Re: [gmx-users] -center -fit dodecahedron : dimer

Hi Nahren, > trjconv -f promd.trr -s proem.tpr -pbc nojump -o nojump.xtc > trjconv -f nojump.xtc -s proem.tpr -pbc mol -ur compact -center -boxcenter > tric -o center.xtc > trjconv -f center.xtc -s proem.tpr -fit rot+trans -o fit.xtc > 1. The above procedures does not center the molecule in the

Re: [gmx-users] No such moleculetype Na

Hi Swati, Sorry, I wasn't paying that much attention indeed and failed to notice you were dealing with Amber. There's nothing wrong with your installation in this regard; Gromacs just does not have Amber included by default. I'm not sure if there's an ions.itp for Amber somewhere, but it's not to

Re: [gmx-users] No such moleculetype Na

Hi Swati, > Fatal error: > No such moleculetype Na > > But the atom type is present in ffamber03.rtp. I tried changing the atom > name to NA and Na+. But I still get similar error. Kindly help. It doesn't complain about the atom type, but about the moleculetype. Did you #include "ions.itp"? That

Re: [gmx-users] about the bond connection between different groups

Hi He Yang, Justin, >> You have said bonds between distinct molecules require a merged topology. >> Is >> there any introduction in the manual or Do you have any example about the >> merged topology? >> > > A merged topology contains multiple moleculetype definitions in one > topol.top. Discussion

Re: [gmx-users] Problem with grompp?

dout.mdp was created correctly, I hadn't noticed this > error. > > Thank you everyone for your help! > Bram van Hoof > > -Original Message- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On > Behalf Of Tsjerk Wassenaar > Sent: dond

Re: [gmx-users] Problem with grompp?

Hi Bram, Check the creation times for topol.tpr and minimized.gro. First test the assumption that the former was created later than the latter. If it's not, then check the grompp output for errors. Maybe pasting it here can help. Cheers, Tsjerk On Thu, Apr 16, 2009 at 10:57 AM, Hoof, B. van wr

Re: [gmx-users] problem during inflatgro process

Hi Nitu, First of all, please try to use proper english for communication. This way 'u don't make it EC-r 4 us'. Second, you'd be better off getting some understanding of how topologies and coordinate files are put together before trying to do these things. A question like 'can I remove something

Re: [gmx-users] How to restrain ligand atom position

Hi Hitesh, The posre.itp file only contains a header [ position_restraints ] followed by a list of atom numbers and restraint force constants. Check chapter 5 of the manual for how and what. For a ligand it's probably best to directly add the [ position_restraints ] section in the file with the [

Re: [gmx-users] calculating com-com distances.

algorithm of how such things are calculated? > > Thanks again! > > Fernando. > > > > > > -- > And Noel Gallagher said: Gromacs is gonna live forever! > > 2009/4/13 Tsjerk Wassenaar > > > > Hi Fernando, > > > > > > > I'

Re: [gmx-users] problem in energy minimisation during inflategro process.

Hi, In addition to Mark's comments: > ; Include chain topologies > #include "rr1_A.itp" > #include "rr1_B.itp" > > ; Include position restrain protein > #ifdef POSRES_PROTEIN > #include "rr1_A_pr.itp" > #include "rr1_B_pr.itp" > #endif > This is rubbish. Position restraints are defined as part o

Re: [gmx-users] Mg ion not recognize.

Hi. Mg is probably in the force field already. You don't need to run it through pdb2gmx. Add it manually after generation of the topology for the protein. #include "ions.itp" in the topology file and add the correct name (check ions.itp) under [ molecules ]. Be sure to have all atoms matching in o

Re: [gmx-users] calculating com-com distances.

