha
> > carbons?  Thanks!
>
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Re: [gmx-users] time of dynamic

[Omer Markovitch]

>
>
>> would you please tell me for compare dynamic peptide what time for MD
>> is enough by gromacs?generally.
>
>
You can take your 20 ns simulation, and divide it into 2-4 parts, each 10
(or 5) ns long.
Then, calculate the property you are interested in for each part seperately.
If 20 ns is more then enought, then the difference between the parts should
be minimal.
Another option is to calculate the variance of the propery you are
calculating, vs. time.

--Omer.
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Re: [gmx-users] Analyzing a trajectory split over multiple files

[Omer Markovitch]

On Tue, Nov 25, 2008 at 01:47, Suman Chakrabarty
<[EMAIL PROTECTED]>wrote:

> Dear all,
>
> I have a very long trajectory split over a large number of files. What
> would be the most efficient way to use the analysis programs over them?
> Do they support multiple input for trajectory? Or I need to combine all
> files into a single one anyway?
>

You should analyze each individual part on its own, and output the raw data
of the result, then average the parts together.

For example - say you are interested in coordination number of molecule X:
For each part, output both the total number of X's found, plus the total
number of X neighbors found. The coordination number is then the sum of
neig. divided by the sum of X's, from ALL parts.
It might be an issue if each part has different time length, then averaging
the coordination number of each part might give more statistical weigh to
short parts then they should have.

In other words, you should first collect the data of each part together, and
only then avg..

--Omer.
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Re: [gmx-users] Replacing molecules in .gro coordinate file

[Omer Markovitch]

>
>
> Supposed I have a .gro file of 38 molecules of A which are already in
> equilibrated conformations. Now I want to transform 15 molecules of A into B
> therefore I will have the binary mixture of A/B with 13:15 molar ratio in
> the final structure. How can I do this? Any suggestions will be appreciated.
>

Maybe open A & B in vmd together, and then save them as one PDB? Omer.
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[gmx-users] small protein & big frozen group - exploding

[Omer Markovitch]

Dear,
I am simulating a small protein (less then 50 amino acids) at room
temperature, with no additional atoms and/or molecules and/or ions. The
simulations seems to proceed ok (in terms of avg. kinetic energy and other
energy terms).
Then, I take the same protein, and introduce a "surface" to the system.
My surface is just a set of identical hard sphere atoms, here is how a
surface atom is defined inside my .TOP file:
 [ atomtypes ]
  ;name  mass charge   ptype c6   c12
 X 1.0000.000 X0.000  0.600E-09
And there are 10 times more surface atoms then protein atoms.

In my .MDP file, there are two energy groups: protein & non-protein. The
surface is frozen in all xyz directions.
Now, the problem is that with the surface, my protein quickly explodes, and
I have no idea why. The surface and protein each coupled to its own
thermostat.

Your help and ideas/comments are appreciated. Omer.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
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Re: [gmx-users] temperature coupling strength

[Omer Markovitch]

On Mon, Nov 10, 2008 at 17:42, Seunghyun Chung <[EMAIL PROTECTED]> wrote:

> Deal all,
> Is there any practical approach to choose the right temperature coupling
> strength for a simulation? For example, if a system behaves differently with
> weak coupling and strong coupling, which result I should trust?

In general, the coupling lifetime should not interfere with any fast degrees
of motion you might have.
For example, for pure water (where hydrogen bond lifetime is in the ps
region, and OH vibration is in the fs lifetime), the thermostat coupling
might be ~0.5 ps, but for a protein, perhaps a value in the area of 1 ps and
above might be more suites.
Plotting the temperature devations and/or averages might direct you to the
better value.



> Also, I thought giving a very weak nose-hoover thermostat coupling would be
> similar to the NVE simulation. However, when I run the simulation, the
> system behaves very weirdly by constantly accelerating and slowing down.
> will there be any explanation on this behavior?
>
I agree. But did you start applying the weak coupling before or after the
system was already equilibrated?


  --Omer.
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Re: [gmx-users] stochastic dynamics , langevin

[Omer Markovitch]

Thanks for the quick reply Berk.


