Re: [gmx-users] Missing Residues are list ind pdb file

Hi Jack, On Fri, Jan 15, 2010 at 8:05 PM, Jack Shultz wrote: > I'm trying to prep Fe-Hydrogenase again (1YQW). I took out all the > non-standard residues. Re-named n-terminal and c-terminal residues. Took out > connects because that worked last time though I'm uncertain if connect > really mater

Re: [gmx-users] The size of the domain decomposition grid (1) does not match the number of nodes (8).

Hi Chris, Don't have an answer too this one, but noticed the argument to the -np option > -np $(wc -l $PBS_NODEFILE | gawk '{print $1}') Maybe it's a bit easier on the eye to use: -np $(sed -n $= $PBS_NODEFILE) Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Ch

Re: [gmx-users] dynamic cross correlation map (DCCM)

Hi, Well I'd say that 'DCCM' refers to the matrix (map) of correlations and not to that of covariances. More specifically, it refers to correlations of positional fluctuations. PCA, on the other hand, refers to the extraction of components or axes which better describe the data than the original a

Re: [gmx-users] occupancy

Hi Carla, You can do lots of things. You can edit the occupancy field by hand, or do it with a tool like sed. You can also neglect the warning, provided that you're pretty sure the structure is okay. Partial occupancies occur when atoms can not be exclusively assigned to a single position. In thos

Re: [gmx-users] how to analysis crystal structure and 2D projections by PCA?

Xi Zhao, Find some elementary text on PCA and read it thoroughly. Tsjerk On Wed, Jan 20, 2010 at 2:40 PM, xi zhao wrote: > > Dear users: > I want to analyse a crystal structure by PCA, and want to show its 2D > projection, but I meet errors" segment fault" > my procedure: > g_covar_d -f crysta

Re: [gmx-users] Lipid parameters for GROMOS96 force fields

Hi, Well, we have compared the G53a5/6 force field with the 43a2 one and found consistently larger radii of gyration and higher RMSDs, suggesting decreased stability. There's a thorough account of it in my thesis (http://dissertations.ub.rug.nl/FILES/faculties/science/2006/t.a.wassenaar/04emb_c4.

Re: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial

Hi Vivek, > Now when I am processing the modified .gro file to generate box, the ligand > and cofactor are going away from the protein molecule and I am not able to > analyze the complex. Gradually going away, or suddenly jumping? In the latter case, read up on periodic boundary conditions. Tsj

Re: [gmx-users] GMXRC Problem

Hi Pawan, Check which shell you're actually running (probably bash), and source the shell specific GMXRC file (GMXRC.bash). Cheers, Tsjerk On Mon, Jan 25, 2010 at 8:19 AM, pawan raghav wrote: > Dear Justin, > > I have some problem regarding GMXRC execution, I got an error while using > gromacs

Re: [gmx-users] Re: about beta port of C27 FF to gromacs

Hi, >> --- >> Program pdb2gmx, VERSION 4.0.7 >> Source code file: resall.c, line: 344 >> >> Fatal error: >> in .rtp file in residue cmap at line: >>       -C      N       CA      C       +N >> :q! >> ---

Re: [gmx-users] Re: about beta port of C27 FF to gromacs

Hi Pär, I actually refered to the .rtp file. I think that the edit was there. Cheers, Tsjerk On Mon, Jan 25, 2010 at 12:24 PM, Pär Bjelkmar wrote: > Hi, --- Program pdb2gmx, VERSION 4.0.7 Source code file: resall.c, line: 344 >

Re: [gmx-users] running unrestrained MD for tutorial

Hi David, Always check which version a tutorial is written for. And also always mention which version you're running when posting a question/issue to the list. Now, with this error, I know you're running the (broken) GMX 3.3.2. The tutorial was written for 3.3.1, but will also work with 3.3.3. Ch

Re: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial

[gmx-users] Ligand coming out while trying Drug-enzyme >> tutorial >> >> >> >> HI Tsjerk, >> >> Thanks for your reply. But, I can't see if it is going suddenly or >> gradually. >> What i can see is the ligand is away from the molecul

Re: [gmx-users] grompp gives "no molecules were defined in the system"

Hi Marysa, The error is about the definition of mulecules, which suggests that there are no [ moleculetype ] directives. Did you #include the proper .itp file(s) with the necessary moleculetype definitions? If not, you'll have to provide more information, probably posting the topology file itself.