Hi Fernando, > I've obtained the vectors for the rectangular box in g_energy, > using Box_XX, Box_YY and Box_ZZ options; I didn't use the vectors of the > skewed box.) You have to use the three vectors from the tricilinic representation to obtain the correct distance in the periodic system. Check

Re: [gmx-users] Membrane protein tutorial

e are developing a new course within our > department related to molecular modeling. > > As for a handout of the tutorial, I do not have one at the moment, but I'd > be happy to send one to you when I do.  I have my prelim/qualifying exam > next week, so I'll be a bit tied up

Re: [gmx-users] Membrane protein tutorial

Hi Justin, Pretty neat. Thnx! Just a few comments, also on the lysozyme one. I think it's best to name and explain all options you use for a program, to take as much of the 'magic' out as possible. Having unexplained options may make students, mainly undergrads, go into a non-absorbant mode, just

Re: [gmx-users] Problems with Jacobi diagonalization

Hi Dayle, Quite a number of posts here :) Okay, so there may indeed (still) be a mismatch. Maybe good noting that g_covar will also accept a .pdb file as reference. One way to be sure that things go right is to convert the .tpr to .pdb using the index with the group 'TDR': editconf -f topol.tpr

Re: [gmx-users] Problems with Jacobi diagonalization

Hi Dayle, Errm, really, the only cases I know of this error to occur is when I had a mismatch between the reference and trajectory. Did you specify xtc-groups? Did you shuffle the system? How did you assert that you have matching series? Have you tried using the reference and the trajectory to con

Re: [gmx-users] How to calculate the dihedral angle variations ???

Hi Venkat, What exactly do you mean with variations. Do you want to follow the angle over time, or do you want distributions with mean and variance estimates? g_angle and g_chi seem to be the appropriate tools. You mention you tried all suitable options, but fail to explain what you tried and what

Re: [gmx-users] solvent box outside protein

No, not this one again! Why not search the archives? Or browse the wiki? Or follow a more extensive tutorial on Gromacs: http://nmr.chem.uu.nl/~tsjerk/course/molmod/ ? Tsjerk 2009/3/30 Halie Shah : > > Hi, > > I just finished my energy minimization run on GROMACS 4.0.4 for my > ligand/protein co

Re: [gmx-users] grompp errors

No. Even though you give the grompp output, you haven't told what you tried to do, which force field you're using and what you did to come to this stage. We can't guess what's in you're topology file. You also clearly haven't searched the archive for posts on "No default ... types", and thus give

Re: [gmx-users] drug-enzyme simulation.

Hi Neha, I guess you're referring to John Kerrigans tutorial, but it would usually help if you specified the one you're using. I think the tutorial should have a sentence stating that the ligand mayb be seen away from the protein during the simulations, but that that is due to the periodic boundar

Re: [gmx-users] Re: g_covar

Hi, The covariances are defined as the second central moment, i.e. the mean square displacement about the mean. Thus to make the PCA interpretable straightforwardly, you'll need to calculate the fluctuations with respect to the average structure. This stands apart from fitting. The fit is perform

Re: [gmx-users] Re: About Gromacs

Hi Xi Ouyang, > > Right now I'm doing wavelet-based coarse-graining model of stretching > the protein. Wavelet is easy to play with under Matlab. Now I want to do is > try to do wavelet decomposition (like fourier decomposition) on the > potential function of the protein and try to do the MD, us

Re: [gmx-users] PBC dodecahedron

Hi Nahren. > > I have run my simulation for 12 ns (of a protein dimer ).. I see the box > remain octahedron till about 5 ns after that the sides of the dodecahedron > becomes unequal. > i tried -pbc atom/whole etc, but does not help. > Any advice on the issue will be truly helpful. > > regards, >

Re: [gmx-users] Binding Copper to Protein

Hi, Justin raises a number of problems, but there's another one. Copper is a transition metal with a specific coordination which depends on the oxidation state. If you only use bonds, you sort of assume that the coordination geometry is the result of a size-exclusion effect. In this respect, coppe

Re: [gmx-users] gromacs 4 mpi weirdness

wrote: > Hi Tsjerk, > > I've encountered problem #2 with GMX 4.0.2 before. I'm not exactly sure > what went wrong, but it may have been due to mpi. With lammpi things work. > > Hope that helps, > > Ran. > > Tsjerk Wassenaar wrote: >> Hi, >> >>

[gmx-users] gromacs 4 mpi weirdness

Hi, I'm running in trouble trying to compile gromacs 4.0.x on our national Intel Xeon Linux cluster (Lisa/Sara). The same problem pops up with different compilers (GNU GCC 3.4, 4.1 (default on the cluster :p), Intel). I'm using fftw-3.2.1 and mpich/gnu c.q. mpich/intel. mdrun compiles, but when I

