Re: [gmx-users] Re: Creating a monolayer from Martini bilayer

t all molecules in the box? Sorry > for > being so annoying need a lot of elaboration! > > > Tsjerk Wassenaar wrote > > Hi Neha, > > > > A single structure is like a trajectory with only one frame :p trjconv > > works on those as well. > > Right, s

Re: [gmx-users] Projection of crystal structure on PCA plot

Hi Anirban, The eigenvectors obtained from the simulation are a way of rewriting the coordinates of your structures, not in terms of atoms-XYZ, but as combinations of these. Because they are combinations of atom-positions, they are defined for the selection of atoms used for the calculation. If yo

Re: [gmx-users] Projection of crystal structure on PCA plot

structure onto the > EV, then I need to consider only the CA atoms of the crystal structure > (which in that case won't be the exact crystal structure) as well. Right? > > Thanks a lot again. > > Regards, > > Anirban > > On Thu, Jun 6, 2013 at 3:56 PM, Tsj

Re: [gmx-users] Eigenvector and eigenvalues

Hi Ankita, Please provide the commands you've run and the screen output from g_covar. Cheers, Tsjerk On Thu, Jun 6, 2013 at 3:44 PM, Ankita naithani wrote: > Hi, > > I wanted to know about the eigenvectors and eigenvalues. I recently > performed the principal component analysis (only the bac

Re: [gmx-users] Eigenvector and eigenvalues

but I really have no idea as to how to > interpret the results and draw conclusions from these 2d plots and also 3d > pdb projections. Could you please guide me in the right direction to > understand these 2d plots and infer the significant results? > > > Kind regards, > > An

Re: [gmx-users] Eigenvector and eigenvalues

lpful insight into protein > motions (Allosteric transitions, effector signalling??). It would however > be intensively complicated to derive for the whole protein considering mine > is a tetramer and a huge system. > > > Kind regards, > > Ankita > > > On Sat, Jun 8,

Re: [gmx-users] Re: distance_restraints

Hi Maggin, Why do you run EM with constraints? Cheers, Tsjerk On Thu, Jun 13, 2013 at 10:53 AM, maggin wrote: > Hi, Justin, > > It's seems no problem at steep energy minimization, except lose H atoms > connect with C, the superposition are very well. > > When I use Pymol to align the NMR st

Re: [gmx-users] Re: distance_restraints

Hi Maggin, The constraints are typically used during MD simulation to allow larger time steps. Cheers, Tsjerk On Fri, Jun 14, 2013 at 9:39 AM, maggin wrote: > Hi, Tsjerk, > > I have one question that in what situation people do constraint ? > > Thank you very much! > > maggin > > > > -- > Vi

Re: [gmx-users] System broken after energy minimization

Hey : When increasing the system size like that, make sure that all molecules in the original box are whole (trjconv -pbc mol). Only then can you, e.g., use genconf to double the system. Cheers, Tsjerk On Sat, Jun 15, 2013 at 1:49 PM, Justin Lemkul wrote: > > > On 6/15/13 6:21 AM, Kieu Thu N

Re: [gmx-users] NVT .gro for NPT

Hi Maggin, Why would that be a problem? Tsjerk On Mon, Jun 17, 2013 at 7:28 AM, maggin wrote: > Hi, all > > I run a small peptide, and after NVT, I got the XXX.gro file like this, > > > > because the peptide not at the center of

Re: [gmx-users] a snapshot of NVT

Hi Maggin, Okay, this image may require a bit of explanation :p VMD has drawn bonds according to the bondedness in a reference file. But the atoms have moved, and some went over the box boundaries. So they show up with long bonds crossing the whole box. It's not a problem, just a visualization art

Re: [gmx-users] sequentially fitting each frame of one trajectory to each frame of another trajectory

Hey Thomas, No, there is no such tool. Sorry. May I ask how you did the MinVar fitting? Cheers, Tsjerk On Mon, Jun 17, 2013 at 12:55 PM, Thomas Evangelidis wrote: > Dear GROMACS list, > > I used minVar to remove global rotations and translations from a > trajectory, but due to memory issues

Re: [gmx-users] Distance travelled from time 0

Hi, g_rmsf doesn't do distances. To answer the question, you can use g_rms with -fit none and a suitable index group. Does depend a bit on what you mean with distance. The distance traveled by a residue could well mean the average distance for all particles in the residue, which is what you'll get

Re: [gmx-users] Visualize Protein ligand complex

Hi Sainitin, You can extract only the protein and ligand, using a suitable index file, or you can limit the number of frames. Cheers, Tsjerk On Thu, Jun 27, 2013 at 5:36 PM, Thales Kronenberger < kronenberg...@gmail.com> wrote: > Don't you wanna try to use the VMD > > use vmd xxx.gro yyy.trr