>
> 1) Is this the proper keywords I should use for Langevin dynamics:
> integrator = sd ;
> bd-fric= 0 ;
> tau_t  = 10 ;
> ref_t  = 300 ;
>

Basically, I want to know if I am using the 4 parameters correctly.
That is - for Langevin dynamics, I should pick bd-fric=0, to allow the
friction to be taken from 1/tau_t ?
Secondly, I am looking for examples of tau_t different people use for
different system.
Thanks, Omer.
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[gmx-users] stochastic dynamics , langevin

[Omer Markovitch]

Dear All,
I am trying to perform Langevin dynamics of large peptides / proteins.
After reading the manual & going over some old mails in this list, I have
two points I hope you could clear for me:
[Gromacs version 3.3.3]

1) I am a bit confused with Brownian vs. Langevin dynamics. Is this the
proper keywords I should use for Langevin dynamics:
integrator = sd ;
bd-fric= 0 ;
tau_t  = 10 ;
ref_t  = 300 ;
With bd-fric=0, the friction is taken as the inverse tau_t.

2) From your experience, what are good values of tau_t (or 1/tau_t) for
simulating a protein? In 2006 list, David has commented that choosing tau_t
is very important (
http://www.gromacs.org/pipermail/gmx-users/2006-July/023089.html ).

Your help is appreciated. Omer.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
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Re: [gmx-users] range of gen_seed

[Omer Markovitch]

I believe that (-1) as the seed takes the time or something as the actual
seed, thus ensuring no two identical seeds, and no two identical velocities.
Omer.

On Fri, Oct 17, 2008 at 12:11, sarbani chattopadhyay <
[EMAIL PROTECTED]> wrote:

>
>
> I want to know that does this ensure that the mdrun starts with diffrent
> velocities ?
>
> Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
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Re: [gmx-users] Simulation of a protein confined in a box

[Omer Markovitch]

Oh, I didn't read carefully.
My suggestion would be, perhaps, to physically put atoms on the sides of the
box (possibly, fill each side completely), and to place on them very high
repulsion.
You might want to freeze them up, and exclude their self interactions from
the energy calculation.

Good guess Suman. Omer.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Sat, Oct 11, 2008 at 09:26, Suman Chakrabarty
<[EMAIL PROTECTED]>wrote:

> Possibly what he is interested in is a system WITHOUT PBC? I don't think
> with PBC the system is really "confined", since there is no true wall to
> reflect the colliding molecules. Thus to study the effect of real
> confinement, it is necessary to remove PBC and impose reflective
> boundary conditions. I am only guessing! :)
>
>
> --Suman.
>
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Re: [gmx-users] Simulation of a protein confined in a box

[Omer Markovitch]

In short - you can apply PBC in all directions (XYZ) by choosing the proper
keyword in the .mdp file, I believe the box dimensions are defined in .gro
file.
Omer.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Fri, Oct 10, 2008 at 16:00, Lee Soin <[EMAIL PROTECTED]> wrote:

> Maybe I didn't put it clearly. My intention is to simulate a protein
> confined in a box, and the problem is that I don't know how to define a
> boundary, or a wall, in GROMACS.
>
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Re: [gmx-users] Simulation of a protein confined in a box

[Omer Markovitch]

Boundary should not "precisely" be around the protein, otherwise some parts
of the protein would "feel" other parts via the boundary.
In general, if you apply periodic boundary conditions (PBC), take the
dimensions as such so the protein would NOT feel the PBC.

Say you have an unfolded protein (or a MD during which a protein unfolds)
whose length is about 20 Angstroms, and you use no explicit solvent. You
might not want to take the dimension of the box to be smaller they, say, 40
Angstroms.
Its just an example.

Omer.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Fri, Oct 10, 2008 at 11:03, Lee Soin <[EMAIL PROTECTED]> wrote:

> But the problem is: how to define a boundary?
>
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[gmx-users] trjconv - converting trajectory into a pdb

[Omer Markovitch]

Hello,
I have ran some MD with GROMACS v3.3.3, and used the command "trjconv -f
traj.xtc -o traj.pdb -s file.gro" to generate a pdb movie.
My simulation includes charged atoms in some residues, but the output pdb
does not seem to include the formal charge data.
My question is, is this a known issue (that GROMACS does not print the
charge info. in the pdb), or, perhaps, it is a symptom of something I did
wrongly?
(its not a big deal, but still - it would be nice to have this data directly
in the movie)
Thank you for the help, Omer.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
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Re: [gmx-users] Hydrogen Bond Lifetime

[Omer Markovitch]

Please see also my reply under "HB lifetime" to Christopher Daub.
I think that JCP 129, 84505 (2008) should be read when dealing with C(t) in
general & HB lifetimes in particular.
** link: http://dx.doi.org/10.1063/1.2968608

Omer Markovitch.
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Re: [gmx-users] HB lifetime

[Omer Markovitch]

Please see my comments below.