Re: [gmx-users] pdb2gmx error

Hi, >>        --- >>        Program pdb2gmx, VERSION 4.0.3 >>        Source code file: pgutil.c, line: 87 >> >>        Fatal error: >>        Atom N not found in residue 1094904186 while adding improper >> >>        --

[gmx-users] Fwd: using oplsaa in Gromacs

I refuse to act as a mailing-list subsitute. And there are others better fit to point you to: http://www.catb.org/~esr/faqs/smart-questions.html http://wiki.gromacs.org/index.php/Parameterization Tsjerk -- Forwarded message -- From: oguz gurbulak Date: Sun, Mar 15, 2009 at 2:50

Re: [gmx-users] Triclinic water box for a protein MD

try and implement something like these > restraints for ages but never got round to it, you know how it is ... > > Tom > > --On 13 March 2009 21:06 +0100 Tsjerk Wassenaar wrote: > >> Or, you use our server (http://haddock.chem.uu.nl/Squeeze/) to get an >> optimally

Re: [gmx-users] Triclinic water box for a protein MD

trajectory, bearing in mind if they do then you will have wasted > a lot of time. > > If you do want to use a triclinic box having a larger amount of water > surrounding the complex may be advisable as this makes images interacting > less likely > > Tom > > --On Friday

Re: [gmx-users] Triclinic water box for a protein MD

Hi, You have to make sure that you're molecule doesn't rotate. Otherwise it will cause direct interactions over the PBC. The same holds true for large conformational changes. Cheers, Tsjerk On Fri, Mar 13, 2009 at 7:26 PM, Justin A. Lemkul wrote: > > > Lucio Montero wrote: >> >> I want to simu

Re: [gmx-users] Variance in ED

Hi Andrea, You're welcome. I forgot to mention that my MD tutorial also has a part dedicated to PCA: http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis.html Maybe you'll find it useful. Cheers, Tsjerk On Fri, Mar 13, 2009 at 4:44 PM, andrea carotti wrote: > Dear Dr. Wassenaar, > many thank

Re: [gmx-users] Fwd: Force Field - Gromos96

Hi C Kim, The GROMOS96 force _is_ a united atom force field. Cheers, Tsjerk On Fri, Mar 13, 2009 at 5:30 AM, Tree wrote: > > > -- Forwarded message -- > From: tree > Date: Thu, Mar 12, 2009 at 10:09 PM > Subject: Force Field - Gromos96 > To: gmx-users@gromacs.org > > > Dear Al

Re: [gmx-users] Variance in ED

Hi Andrea, The variance associated with an eigenvector is the eigenvalue. The sum of the eigenvalues captures the total variance. Accordingly, dividing an eigenvalue by the sum of all eigenvalues gives the part of the total variance explained by the eigenvector. Cheers, Tsjerk On Thu, Mar 12, 2

Re: [gmx-users] metal ion go out of protein after md

Nothing, except reading more about periodic boundary conditions. It doesn't hurt though to understand that binding of ions such as Mn to proteins involves charge transfer effects, that are hard to model properly. This will cause a (further) deviation between your results and reality. So be careful

Re: [gmx-users] Fatal error: 2 atoms are not part of any of the T-Coupling groups during md simulation.

Hi Chitrita, > I am not very clear about the parameters used in mdp files. So I am sending > the mdp file here. This is of course vital when performing simulations. Do read up on these things. This is the part of the .mdp file that determines the how and what of temperature coupling: > ; Beren

Re: [gmx-users] Fatal error: 2 atoms are not part of any of the T-Coupling groups during md simulation.

Hi Chitrita, You'll have to make sure that whatever t-coupling groups you've specified (referring to groups in pr.ndx) together capture all atoms. This stands apart from the topology and coordinates. If you're not sure, paste the temperature related mdp options for us to be able to help you furthe

Re: [gmx-users] Gromac4 grompp -v Err

Hi Li Bei, You're using an old .mdp parameter file. Use a new one. If you make an empty .mdp file (touch empty.mdp) and use it as input to grompp, a .mdp file with all parameters set to default will be generated (mdout.mdp). Cheers, Tsjerk On Tue, Mar 10, 2009 at 9:59 AM, li bai wrote: > Hello

Re: [gmx-users] Isn't dt=0.0001 very small?