Re: [gmx-users] PBC problem

Hi Yutian Yang, Yes. That is, if the chain is interacting with itself. If it remains curled up, then it won't be a problem. Cheers, Tsjerk On Thu, Jun 27, 2013 at 10:10 PM, Yutian Yang wrote: > Hi all, > > I have a question about PBC. If I have a polymer chain that is longer than > the box l

Re: [gmx-users] Covariance file format

Hi Ankita, The fie contains the eigenvectors as x1 y1 z1 x2 y2 z2 ... xN yN zN Hope it helps, Tsjerk On Mon, Jul 1, 2013 at 1:38 AM, Ankita naithani wrote: > Hi, > > I wanted to know the exact format of covariance.dat file as generated by > g_covar during covariance analysis. The file format

Re: [gmx-users] Re: Covariance file format

where N is the number of atoms and n is the number of frames :p T. On Mon, Jul 1, 2013 at 8:29 AM, Tsjerk Wassenaar wrote: > Hi Ankita, > > I should not answer questions before coffee!! Sorry. > > It's the covariance matrix! So it's > > 1/n sum x1x1 1/n su

Re: [gmx-users] Re: Covariance file format

delta ri dot delta rj so I don't think so I can use the > eigenvectors > > > Kind regards > > Ankita > > On Monday, July 1, 2013, Tsjerk Wassenaar wrote: > > > Hi Ankita, > > > > The fie contains the eigenvectors as > > > > x1 y1 z1 >

Re: [gmx-users] Re: Covariance file format

I. Which the first column wud have > alpha atom one second column would have 2nd aloha atom n third would have > correlation between them? > > > > Kind regards, > > Ankita > > On Monday, July 1, 2013, Tsjerk Wassenaar wrote: > > > Hi Ankita, > > > >

Re: [gmx-users] D-aminoacids in input file

Hi Shima, You can use the same parameters. There is no difference other than the position of atoms. Cheers, Tsjerk On Mon, Jul 1, 2013 at 9:52 AM, Shima Arasteh wrote: > Dear gmx users, > > I have D amino acids in my input .pdb file. The force field which I aim to > use, is CHARMM. I am wond

Re: [gmx-users] TRACE OF RMSD COMPARISON MATRIX

Hi Richa, >From your explanation, I understand you want to know the sum of distances between each frame and its corresponding filtered frame. I think it makes more sense to sum squared distances, but that's a minor detail. The (non-mass-weighted) RMSD between two structures, written as positional

Re: [gmx-users] Problem calculating RMSD with gromos

Hi Melchor, So what did you expect, what did you do, and what did you get? Cheers, Tsjerk On Tue, Jul 2, 2013 at 2:45 PM, Melchor S. wrote: > Hi all, > > I am trying to calculate an RMSD of two simulations. All the setting are > equal for both, but i use OPLS in one and for the other gromos

Re: [gmx-users] Re: Problem calculating RMSD with gromos

Hi Melchor, Have you looked at the structures? The GROMOS people suggest using twin-range cut-off with reaction field correction, and the Vanderwaals cutoff you use seems a bit small, as 1.4 nm is commonly used with GROMOS. Maybe that makes a difference. Cheers, Tsjerk On Tue, Jul 2, 2013 at 3

Re: [gmx-users] Cannot get velocities from the trajectory file

Hi Silvia, The .xtc file does not contain velocities. You'll need to use the .trr file. Cheers, Tsjerk On Tue, Jul 2, 2013 at 8:25 PM, Silvia wrote: > Dear users and experts, > I am new in the list and I am writing because I have a problem to get > velocities from the trajectory file. When I

Re: [gmx-users] Help needed in installation

Hi Sonika, cmake needs a specification of the path where the source code is. In addition to that, it is best to build it in a separate directory. As explained on the website, in your gromacs directory: mkdir build cd build cmake ../ make make install Hope it helps, Tsjerk On Tue, Jul 2, 2013

Re: [gmx-users] unwrap trajectory file using -pbc nojump

Hi Yutian Yang, I don't think it's because of the size of the system. Can you run trjconv without -pbc nojump? And did you check the trajectory with gmxcheck? Does the output file exceed a maximum file size limit? Hope it helps, Tsjerk On Wed, Jul 3, 2013 at 9:22 PM, Yutian Yang wrote: > De

Re: [gmx-users] pdb files from trajectory

Hi Shima, You need to give a reference structure with the -s option. Otherwise the program assumes you mean to use topol.tpr, which isn't present. Cheers, Tsjerk On Sun, Jul 7, 2013 at 11:51 AM, Shima Arasteh wrote: > Dear gmx users, > > I' d like to get pdb files from trajectory, then used t

