Re: [gmx-users] Combining LJ and buckingham potential

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

Re: [gmx-users] Re: Alternative TRP residue

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/ ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/

Re: [gmx-users] PBC

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/ ___ gmx-users mailing listgmx-us

[gmx-users] non squares box

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

Re: [gmx-users] non squares box

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/Lev

Re: [gmx-users] non squares box

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 w

Re: [gmx-users] Protein going out of the box

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

Re: [gmx-users] Periodic Boundary Condition Issues

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

[gmx-users] table extension

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, angle

Re: [gmx-users] table extension

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-e

Re: [gmx-users] table extension

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 c

Re: [gmx-users] table extension

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

Re: [gmx-users] Large fluctuation of protein temperature with nose hoover thermostat

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

Re: [gmx-users] 1-4 interaction between atoms in PBC mode

> > > 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

Re: [gmx-users] Trajectory files in vmd

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

Re: [gmx-users] question about energy minimization

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.

Re: [gmx-users] Parameter to for randomizing simulation

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/ O

Re: [gmx-users] problem in loading xtc in VMD

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 ht

Re: [gmx-users] option for finding forces between two groups

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

Re: [gmx-users] Making Commands Non-Interactive

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/

Re: [gmx-users] reduced units

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 u

Re: [gmx-users] Coarse-Grain: GROMACS bond information to VMD

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,

Re: [gmx-users] g_rdf and number of atoms to include

, 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. _

Re: [gmx-users] g_rdf and number of atoms to include

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 thre

Re: [gmx-users] Decreasing MSD of ligand ?

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 tim

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

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 W

Re: [gmx-users] Normalization in g_rdf

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 l

Re: [gmx-users] g_msd => The MSD and periodic boundary condition

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 ha

Re: [gmx-users] Simulation at unrealistic temperatures

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 s

Re: [gmx-users] trajectory info

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 ca

Re: [gmx-users] diffusion coefficient

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 >

[gmx-users] searching the archives

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. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search th

[gmx-users] Fwd: charges,resonance and electrostatics

late 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 mista

Re: [gmx-users] Fwd: charges,resonance and electrostatics

> > >> 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, wh

Re: [gmx-users] HB lifetime

ows 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 ra

Re: [gmx-users] Hydrogen Bond Lifetime

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. _

[gmx-users] trjconv - converting trajectory into a pdb

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

Re: [gmx-users] Simulation of a protein confined in a box

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

Re: [gmx-users] Simulation of a protein confined in a box

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:

Re: [gmx-users] Simulation of a protein confined in a box

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 gue

Re: [gmx-users] range of gen_seed

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 s

[gmx-users] stochastic dynamics , langevin

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 prope

Re: [gmx-users] stochastic dynamics , langevin

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

Re: [gmx-users] temperature coupling strength

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

[gmx-users] small protein & big frozen group - exploding

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

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

> > > 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 ap

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

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

Re: [gmx-users] time of dynamic

> > >> 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

Re: [gmx-users] RE: How to output a single index group

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

[gmx-users] Barostat & Density decreasing to zero

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

Re: [gmx-users] Turning off electrostatic or Van der Waals interactions

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 simulatio

Re: [gmx-users] Diffusion coefficients ( Exp X Simul )

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

Re: [gmx-users] initial velocities Langevin dynamics

scaled 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.

Re: [gmx-users] is there a possibility to convert .gro files directly to PDB?

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/ ___ gmx-users mailing listgmx-users@gromacs

Re: [gmx-users] (no subject)

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 neibo

[gmx-users] printing coords ; energies

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_c

Re: [gmx-users] printing coords ; energies

OTECTED]> 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. > >

Re: [gmx-users] installation and fftw

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

Re: [gmx-users] RE: manipulation of trajectory data

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! > > >

Re: [gmx-users] RE: optimizing the mailing list

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 r

Re: [gmx-users] How to convert gromacs traj file(.xtc) to amber traj file?

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.weizma

Re: [gmx-users] D2O

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

[gmx-users] defining group

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/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman

Re: [gmx-users] defining group

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

Re: [gmx-users] kill some atoms

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 ph

Re: [gmx-users] GROMACS sample procedure

arest 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, Christophe

Re: [gmx-users] RE: Time step in md

s 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. __