Hi Andrew, > I'm doing this tutorial: > https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf > and I have an error with dt=0.002 or even dt=0.001 in pr.mdp during > equilibration. It works only with dt=0.0001 which seems very very small step > for me. Your observation is correct:

Re: [gmx-users] genion command with PDB files for amber03 force field

Hi, To set things straight a bit. >> "If you are using ion-related GROMACS tools, such as genion, you will need >> to enter the AMBER ion definition to the ions.itp file in the "top" >> directory of the GROMACS distribution." > > This isn't too tough, as all the parameters for the ions are includ

Re: [gmx-users] Can not open file: topol.tpr

Hi, You mentioned it was from following a tutorial. In that case also always check whether your line reads exactly the same as is stated in the tutorial. Besides, indicate which tutorial, as there are many, and if you find that it was an error in the tutorial rather than your typo, also report tha

Re: [gmx-users] How to handle incomplete PDB file?

Read all mails in this thread... (and the archives) Tsjerk On Tue, Mar 3, 2009 at 2:08 PM, Lee Soin wrote: > Then what should I do? > > 2009/3/3 Justin A. Lemkul >> >> >> Justin A. Lemkul wrote: >> Specifying -missing in pdb2gmx doesn't work. >> >> Also, don't do this.  Note from the pdb2g

Re: [gmx-users] trjconv fit subset of atoms

Josh, -n indicates that groups are to be read from the index file, rather than using the standard groups. It's not related to what the group is being used for. Cheers, Tsjerk On Thu, Feb 26, 2009 at 11:34 PM, Joshua Adelman wrote: > I'm using 4.0.2. There are three optional ndx flags, -n -sub

Re: [gmx-users] trjconv fit subset of atoms

Hi Josh, When fitting, trjconv asks for separate groups for performing the fit and for the output. No need to hack anything. You can make a suitable index file using make_ndx. Cheers, Tsjerk On Thu, Feb 26, 2009 at 7:47 PM, Joshua Adelman wrote: > I am trying to use trjconv to generate a new .

Re: [gmx-users] problem in creating topol.tpr file

Read for yourself. Think for yourself. If we are to answer a question, we want to know that the receiver is capable of reading (the answer) and to comprehend (the answer). It's up to you to show that you are so capable (by showing you've read the output and thought it over) that answering your ques

Re: [gmx-users] Atom H2 not found in rtp

Hi Varsha, What force field did you use? What atoms are listed for residue 'BEN' in that force field? What atoms are listed for residue 'BEN' in the .pdb file? Tsjerk On Thu, Feb 26, 2009 at 5:41 AM, varsha gautham wrote: > Hello, gmx-users， >i used command"pdb2gmx -f a.pdb -ign

Re: [gmx-users] How to define new residue in GROMACS?

Hi Yiming Chen, In this case there's no need to add GTP as a building block. Have a look at John Kerrigan's drug - enzyme tutorial to see how to include a prodrg topology in your simulation: http://wiki.gromacs.org/index.php/Tutorials Also, do note the caution regarding non-standard groups in yo

Re: [gmx-users] problem in running gromacs

Hi, Hmm, once you manage to deal with that issue, you're in for a gmx_sumi fatal error. What's the thing with version 3.3.2 these days? You really should try to get another version of Gromacs before continuing. Cheers, Tsjerk On Sat, Feb 21, 2009 at 11:33 AM, Mark Abraham wrote: > nitu sharma

Re: [gmx-users] pre-compiled MacOS 3.3.2 gmx_sumi error

Hi Dean, Apparently I stopped reading somewhere before the end of your mail. Our IT department had installed Gromacs 3.3.2, and most of the students ran into the gmx_sumi error during the tutorial mentioned :( A few students ran through the tutorial with Gromacs 4.0.2 without problems. The only di

Re: [gmx-users] pre-compiled MacOS 3.3.2 gmx_sumi error

Hi Dean, That bug has been fixed for all later versions. Tsjerk On Fri, Feb 20, 2009 at 6:16 PM, Dean Cuebas wrote: > Dear users, > > I have the precompiled macosx 3.3.2 package, and I'm getting the following > error during a PR mdrun: > > ---