Re: [gmx-users] Re: including a custom itp file in topology

Hi, rtp stands for 'Residue ToPology' and is used exclusively for building block definitions, which are only used by pdb2gmx. itp stands for 'Include ToPology' and can contain any part of a topological description of a system, atom types, bond types, moleculetypes, definitions, to be #included at

Re: [gmx-users] Re: Step 6 of lysozyme tutorial

Hi Bharat, Besides the notes of Justin, which lysozyme tutorial? And for which GMX version was that tutorial written? Tsjerk On Sat, Jan 30, 2010 at 12:53 PM, Justin A. Lemkul wrote: > > > bharat gupta wrote: >> >> Hi >> >> I am getting the follwing error while running the mdrun command given >

Re: [gmx-users] last line in .gro file

Hi Vishal, Here is a python function that generates a triclinic representation given a definition with lengths and angles. The argument L is a tuple or list containing the lengths and angles. def triclinic(L): B = [[0,0,0],[0,0,0],[0,0,0]] x, y, z, a, b, c = L[:6] B[0][0] = x i

Re: [gmx-users] best interval for saving configurations ?

It also strongly depends on what analysis you try to do. For autocorrelation you should sample frequently enough, for other configurational analysis, you don't need so many points, for covariance analysis you should aim for a number of frames three times the number of atoms you want to analyze. Ch

Re: [gmx-users] Problem - can't set dodecahedrons box

Hi, > You can post-process your trajectory using "trjconv -pbc mol -ur compact" to >see the real > representation. The real representation is the infinite periodic system; there is no box shape there. For representation of a single unit cell you can take any cut that is consistent with the latti

Re: [gmx-users] Same starting structure but different trajectories

Hi Emanuel, Anything small can cause trajectories to diverge, it's chaos. The machine on which is run can make the difference. This is also covered in the list archives. > ;Temperature coupling > tcoupl           = nose-hoover > tc-grps          = protein NA+ CFP SOL > tau_t             = 0.1  0.

Re: [gmx-users] pbc whole

Hi Carla, Justin's recipe should've worked. As he suggested, maybe the ligand is not with the protein. You can check by multiplying your system with genconf: genconf -f in.pdb -o out.pdb -nbox 2 2 2 If the ligand is with the protein, one copy will be located in one of the copies of the protein.

Re: [gmx-users] pbc whole

p me analyze my results. > > Carla > > On Wed, Feb 17, 2010 at 10:25 AM, Tsjerk Wassenaar > wrote: >> >> Hi Carla, >> >> Justin's recipe should've worked. As he suggested, maybe the ligand is >> not with the protein. You can check by multiplying

Re: [gmx-users] pbc whole

Hi Carla, > I checked with genconf & now I'm certain that my ATP molecule is still with > the protein That's good to know :) >>> trjconv -s a.tpr -f b.xtc -o c.xtc -center -ur compact -pbc mol >>> (centering on "Protein") So what did come out of this then? It should have given you a compact rep

Re: [gmx-users] Help with Segmentation fault!!!