>
> Hi,
>
> The HB definitions and associated lifetimes are a bit arbitrary, so there'
> s always going to be some ambiguity here.  That being said, the reason the
> integral of the HB correlation function C(t) isn't an ideal definition is
> that C(t) is only roughly exponential.  Same argument goes for getting the
> lifetime from a fit to C(t), or looking for the time where C(t)=1/e, or
> similar simple approximations.
>

I disagree. HB lifetime is only slightly dependent on the exact values of
the geometric parameters, around the usual values of R(O...O)= 3.5 Angstrom
& angle(O...O-H)= 30 degrees, please see JCP 129, 84505 (a link to the
abstract is given below).
C(t) of a HB obeys the analytical solution of the reversible geminate
recombination (see a short review in JCP 129), and so its tail follows a
power law: C(t) ~ Keq*(D*t)^-3/2, which is indicative of a 3 dimensions
diffusion.


> What Luzar recommends is to think about an equilibrium between bound and
> unbound molecules, so that they interact with a forward and a backward rate
> constant k and k'.  k gives the forward rate, ie. the HB breaking rate, and
> k' gives the HB reformation rate... they are not equal due to the diffusion
> of unbound molecules away from the solvation shell.  There are a few
> advantages of going this route, not the least of which is that you tend to
> get similar lifetimes regardless of small changes in the HB definition, and
> whether you use geometric or energetic criteria, etc.
>

The reversible geminate recombination deals with the A+B <---> C, here
A=B=H2O & C=(H2O)2, the bound water dimer.
>From a single fit to C(t) one receives the bimolecular forward & backward
rate constants, which are well defined.
k' you suggest is an apparent unimolecular rate constant, which appears to
be more suited for short times.


>
> Extracting these rate constants is a bit tricky (I usually do it by hand),
> but I guess gromacs has a scheme to do it... I haven't actually looked at it
> (though I really should!).  I'd recommend some caution though, a scheme that
> works well for HB's between water molecules in bulk may need to be adjusted
> to properly model HB's between water and polar atoms.
>

I have to disagree again. The A+B=C problem has an analytical solution.
Technically, ones only need to know how to calculate an error-function and
to solve a cubic equation, please see eq. 9, 10 at JCP 129.
The geminate problem is robust in the sense that it describes C(t) of ANY 2
particles, as long as their behavior is controlled by diffusion, it
describes the water pair, but should describe also, for example, liquid
argon. For the second case, ofcourse, different rate constants are expected.

One should NOT see JCP 129 as a "proof" that previous works were absolutly
wrong !
Instead, it shows that the postulate by Luzar & Chandler, that C(t) of water
is controlled by diffusion, is right, and that with the analytical solution
of the geminate problem one can understand some aspects of the water dimer.
For example - what causes the activation energies of the forward & backward
rate constants to be about similar rather then being different by the
strength of 1 HB?

Hope I was clear.
Omer Markovitch.

** a link to JCP 129, 84505 (2008) http://dx.doi.org/10.1063/1.2968608
** supporting information includes a short trajectory movie
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Re: [gmx-users] Fwd: charges,resonance and electrostatics

[Omer Markovitch]

>
>
>> There is no non-bonded interaction between these two oxygens, unless you
>> are using an Urey-Bradley potential for the angle, like in the CHARMM force
>> field. Most (if not all) of the standard force fields in Gromacs treat the
>> interaction of these oxygens within an angle definition, which is a bonded
>> term.
>>
>> -Justin
>
> So no coloumb law between the two oxygens?  10x, Omer.
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[gmx-users] Fwd: charges,resonance and electrostatics

[Omer Markovitch]

 Hello,
There is a point, I want to clear out for myself:
Say we focus on the aspartate residue. It has a formal charge of -1.
This charge on either oxygen of the carboxyl is -0.8 (oxygens OD1 & OD2),
according to one of the force fields employed in GROMACS.

What is the right way to calculate electrostatics here:
1) "As is", and letting the two oxygens repel one another.
2) Ignore this specific pair when calculating?

How does GROMACS operates? I think that (1) is the common practice, but I
want to be sure.