Re: [gmx-users] Virtual atom

Hi, The virtual atoms are residue-bound and will have the same residue name as the atoms it is constructed from. There's no residue name DUM introduced. Tsjerk On Thu, Feb 19, 2009 at 4:06 PM, Georgios Patargias wrote: > Hello > > When a virtual atom is constructed from a two protein atoms, is

Re: [gmx-users] Problem in preparation of the enzyme/substrate complex

with force field parameter as Justin said. Maybe i should take the > feasibility of my original plan into a good consideration. Anyway, so much > thanks to you guys. Mark, Tsjerk, Justin and everyone here. > > Regards > Ji > > On Thu, Feb 19, 2009 at 8:43 PM, Tsjerk Wassenaar wrot

Re: [gmx-users] Problem in preparation of the enzyme/substrate complex

dduct such as you've shown > has not been parameterized within the Gromacs implementation of Gromos96. > If other researchers have done it, then your best bet is to see how they > did it and hopefully apply it to your situation. > > Otherwise, you have a long project ahead of y

Re: [gmx-users] Problem in preparation of the enzyme/substrate complex

s 96 > force field (may be he modified these force field too) to a similar > enzyme/substrate system, and hope i can get some information from him. Even > though, i really eager to get some knowledge from all of gmx-users. Anyway, > I'm always grateful for your comment. &g

Re: [gmx-users] Problem in preparation of the enzyme/substrate complex

Hi, > I'm not familiar with > i can't tell myself which > guess i can > I have no idea whether This is the worst possible basis for trying to modify a force field. First get well acquainted with molecular dynamics and the role and whereabouts of force fields. Then you can start thinking of using

Re: [gmx-users] NVT or NPT ?

And not to forget: most experiments are performed under (more or less) constant pressure. In that sense, NPT simulations are 'more like the real thing'. Cheers, Tsjerk On Wed, Feb 18, 2009 at 5:21 AM, wrote: > short answer: volume equilibration and therefore density equilibration. Even > peopl

Re: Re (in reply to Tsjerk): [gmx-users] Porcupine Plots

ahren manuel wrote: > Dear Dr. Tsjerk, > > thanks for your reply. I got the clue from your reply and i did the same via > VMD. But can you please be little more speicific about Pymol. I am not quite > used to that software. > > regards, > nahren > > > --- On M

Re: [gmx-users] about dumping the last frame

Hi Shirin, The sed-solution is: sed -ne '/^MODEL/,/^ENDMDL/{/^MODEL/{x;d};H}' -e '${x;p}' traj.pdb Which might come in handy as an alias (csh-style:) alias lastmodel "sed -ne "/^MODEL/,/^ENDMDL/{/^MODEL/{x;d};H}" -e "${x;p}" \!*' Hope it helps, Tsjerk On Mon, Feb 2, 2009 at 8:03 AM, nahren

Re: [gmx-users] Porcupine Plots

Hi Nahren, Gromacs does not include a tool for generation of porcupine plots. But if you're offered a means to do it through a webservice, all you really need is to take the extreme projections (two frames: g_anaeig -extr) and submit them. In a sense, you'll get the same thing if you load the extr

Re: [gmx-users] query about random velocity generation

Hi Sangeeta, Different temperatures always come with different velocities, as these are related to each other. If you want to have different simulations for the same temperature then you have to change the number for gen_seed. As for the range, you're stuck with that for a signed (?) int, but that

Re: [gmx-users] Help

Hi Jason, Unfortunately for you this is not the gmx.com-mail-users forum, but the gmx-shorthand-for-the-gromacs-program-users forum. So unless you want to try and simulate wildlife - for which there are better programs - you're probably better off at www.gmx.com. Now, if I help you out, am I ellig

Re: [gmx-users] restore pbc after a rotation

Hi Xavier, By when do you need it? You can send me one frame ( .gro) and I can see what I can do. But no guarantees, and no time indication :( Cheers, Tsjerk On Mon, Jan 26, 2009 at 7:11 PM, XAvier Periole wrote: > > On Jan 26, 2009, at 12:58 PM, Tsjerk Wassenaar wrote: > >