Hi Deisy, > define   = -DFLEXIBLE > integrator   = md Well, probably you'd be better off with 'integrator = steep'. If you're doing MD, better not define -DFLEXIBLE. But for the rest, you give little account of what you're doing. What about the workflow, where in your

Re: [gmx-users] (no subject)

Hi E R Azhagiya singam, You first have to ask yourself whether you're up to it. This is considered an advanded topic. In particular for groups like these. To start with, do you know the protonation state of the Zn(Cys)4 group in your case? Cheers, Tsjerk On Fri, Feb 19, 2010 at 9:14 AM, babu go

Re: [gmx-users] Normal Mode analysis

> Aside from that, search the literature; published papers should have > reproducible methodology :) And.., methodology in published papers has proven to be publishable. :) Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing l

Re: [gmx-users] Re: Protein carbohydrate interaction simulation

Ooh, this is just too funny :) >> Its me, Pawan. Hi Pawan! >> Dont post questions like these in the forum. >> Say to people that u did any ground work for what u want to study in. >> Like what all ppaers u got, what exactly u want to work in and what is ur >> control study and all that. >> If u

[gmx-users] Re: tautology (Normal Mode Analysis)

Hi Ken, To stay close to tautology, although not being strictly tautological, I think the answer to "I want to do normal mode analysis, could you tell me how" should be "If you don't know how to do normal mode analysis, then you shouldn't be doing normal mode analysis." (Bounced to the user li

Re: [gmx-users] Energy minimisation of solvated protein - Tutorial

rying to go through the 'Introduction to Molecular Dynamics > Simulations and Analysis' tutorial written by Tsjerk Wassenaar, one of the > tutorials listed on the GROMACS website. > > I've got to the stage where I am performing energy minimisation on my > solvated protein

Re: [gmx-users] g_sas

Hi Pawan, The legends are contained in the .xvg file. Try viewing the file. Cheers, Tsjerk On Mon, Mar 1, 2010 at 8:29 AM, pawan raghav wrote: > I executed the following command. > > g_sas -s mdrun.tpr -f mdrun.trr -or mdrun.xvg > > xmgrace -nxy mdrun.xvg > > I get two sets of values: one is b

Re: [gmx-users] Continuous trajectory from trjconv?

Hi Pablo, You want to mutually exclusive things. That is by definition impossible. Sorry, Tsjerk On Mon, Mar 1, 2010 at 11:02 AM, Pablo Englebienne wrote: > Hi, I made an NpT MD simulation of 10 copies of the same small molecule in > CHCl3 (dodecahedron unit cell) for 20 ns. I want to visualiz

Re: [gmx-users] gromacs memory usage

Hi Amit, I think the presentation gives right what you want: a rough estimate. Now as Berk pointed out, to allocate more than 2GB of memory, you need to compile in 64bit. Then, if you want to have a real feel for the memory usage, there's no other way than trying. But fortunately, the memory requi

Re: [gmx-users] g_mindist periodic boundary condition

Hi Dian, Which version of gromacs are you using? Can you assert that the pdb file has the correct box? It should have a line starting with CRYST1 (grep "^CRYST1" file.pdb). Some versions of gromacs (3.3.2 I think) didn't write the CRYST1 record, and thus disallow PBC related operations. Cheers,

Re: [gmx-users] g_mindist periodic boundary condition

quot;CRYST1 24 24 24" in the first line? > By the way is it CRYST1 or CRYSTL? > > And the command I was running was "g_mindist -f 1001.pdb -n 1001.ndx -od > 1001_C". > > Dian > > On Thu, Mar 4, 2010 at 12:38 AM, Tsjerk Wassenaar wrote: >> >> Hi Dian,

Re: [gmx-users] g_rms warning

Hi Carla, You'll have to use index groups to extract a trajectory and reference that correspond. If you have those you can get on with the RMSD. Cheers, Tsjerk On Mon, Mar 8, 2010 at 11:44 AM, Carla Jamous wrote: > Hi everyone, please I just need a precision: > > I need to calculate the RMSD o

Re: [gmx-users] Regarding defining termini in new rtp entry

Hi Ilya, If it is an amino acid, albeit modified, you can make pdb2gmx recognize it as such by adding it to the file 'aminoacids.dat'. This file is in the installation directory. You can also copy it to your working directory and change it there, as it will then take precedence over the other one.