Thank you, Omer Markovitch.
(this email was sent to gmx-dev. by mistake)

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
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[gmx-users] searching the archives

[Omer Markovitch]

Shalom,
Is it just me or there is a bug in the archives search page
http://www.gromacs.org/search ?
(error 404 - page not found)
--omer.
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Re: [gmx-users] RE: Time step in md

[Omer Markovitch]

On Sat, Sep 20, 2008 at 10:29, Vitaly Chaban <[EMAIL PROTECTED]>wrote:

> > could you explain my the secret of choosing to time step for md
> > integrator?
>


The secret is, to have the timestep small enough so that you could "truly"
say between two consecutive steps the forces are linear, and to have it
large enough so the computation would be feasible.

Other then that, look at the previous answers you got for a more "hands on"
approach. You might also want to read about integrating MD.
--Omer Markovitch.
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Re: [gmx-users] GROMACS sample procedure

[Omer Markovitch]

I think there are example files, look at the gromacs web site.
A super brief answer would be as follows:
File.top is the topology file. It holds description of atom types
& potentials.
File.gro holds the initial coordinates, and box dimensions.
File.mdp holds run parameters (how many steps, temperature, output control,
simulation type, etc`).
The command "grompp" reads some input files, and prepares file.tpr, which is
then used as an input to "mdrun" - the ultimate command that does the actual
MD.
The number of different initials of G.R.O.M.A.C.S., minus the nearest prime
number is 17.
Gromacs has healing powers.
Please refer to the gromacs manual for more details, and to the gromacs wiki
aswell.

Omer Markovitch.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Thu, Sep 18, 2008 at 12:03, Christopher Ambe <[EMAIL PROTECTED]>wrote:

> I am new to GROMACS and have not tried any calculation using it. I have
> installed grmx on scientific linux. Can anyone help me find a sample
> procedure of using GROMACS for molecular dynamics simulation (or even for
> simple energy calculation)? I am interested in doing research on Molecular
> Dynamics using GROMACS, but so far, I really dont have an idea where to
> start. I hope to hear your advise. Thank you very much
>
>
> Christopher Ambe
> MSU-Iligan Institute of Technology
>
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Re: [gmx-users] kill some atoms

[Omer Markovitch]

What is the reason for shrinking the box?
If it is for technical reasons, for example - nicer visualization etc`, then
perhaps this could be done manually.
If you plan to use the smaller box later, then maybe you could do some part
of high pressure simulation, to reduce box size while keeping it physical.
--Omer.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
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Re: [gmx-users] defining group

[Omer Markovitch]

Thank you both! Omer.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Sat, Sep 13, 2008 at 15:57, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:

>
>
> Omer Markovitch wrote:
>
>> Hello,
>> I would like to ask for your help in defining groups:
>> Say I have a protein. I would like to have two groups (1) the Calpha
>> backbone (2) everything else.
>> Later on, I will want to freeze the Calpha group.
>> How can I define these groups? Where?
>> I have looked in the manual, but I do not understand how to do it and in
>> which files.
>>
>
> Groups are defined in index files (.ndx), which are created with make_ndx.
> Calpha is a default group read in from a protein structure.  To create a
> group that is everything but Calpha (group 3 in the make_ndx list), you
> would use
>
> !3
>
> at the make_ndx prompt.
>
> -Justin
>
>  Thank you, Omer Markovitch.
>>
>> Koby Levy research group,
>> Weizmann Institute of Science.
>> http://www.weizmann.ac.il/sb/faculty_pages/Levy/
>>
>>
>> 
>>
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>>
>
> --
> 
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>
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[gmx-users] defining group

[Omer Markovitch]

Hello,
I would like to ask for your help in defining groups:
Say I have a protein. I would like to have two groups (1) the Calpha
backbone (2) everything else.
Later on, I will want to freeze the Calpha group.
How can I define these groups? Where?
I have looked in the manual, but I do not understand how to do it and in
which files.
Thank you, Omer Markovitch.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
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Re: [gmx-users] D2O

[Omer Markovitch]

Quote: "*A D2O gromacs mailing lists query will produce (among others) the
following results which might be of assistance to you:* "
I would like to know how do such a query. I think that under the web
interface one can access archive per date, w/out searching.
  --Omer Markovitch.
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Re: [gmx-users] How to convert gromacs traj file(.xtc) to amber traj file?