Re: [gmx-users] restore pbc after a rotation

Hi XAvier, Unfortunately, you're out of luck. The coordinates do not contain information regarding the proper orientation with respect to the coordinate system. That's the short answer. I guess you did save all atoms, at least of proteins and lipids, in which case you could do a search for a rota

Re: [gmx-users] g_rms: Too many iterations in routine JACOBI

Hi, On Sat, Jan 24, 2009 at 12:04 PM, nishtha pandey wrote: > Hello everyone, > While trying to do the RMSD analysis of my trajectory > file I am facing the error " Too many iterations in routine JACOBI". I have > gone through the archives which suggests that such problem ari

Re: [gmx-users] problems with pdb2gmx command

Hi Jacob, Check the output from pdb2gmx. It works with the tutorial files, so the problem is with your input, not with the program. Tsjerk On Thu, Jan 22, 2009 at 5:39 PM, wrote: > I'm having issues with the pdb2gmx command in gromacs. It does not seem to be > creating the .gro file for some r

Re: [gmx-users] MD vs Scattering

Hi Lin, Have you tried searching some articles on the matter? You're 10+ postings to this list on the subject haven't yielded much to date. If you want a better answer, you'll have to be more specific in what type of data you want to reproduce. Key thing is to understand what you get from scatteri

Re: [gmx-users] how to identify the hydrophobic core residue to calcuate gyration

What do you want to do? Please take some time to phrase a proper question. Tsjerk On Thu, Jan 22, 2009 at 7:04 AM, ravi sharma wrote: > > Hello guys, > neone have idea how to mark which are the hydrophobic residue to supply with > make index command and have to calculate the gyration curve. > >

Re: [gmx-users] is there any Problem in V. 3.3.3?

Hi Bala, My guess is you're running with position restraints on. Check the manual. And while you're at it, google for "how to ask questions the smart way". Tsjerk On Fri, Jan 16, 2009 at 3:00 PM, bala ms wrote: > Hi > I am new to Gromacs, I am using V3.3.3. I have run the MD simulation > (

Re: [gmx-users] atom H is missing in the first residue in a chain

Hi Justin/Zhong Zheng, > > Use -ignh to allow the relevant .hdb file to add the appropriate hydrogens. > The problem is that, without -ignh, pdb2gmx expects all atoms (including H) > to be present in the .pdb file. If you are using a crystal structure, this > requirement will not be satisfied. >

Re: [gmx-users] eigenvalues

f people use PCA on short trajectories, even > of large systems, which to me is confusing > > Thanks for any insights you can give > > Tom > > --On Saturday, January 10, 2009 11:49:18 +0100 Tsjerk Wassenaar > wrote: > >> Hi Sanjay, >> >> Imagine yourself zi

Re: [gmx-users] eigenvalues

Hi Sanjay, Imagine yourself zig-zagging along a line from one place to another. If you look at you're motion (and the variance), you'll find that if you only look at blocks most of it is explained by the zig-zag and nicely periodic (no cosine content as in Berk Hess' paper). Good, you think. But i

Re: [gmx-users] re : heme group

Well, if you look into the .rtp files for the GROMOS force field, you'll find heme in there, but maybe not in the right form or not in the format you have in the .pdb file. Whether something is in the residue (building block) topology libaray is not prinicply related to being amino acid. As if the

Re: [gmx-users] eigenvalues

Hi Monika, > As far as I know, PCA analysis breaks your total motion in system, or rather > decouples it into respective motions. Well, formally, PCA tries to provide an explanation of the total variance in the system, in terms of a set of new, linearly unrelated variables. > And by the eigenvec

Re: [gmx-users] eigenvalues

Hi, Well, the trace of the covariance matrix (thus the sum of the eigenvectors), should say something about overall flexibility. In that case, the observation that the protein with ligand seems more flexible than without is not completely incorrect. However, the question arises regarding the natur

Re: [gmx-users] Saving trajectories of a particular group within the system

re is > ignored", is incorrect according to you? Or is it only incorrect for the > option "xtc-groups"? > > If incorrect I'd say this should be changed asap. But actually I believe > it is correct, at least for the options I've tried. > > Thanks, >