Re: [gmx-users] rmsf question

Hi Andrei, You can do it this way. But do mind that the ensemble from NMR is not meant to reflect the Boltzmann distribution. Rather it is meant to provide a number of plausible solutions given the (positive) restraints from the experiments and the force field used for the refinement. This means t

Re: [gmx-users] rmsf question

Hi Andrei, > If I correctly uderstand the RMSF computed on C-alpha in PDB NMR > structure, is a measure of the uncertanty in resolving the structure. No, that's not what I said. You're saying that there's one structure (the structure), but there is uncertainty in resolving it. That's not the case

Re: [gmx-users] cross-correlations as a function of interatomic distance

Hi, Well, since interatomic distances are properties of single conformations and fluctuation covariances/correlations are properties of sets of conformations, it is simply impossible. You might plot the covariances/correlations against the mean distances, if you feel you must. Be sure to use the a

Re: [gmx-users] MD localized in the active site

Hi, You also have to spend a sufficient amount of thought on the question whether an approach like that will give you what you're after. It's not going to sample a relevant ensemble and you're disabling the long range correlations that may be of influence on ligand binding. Cheers, Tsjerk On We

Re: [gmx-users] about g_sas analysis

Hi, Recently there was a relatively extensive discussion on the list regarding g_sas. Check the archives. Cheers, Tsjerk On Thu, Mar 18, 2010 at 9:07 AM, Milan Melichercik wrote: > supti mukherjee wrote: >> >> Dear gromacs users, >> I have some doubts regarding the options to be selected in g_

Re: [gmx-users] g_covar -ref

Hi Vijaya, Well, to start with that will be something as calculating the 'fluctuation' as sum((xi-ri)^2)/N, with xi and ri denoting the ith atom of the conformation x and the reference structure r and the sum is over time/observations. In the case of no variation in xi, the value you get will stil

Re: [gmx-users] g_covar -ref

Hi Vijaya, I'm sorry if I didn't quite get that first sentence of yours. Did you meant to start it with "I thought that ..."? Or were you trying to explain me something you thought I missed? PCA stands for 'principal component analysis', not 'covariance analysis'. For instance, PCA can be applied

Re: [gmx-users] g_covar -ref

Hi Vijaya, > Your answer truly eludes me, unless -ref is an useless option. Well, that's pretty close to the conclusion. The use is limited to a few very specific cases and it might be better to hide the option from the view of casual users. But apparently you didn't catch the why yet. If you im

Re: [gmx-users] g_covar -ref

Hi Vijaya, Hmmm. Well, it may make some sense to take a defined extreme point to take deviations from. Like for motion on an arc, it may make sense to take the center of the circle to determine the deviations. But what that will yield; how that translates to wiggling proteins... :S Cheers, Tsjer

Re: [gmx-users] Dynamics cross correlation map

Hi Sukesh, You've posted this question several times now, without changing the phrasing. Did it occur to you that maybe nobody felt equipped to or sufficiently triggered by your post to reply? What do you mean with a 'dynamics cross correlation map' for 'residues or groups of residues'? Being more

Re: [gmx-users] Dynamics cross correlation map

Hi Sukesh, Great. This makes things much clearer. So basically what you'd need to do is to divide each i,j-th element of the covariance matrix you obtained (covar.dat) by the sqrt of the ii-th and jj-th diagonal element. That will commonly turn a covariance matrix into a correlation matrix. But,

Re: [gmx-users] how to analye a single structure (NMR or X-ray) by PCA?

Hi, Now that particular reference was not a very suitable one for this question :) The proper reply here is: There are no collective motions in a single structure, period! Do some background reading on PCA, and some more on PCA as applied to MD simulations. There is some information in the manua

Re: [gmx-users] trjconv and ions

Hi Joe, Probably you have a mismatch between your reference structure and the trajectory. So trjconv assumes coordinates associated with ions, while they actually belong to water. Hope it helps, Tsjerk On Mar 25, 2010 7:22 PM, "Joe Joe" wrote: I am seeing weird behavior when I trjconv my traj

Re: [gmx-users] g_covar & g_anaeig problems

Hi Jared, Can you post the exact series of commands you used to come to this point, including the selections you used and what constitutes these selections if they are not standard? Please also indicate what was in the trajectory you started off with (xtc-grps). Cheers, Tsjerk On Thu, Mar 25, 2

Re: [gmx-users] RE:directed trajectories

Hi Stephan, With 'collide in a specific way based on Docking', do you mean to pull them together? I'm not certain that will be protocollized easily. And your ligands, are they protein/peptide too, or do you have topologies for them? If not, it is likely to become more dirty than quick. Interest

Re: [gmx-users] how to get averaged coordinates for a residue in a time interval?