[Omer Markovitch]

Are you sure this will be done automaticaly if you'll procide gromacs with
an output file called filename.trj?
There is also the option of converting into PDB: "trjconv -f traj.xtc -o
trajtraj.pdb -s coordinates.gro".
omer.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Mon, Sep 8, 2008 at 20:14, ranqi zhu <[EMAIL PROTECTED]> wrote:

> Hi, Everyone,
>
> I just want to use the clustering tool in amber which only take trj file.
>
> Thanks
>
> -Ranqi
>
> --
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Re: [gmx-users] RE: optimizing the mailing list

[Omer Markovitch]

Using emails, this might be done "manually" - each user will add to the
TOPIC something like: "tag install", etc`.
Then each user could define his own rule, in his personal email account, how
to deal with messages that contain "tag xxx" & "gromacs" in the topic.
Just a thought... Omer.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Mon, Sep 8, 2008 at 21:17, David van der Spoel <[EMAIL PROTECTED]>wrote:

> Vitaly Chaban wrote:
>
>> it's called internet forum... :)
>>
> we've had this discussion before.
> On a forum many of the hardcore gromacs people (like me) would probably not
> respond anymore.
>
>
>> I suggest that we consider ways in which the mailing list can be
>>> optimized. My initial thought is to allow submitters to flag messages  as
>>> belonging to some particular topic(s).
>>>
>>> e.g.
>>> "program crash"
>>> "force fields"
>>> "protein"
>>> "free energy"
>>> "coarse graining"
>>> "lipids and detergents"
>>> "unknown"
>>> etc.
>>>
>>> Since the submission is by regular email and hence there is no
>>>  possibility of introducing a radio box with topic options, this could  be
>>> implemented by allowing any user to define the topic to which a  particular
>>> message belongs. Ideally, the submitter would go to the  website after
>>> submission and set the topic of their own submission.
>>>
>>> If the archives then allowed a user to view only a particular topic,
>>>  then this would offer an alternative to the search tool, and also a  link
>>> to such a topical list could be posted in the relevant pages on  the wiki.
>>>
>>> I realize that the actual coding of such an interface may not be
>>>  available at this time. But I suspect that somebody on this list knows
>>>  some type of useful optimizations that are possible at this time.
>>>
>>> Chris.
>>>
>>
>>
>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
> [EMAIL PROTECTED][EMAIL PROTECTED]   http://folding.bmc.uu.se
>
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Re: [gmx-users] RE: manipulation of trajectory data

[Omer Markovitch]

to me too.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Mon, Sep 8, 2008 at 16:30, Vitaly Chaban <[EMAIL PROTECTED]>wrote:

> gurgo> If anyone has a simpler example along the lines of my interests,
> gurgo> please send me it!
>
>
> and to me...
>
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Re: [gmx-users] installation and fftw

[Omer Markovitch]

Regarding buildit FFT - I believe they say it is slower then other packages.
Omer.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Thu, Sep 4, 2008 at 21:54, Myunggi Yi <[EMAIL PROTECTED]> wrote:

> I have done the compilation.
> Thank you so much.
>
>
>
> On Thu, Sep 4, 2008 at 12:08 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
>
>>
>>
>> Myunggi Yi wrote:
>>
>>> Thank you for your answer, but I can't really get you.
>>> I am using gromacs 3.3.3. .> on CentOS
>>> with AMD64 clusters with infiniband connection.
>>> I have both INTEL and GNU copilers (gcc4.1.2 and gcc3.4) and openmpi
>>> (intel and gnu).
>>> You are saying I don't have install fftw by myself, aren't you?
>>> Then how can I compile? What is the best option for the performance?
>>> I did the followings.
>>>
>>> ==
>>> ./configure --prefix=$HOME/gromacs/ --with-fft=fftw2
>>> make
>>> make install
>>>
>>> make clean
>>> ./configure --enable-mpi --disable-nice $HOME/gromacs/ --with-fft=fftw2
>>> --program-suffix=_mpi
>>> make mdrun
>>> make install-mdrun
>>> ==
>>>
>>> Is this wrong?
>>>
>>
>> Seems reasonable, did it work?
>>
>> Can I compile it with intel compiler?
>>>
>>
>> It is easy to use gcc, and definitely do *not* use gcc-4.1.2; use 3.4.
>>  There are step-by-step instructions on how to install both FFTW and Gromacs
>> on the Gromacs website:
>>
>> http://www.gromacs.org/content/view/23/33/
>>
>> Following these directly will give you the standard installation, in
>> serial and parallel, and single and double precision, if you choose.
>>
>> -Justin
>>
>>
>>> I'm sorry. I have so many questions.
>>> Please let me know how to compile it.
>>>
>>> Thank you.
>>>
>>>
>>> On Thu, Sep 4, 2008 at 11:40 AM, Roland Schulz <[EMAIL PROTECTED] >> [EMAIL PROTECTED]>> wrote:
>>>
>>>Hi,
>>>
>>>Gromacs has it's own parallel FFT which only uses FFTW for the local
>>>FFT. Thus a non-MPI FFTW is fine. and FFTW 3 is faster than 2.
>>>
>>>Roland
>>>
>>>On Thu, Sep 4, 2008 at 8:53 AM, Myunggi Yi <[EMAIL PROTECTED]
>>>> wrote:
>>>
>>>Dear gmx users,
>>>
>>>fftw3 seems doesn't support MPI.
>>>Why is the gromacs configuration default fftw3 not fftw2?
>>>Which version should I use for parallel computing?
>>>
>>>Thank you.
>>>
>>>
>>>--Best wishes,
>>>
>>>Myunggi Yi
>>>==
>>>KLB 419
>>>Institute of Molecular Biophysics
>>>Florida State University
>>>Tallahassee, FL 32306
>>>
>>>Office: (850) 645-1334
>>>http://www.scs.fsu.edu/~myunggi <
>>> http://www.scs.fsu.edu/%7Emyunggi >
>>>[EMAIL PROTECTED] 
>>>
>>>___
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>>>.
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>>>
>>>
>>>
>>>--ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
>>>
>>>
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>>>
>>>
>>> --
>>> Best wishes,
>>>
>>> Myunggi Yi
>>> ==
>>> KLB 419
>>> Institute of Molecular Biophysics
>>> Florida State University
>>> Tallahassee, FL 32306
>>>
>>> Office: (850) 645-1334
>>> http://www.scs.fsu.edu/~myunggi
>>> [EMAIL PROTECTED] 
>>>
>>>
>>> 
>>>
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>>
>> --
>> 

Re: [gmx-users] printing coords ; energies

[Omer Markovitch]

Thank you.
Sorry for not being clearer. I meant where in the source code are the energy
related functions & variables?
Omer.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Thu, Sep 4, 2008 at 16:19, Jochen Hub <[EMAIL PROTECTED]> wrote:

> Omer Markovitch wrote:
> > Dear All,
> > I would like to consult you on the following two things:
> >
> > 1) I have a small, preanalysis, routine I would like to run each time a
> > frame is written and added to the trajectory file.
> > After some checking, I believe that, in the file "*stat.c*", the routine
> > "*void write_xtc_traj(FILE *log,t_commrec *cr,
> >   char *xtc_traj,t_nsborder *nsb,t_mdatoms *md,
> >   int step,real t,rvec *xx,matrix box,real prec)*"
> > is the routine actually printing each frame.
> > Is this true or perhaps I've missed something?
> >
> > 2) Regarding energies - where are the energies stored? I mean the energy
> per
> > type?
>
> The energies of the energy groups (as defined in the mdp file) are
> stored in the edr file (ener.edr by default).
>
> jochen
>
> > In which file & variable is this defined?
> > I understand that these values are printed to the log file (usually named
> > md.log), but I failed to locate the exact functions dealing with this.
> >
> > Thanks, Omer.
> >
> > Koby Levy research group,
> > Weizmann Institute of Science.
> > http://www.weizmann.ac.il/sb/faculty_pages/Levy/
> >
> >
> >
> > 
> >
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> --
> 
> Dr. Jochen Hub
> Max Planck Institute for Biophysical Chemistry
> Computational biomolecular dynamics group
> Am Fassberg 11
> D-37077 Goettingen, Germany
> Email: jhub[at]gwdg.de
> Tel.: +49 (0)551 201-2312
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[gmx-users] printing coords ; energies

[Omer Markovitch]

Dear All,
I would like to consult you on the following two things:

1) I have a small, preanalysis, routine I would like to run each time a
frame is written and added to the trajectory file.
After some checking, I believe that, in the file "*stat.c*", the routine
"*void write_xtc_traj(FILE *log,t_commrec *cr,
  char *xtc_traj,t_nsborder *nsb,t_mdatoms *md,
  int step,real t,rvec *xx,matrix box,real prec)*"
is the routine actually printing each frame.
Is this true or perhaps I've missed something?

2) Regarding energies - where are the energies stored? I mean the energy per
type?
In which file & variable is this defined?
I understand that these values are printed to the log file (usually named
md.log), but I failed to locate the exact functions dealing with this.

Thanks, Omer.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
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