Re: [gmx-users] Saving trajectories of a particular group within the system

Hi Wade, > > I intend to generate only the trajectories of my protein alone, > without outputing trajectories of the solvents. This is since the > output files can get really massive. So looking at the manual, I've > inserted the line: "xtc_grps = Proteins" into the .mdp input file and > did a sho

Re: [gmx-users] g_rmsd

Hi sh-karbalaee, g_rmsf by default uses deviations from the average structure. You can write out that structure and use it as reference for g_rms. Cheers, Tsjerk On Thu, Dec 4, 2008 at 6:52 AM, shahrbanoo karbalaee <[EMAIL PROTECTED]> wrote: > Dear justin > I want to calculate rmsd or rmsf fro

Re: [gmx-users] Re:Re: x2top

Hi, > > if i just use the topology of the sugar without the protein then the > simulations starts but the atoms are not moving during the simulation. they > are exactly at the same position in frame 1 and frame n. therefore had the > idea to use the build-in x2top function. so i would be glad to g

Re: [gmx-users] print out the velocities and forces using template.c

Hi Qiang, You'll have to check whether the frame contains velocities (fr.bV == TRUE) or forces (fr.bF == TRUE). Also make sure you set the flags right to read velocities/forces. Check the source of g_traj or trjconv for examples. Cheers, Tsjerk On Fri, Nov 28, 2008 at 10:33 AM, Mark Abraham <[E

Re: [gmx-users] Fatal error with grompp(with detail process)

Hi Jenny, The files lipid.itp/popc.itp contain references to atom types which are not in the G53a6 force field; that combination just doesn't work. lipid.itp/popc.itp were written to be used with another force field. It's generally not a good idea to mix force fields. Cheers, Tsjerk On Fri, Nov

Re: [gmx-users] x2top

Hi Bernhard, >> I tried to use the x2top function of gromacs 4 on a sugar-molecule. >> Library file ffG43a1.n2t not found in current dir nor in default Why would you want to use the Gromos96 43a1 force field for this and why use x2top to provide the topology for it? As Justin said, you could use

Re: [gmx-users] problems running grompp with protein-ligand complex

Hi Fabrício, > I've checked wikigromacs, but the solution given there, to simply erase the > second default line does not suit me here. Once I do this, i mean, go to my > ligand.itp file and put a ; before my default section, grompp does not > recognize anymore that my ligand is there and gives ou

Re: [gmx-users] Re: how to show dodecahedron box in VMD

Hi, Can't help you with VMD, but I do have a script to take care of this in Pymol. Cheers, Tsjerk On 11/25/08, xianghong qi <[EMAIL PROTECTED]> wrote: > Dear all: > > I am trying to show the dodecahedron box only in vmd since my simulation box > is dodecahedron. If I include water, I can see t

Re: [gmx-users] trjcat error

Hi QIU YI HUAN, Was it a warning or did it exit without producing output? Please be more complete in your postings. Maybe a good idea to include the output of the program? In case of an error use gmxcheck first on each of the trajectories. It seems that one of them is giving an error. Then, if yo

Re: [gmx-users] Re: grompp NOTE mdp file concerning steps

t; > A run I have now, which while was compiled gave the same note, has surpassed > the 32299167 > steps I found out that as a limit for this note. In other gromacs' I do not > get such errors. > > Good to have you back, > Nikos > > > > > > --- Tsjerk Wasse

Re: [gmx-users] mdrun in parallel

Hi Alessandro, With gromacs versions <4 you have to generate the .tpr file with grompp using the flag -np 16 to be able to run on 16 processors. But why not upgrade to gromacs 4.02 and get much better scaling? Cheers, Tsjerk On Fri, Nov 21, 2008 at 12:06 PM, <[EMAIL PROTECTED]> wrote: > Hi All

Re: [gmx-users] Re: grompp NOTE mdp file concerning steps

Hi Nikos, You mention it raises a note. What happens to the .tpr file? Can you look for nsteps in the output from gmxdump? Cheers, Tsjerk On Wed, Nov 12, 2008 at 2:45 PM, Claus Valka <[EMAIL PROTECTED]> wrote: > Hello, > > searching further the issue, I realized that no more than 32299167 numbe

Re: [gmx-users] flood of gmx's mails in my mailbox

...or use gmail. Tsjerk On Tue, Nov 11, 2008 at 1:31 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > > > Pathumwadee Intharathep wrote: >> >> Dear gmx-user, >> My mailbox has flood of gmx's mails. What should I do to digest them. >> > > Use the WWW interface to change your preferences to diges

Re: [gmx-users] g_rms

Hi Tatsiana, No. g_rms requires the input trajectory and the reference structure to match. Actually, the trajectory (if .xtc format) does not even contain information regarding the atoms; only coordinates. Tools depend wholly on the reference structure for information on atom/residue names, etc.