Well, you could also use g_rmsf with -b and -e, and a suitable index file... Cheers, Tsjerk On Thu, Apr 1, 2010 at 6:18 PM, Justin A. Lemkul wrote: > > > Wu Rongqin wrote: >> >> Dear all, >> >> How to get the averaged coordinates for a short time range say, 10 ps? >> which utility should be use

[gmx-users] Lindemann parameter

Hi Dmitri, Better to start a new thread for a new issue. It would also help if you give an equation for the Lindemann parameter. Is it really about fluctuations in the intermolecular distance, or in the intramolecular distance? The first would be a bit tough. For the latter you want to have a look

Re: [gmx-users] MD for two merged chains

Hi Dimitry, Well, you can use pdb2gmx with -merge to merge chains. Hope it helps, Tsjerk On Mon, Sep 22, 2008 at 4:12 PM, DimitryASuplatov <[EMAIL PROTECTED]> wrote: > Hello, > I have a two-chain protein. I want to merge N-terminal residue of chain > A with C-terminal of chain B. I can tweak th

Re: [gmx-users] dna-protein simulation

Hi Prasun, It was already pointed out that you shouldn't change the names in the force field files. ADE stands for RNA-Adenine and DADE stands for DNA-Adenine, keep it that way! Change the PDB file instead, but do it properly. So, do a restart: Take the original pdb file. Check the residue names,

Re: [gmx-users] TIP4P, TIP4P-Ew

Hi Lin, That tutorial doesn't really give a good procedure for production work simulations. Use a rhombic dodecahedron instead, with a distance to the wall (-d) of at least 1 nm. Maybe it's better to try the tutorial I put up on http://nmr.chem.uu.nl/~tsjerk/course/md-tutorial/ It's not as good on

Re: [gmx-users] TIP4P, TIP4P-Ew

Hi Lin, >From the amount of questions you pose on the user list and the unfamiliarity you display with Gromacs/MD basics, it seems that you're not as experienced with 1. MD, 2. Gromacs and 3. Force fields as you should be when you modify parameters. That's an experienced-level topic on which you c

Re: [gmx-users] Re:Question regarding Gromacs

Minnale, > Thanks for the reply, what may be the reason GROMACS became great? Check the JCC 2005 paper: http://www.ncbi.nlm.nih.gov/pubmed/16211538 > sometimes though system explodes it will generate energy minimisation > output.gro file we cant use this file for further run? Need more inform

Re: [gmx-users] #define gi_2 ; tetrahedral centres

Hi On Sun, Sep 28, 2008 at 6:39 ALin, That's not really necessary, the tetrahedral geometry is kept by the angles. It only needs to be imposed in the case of a CHXYZ group with united atoms. Cheers, Tsjerk M, Chih-Ying Lin <[EMAIL PROTECTED]> wrote: > > Hi > > I found this improper dihedral a

Re: [gmx-users] charge changes in Free Energy calculations

Hi Qiang, Couldn't you do it by shortening the chain, turning on/off one of the CH2 groups? You only have to mind perturbing the bonding and such in the right way then. Cheers, Tsjerk On Sat, Sep 27, 2008 at 6:32 PM, friendli <[EMAIL PROTECTED]> wrote: > Dear all, > > I have a mutation free ene

Re: [gmx-users] different versions of Gromacs

Hi Sudheer, It depends mainly on what it is you want to look at. You cannot exclude though, that the version has an effect on your results. Therefore you either have to do all simulations using the same version, or you have to randomize the versions over the simulations. I do hope that you meant t