Re: [gmx-users] bad box in protein.gro

Hi Alessandro, editconf encounters a bad box in the input file and I think it first replaces that with a standard box internally. Check the box at the end of box.gro to see if the result is what it should be (nine numbers, according to the specification of the rhombic dodecahedon in Chapter 3 of t

Re: [gmx-users] Gromacs-4.0.2 is out

Hi, Thanks for the release. I notice that the modifications I sent for trjconv didn't make it. For those who are interested, replacing the distribution gmx_trjconv.c with the one attached will add the molecular shaped box to the unit cell options. This allows distributing the solvent around a solu

Re: [gmx-users] position restraint and pdb

Hi, > Yes. You can use GROMACS to simulate traffic if you want to. :-) Mark, do you have a force field for that? >> As i had done it with 4 residue with blocking group. But then i got the >> error for rvdw and rlist as they should be nearer to cutoff value. >> So instead of decreasing the value

Re: [gmx-users] g_rms

Hi Tania, The boolean options to the gromacs programs are (usually) set using (e.g.) -mw | -nomw Cheers, Tsjerk On Sat, Nov 8, 2008 at 5:00 AM, Mark Abraham <[EMAIL PROTECTED]> wrote: > Tatsiana Kirys wrote: >> >> Hi, >> >> i got strange results using g_rms. >> Does it by default uses mass wei

Re: [gmx-users] Repeating the simulation

Hi QIU YI HUAN, Radius of gyration is a configuration dependent property. You need statistics for that, so you should have more simulations. Jochens example of the rdf is one where the statistics comes from the number of molecules in your system (quite a number for water, versus one self-assembled

Re: [gmx-users] grompp error

hmm, okay, forget whatever you think I replied :) On 11/5/08, Berk Hess <[EMAIL PROTECTED]> wrote: > > Hi, > > There is a bug in the 4.0 grompp which causes problems when you have two > consecutive "blocks" with the same molecule type. > You will have to merge them into one block. > > I have

Re: [gmx-users] grompp error

Hi Supti, > -- > > Program grompp_d, VERSION 4.0 > Source code file: grompp.c, line: 352 > > Fatal error: > number of coordinates in coordinate file (file_b4em.gro, 46634) > does not match topology (file.top, 9977) > - It's just wh

Re: [gmx-users] problem with g_dist (probably solved)

Hi Thomas, To have PBC or not in a run has nothing to do with analysis. Analysis tools don't have a clue of what you put into the .mdp files. Any of tha analysis tools will assume that the box specified in the file involves PBC. Don't know from the top of my head, but I think where possibly necess

Re: [gmx-users] WARNING 1 [file aminoacids.dat, line 1]

Lin, Temperature coupling has nothing to do with having a protein or not. Likewise, pressure coupling, time step, total simulation length, temperature and a lot of other options have nothing to do with having protein or not. These are all basic things of performing simulations. Now, you followed a

Re: [gmx-users] Re: gmx-users Digest, Vol 54, Issue 138

gt;[EMAIL PROTECTED] > > > > You can reach the person managing the list at > >[EMAIL PROTECTED] > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of gmx-users digest..." > > > >

[gmx-users] Fwd: The question from the tutorial: Add water spc216.gro

sjerk -- Forwarded message -- From: Chih-Ying Lin <[EMAIL PROTECTED]> Date: Thu, Oct 30, 2008 at 7:35 AM Subject: The question from the tutorial: Add water spc216.gro To: Tsjerk Wassenaar <[EMAIL PROTECTED]> Hi I have a molecule, which is not a protein. Then, I made a .to

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