Re: [gmx-users] help extracting .pdb frame out of run

Hi Fabricio, You can also sue the option -dump 1 to extract a frame. But it's not related to your error. Have you done any fitting and pbc related stuff or did you shuffle/sort your system prior to running? Cheers, Tsjerk On Tue, Sep 30, 2008 at 5:02 PM, Ragnarok sdf <[EMAIL PROTECTED]> wro

Re: [gmx-users] g_hbond, residue selection and boundary conditions

Hi Nicolas, > 1. Does g_hbond takes into account the periodic boundary conditions > or should first I center the system on my molecule, then run g_hbond? Yes (pretty much all tools do). > 2. When I run g_hbond, it prints the message "No option -sel" the > usual welcome message and run no

Re: [gmx-users] least squares fit

Hi Ram, Yes. Tsjerk PS. Do mind that the PBC are not preserved in that case. On Thu, Oct 2, 2008 at 7:54 PM, rams rams <[EMAIL PROTECTED]> wrote: > Dear users, > > While doing the least squares fit, if I choose the "protein" as input group > and "system" as output group, does it mean that the p

Re: [gmx-users] GMX 4.0 RC2: mdrun writes broken molecules?

Hi Justin, It's indeed the case that mdrun now writes broken molecules. Has to do with the domain decomposition and processors only keeping track of 'their' atoms. Too bad, but you'll just have to keep a .tpr around to make molecules whole again afterwards. Using trjconv -nojump with a suitable re

Re: [gmx-users] g_rmsf over time windows

Hi Giordano, Do you have a conformational change? If you consider unidirectional motion, in one or N coordinates alike, you would expect just what you see for the fluctuations. In fact, it's not really fluctuation then. 10 ns is also pretty short for a simulation of a protein. It's likely that you

Re: [gmx-users] g_rmsf over time windows

Hi Giordano, > I agree that 10 ns > are a short sampling but the total simulation time is 15 ns + 2 ns I > used to reach 298K; Whether that's enough is largely dependent on the size of your protein You should check whether you went beyond relaxation by inspecting the cosine content of the first f

Re: [gmx-users] editconf subroutine

Hi Maria, The answer is in the source code of course. But here's a python/pymol function which does the same thing, and which I wrote after the routine in editconf. It takes as input the definition as a list with lengths x,y,z and angles a,b,c and returns the upper triangular matrix: def triclini

Re: [gmx-users] Gromacs 3.3.1. and 3.3.3

Minnale, Hmm, I thought I recalled answering a similar question just recently. But mind you that doing statistics on MD, unless the results are very obvious, you have to be as careful and consistent as can be. That means that you should avoid trying to compare things which are performed under diff

Re: [gmx-users] Gromacs 3.3.1. and 3.3.3

Hi, Fully agree with that one. But the big problem is with simulations for comparison that you have to justify that a bug fix could not be the cause of a difference between simulations (or could even counteract on something which should give a difference). So even with minor revisions, unless you

Re: [gmx-users] Opinion: Can position restraining waters increase the speed of the md simulation?

Hi Art, You could, but should you? What do you think to gain? One layer of water is approximately 2.5 A, so with 6 you'd have about two layers of water 'free'. With position restraints on the rest, you'd still be calculating all forces and such, so there's not much gain there. On top of that, the

Re: [gmx-users] protein coming out of the box

1021 results for "protein out box" on the gromacs search page (mailing list search). The first so many are relevant. Why not checking the archives first? Oh, and it's mentioned in the wiki too. Tsjerk On Sat, Oct 11, 2008 at 11:03 AM, ravi sharma <[EMAIL PROTECTED]> wrote: > > Hello everyone > >

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

Ravi, Just come to terms with PBC: the box has no outside. Chapter 3 of the manual... Tsjerk On Sat, Oct 11, 2008 at 1:30 PM, ravi sharma <[EMAIL PROTECTED]> wrote: > So how could i do this energy conservation, > > > Ravi Datta Sharma > Lecturer, > Bioinformatics, > Department of Microbiology, >

Re: [gmx-users] Fatal Error: number of coordinates in coordinate file does not match topology

Hi Chitrita, Please copy-paste the exact error and the command line in both cases (working and not working). Also, what platform are you working on? Did you by chance edit the .mdp file under windows? Cheers, Tsjerk On Sat, Oct 11, 2008 at 6:46 PM, Chitrita Dutta Roy <[EMAIL PROTECTED]> wrote:

Re: [gmx-users] backup .xtc and .trr

Hi huan, You can split the trajectories in parts using e.g. trjconv Also spend some thoughts on whether you need all that data. Do you really need the velocities/forces/high precision (.trr). Do you need the time resolution you have, or can you do with less. And did you include all solvent? D

[gmx-users] Fwd: gromacs

-- Forwarded message -- From: He, Yang <[EMAIL PROTECTED]> Date: Mon, Oct 13, 2008 at 5:35 PM Subject: gromacs To: "[EMAIL PROTECTED]" <[EMAIL PROTECTED]> Hi , I am using the gromcas to simulate the course grain for DNA. I listed the new atom types in the .atp file like this Ab

Re: [gmx-users] two pdb files

Hi, Gromacs doesn't use residue numbers and atom numbers anyway. No problem just concatenating a la Justin. If you still have to run pdb2gmx, it may be better to have different chain identifiers. On tthe other hand, it may be better to run pdb2gmx before concatenation (which you probably have done

Re: [gmx-users] How can I generate a Input *.gro file of coarse grain model?

Hi Xuji, You'll have to have a coordinate file to start with, just like with your atomistic scale stuff. Whether this would be .pdb or .gro doesn't matter. If you have don't have coordinates, parameters are pretty useless. Maybe the Groningen guys are willingg to share you a .pdb file to play with

Re: [gmx-users] Warning with L-BFGS minimization

Hi Jochen, It's probably the rvdw cutoff (from readir.c): if (ir->eI == eiLBFGS && (ir->coulombtype==eelCUT || ir->vdwtype==evdwCUT) && ir->rvdw != 0) { warning("For efficient BFGS minimization, use switch/shift/pme instead of cut-off."); } Bummer! Tsjerk On 10/24/08, Jochen Hub <[E

Re: [gmx-users] The structure property

Hi Lin, Justin is right on all points. The first is indeed a check you should always perform, but in this case (1LW9), there are no missing residues/atoms. The point is that one should be aware that there could. The same thing goes with the hint for the histidines. I could have not written you sho

Re: [gmx-users] tcoupling

Hi, I haven't really checked how it is with the new version (and you're not telling which version you're using anyway), but grompp used to get confused with multiple molecules and only report the charge on one of them. You can check the total charge from the .tpr file with (bash command line): gm

Re: [gmx-users] override dispalying of options

And, you can even (like for anything that generates output), redirect output to nowhere: (csh) grompp >& /dev/null (bash) grompp &> /dev/null By the way, bringing it to the background (&) doesn't change the binding to the terminal. Oh, and Mark is absolutely right that it is better to save to a

Re: [gmx-users] (no subject)

Hi Cecilia, Please give your posts a descriptive title. Then, this is actually a bash-related issue, which has not much to do with Gromacs. But then again, we're nice people :) The thing is that bash wants to have: export PATH="/usr/local/gromacs/bin:${PATH}" By the way, you can also use: sourc

[gmx-users] Fwd: The question from the tutorial: protein non-protein in .mdp file

lecule separately. Cheers, Tsjerk -- Forwarded message -- From: Chih-Ying Lin <[EMAIL PROTECTED]> Date: Thu, Oct 30, 2008 at 8:20 AM Subject: Re: The question from the tutorial: protein non-protein in .mdp file To: Tsjerk Wassenaar <[EMAIL PROTECTED]> HI First, this webpage

[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

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..." > > > >

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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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

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] 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

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