Re: [gmx-users] On the box type

Hi Cyrus, In a rectangular box (which is a specific case of a triclinic box) your molecule can't rotate freely without significant chance to run into its periodic image, invalidating whatever result you get. So, unless rotation is of no concern, or can be cirrcumvented, you'll need to use a rhombi

Re: [gmx-users] Breaking of disulfisde bridges in human insulin

Hi Vinita, I would guess that the other bond would not be made anyway according to the criteria used by pdb2gmx. Or does it say it's making the bond? Does the bond appear in the .top file? Cheers, Tsjerk On 7/8/13, Vinita Kumari wrote: > Dear gromacs users, > I want to break two disulfide bond

Re: [gmx-users] Frozen covalent bound atoms

constraints freeze_grps virtual_sites Cheers, Tsjerk On Jul 9, 2013 10:36 PM, "Nash, Anthony" wrote: Hi all, I would imagine this has been covered before, yet I don't think I have unearthed the right search inquiry yet. I want to make a dihedral angle along the length of a helical protein us

Re: [gmx-users] Squishing or Stretching Membranes

Hey :) You can use editconf -scale to scale the system to the average box size. Cheers, Tsjerk On Jul 9, 2013 4:28 PM, "Mirco Wahab" wrote: On 09.07.2013 16:11, Neha wrote: > > I had a question about trjconv. After one of my simulations has... You could dump many structures from the last part

Re: [gmx-users] editconf: Invalid command line argument: –f

Hi Jonathan, I suspect the dash is not of the right kind. Did you by chance copy/paste the command? Did you try typing it? Cheers, Tsjerk On Sat, Jul 13, 2013 at 12:03 AM, Jonathan Saboury wrote: > I am following "Tutorial 1" from > https://extras.csc.fi/chem/courses/gmx2007/tutorial1/index.

Re: [gmx-users] Regarding gromos method in g_cluster

Hi Bipin, If A/C have RMSD 0.4 nm, but A/B and B/C both have RMSD < 0.3 nm, they'll end up in the same cluster. Cheers, Tsjerk On Wed, Jul 31, 2013 at 9:45 AM, bipin singh wrote: > Thanks for the reply Prof. David. But in the output it shows that "The RMSD > ranges from 0.0602553 to 0.411066

Re: [gmx-users] concatenating 2 xtc files

Hi Kavya, That shouldn be a problem. Please post your sequence of commands for concatenating and further processing of the trajectory. Cheers, Tsjerk On Thu, Aug 1, 2013 at 8:12 AM, Kavyashree M wrote: > Dear users, > > I ran a simulation for 25ns. First 5ns in 8 core machine > and late part

Re: [gmx-users] Invalid order for directive atomtypes

Hi Jonathan, The itp's for the ligands were given atomtype sections, but atomtypes (and other *types) may only be defined before any moleculetype definition (check chapter 5 of the manual for the topology format). You'll need to remove anything before the moleculetype directive from the itp files

Re: [gmx-users] script to add water in protein

Hi Pooja, Do you mean solvating around the protein, or placing water inside? If you feel brave, you can check out the C code of genbox. Genbox copies a box of solvent to cover the box with the protein, and then removes all solvent which has overlaps with the protein. Cheers, Tsjerk On Mon, Aug

Re: [gmx-users] Help with Error Message

Hey :) Sorry for replying a bit late. But the issues you mention in this and the other posts are usually solved by closely reading the text of the tutorial, not only the commands. Cheers, Tsjerk On Sun, Aug 25, 2013 at 3:44 AM, The One And Only wrote: > Never mind, I'm dumb. I just realized t

Re: [gmx-users] Help with Error Message

y file. > > > On Tue, Aug 27, 2013 at 1:33 PM, Tsjerk Wassenaar > wrote: > > > Hey :) > > > > Sorry for replying a bit late. But the issues you mention in this and the > > other posts are usually solved by closely reading the text of the > tutorial,

Re: [gmx-users] Help with Error Message

An editor is a program to edit the text in a file: gedit, nano, vi, emacs, ... It'll be the equivalent of Windows' Notepad. Can you find a tutor around to help you out with the basic usage of Linux? It's always difficult to plunge into several different things at the same time, here 'using linux',

Re: [gmx-users] Genion command not working

Hi Deepak, You have to set the minimal distance between ions lower. Check the help of genion. Cheers, Tsjerk On Aug 28, 2013 8:04 AM, "Deepak Ojha" wrote: Dear Gmxers, I want to simulate 5M nabr aqueous solution.To add the ions I use genion command and add 22 na and br ions respectively to t

Re: [gmx-users] ERROR : GROMACS finsihed with error 74

Hi Sri, I guess that this simulation was run through the WeNMR GMX portal? It's not really a Gromacs question. Problems with that portal should be directed to the adminstrator, who will send it to me anyway, so I'll respond here :) The error means 1. that I should put time in writing more clear e

Re: [gmx-users] Re: Segmentation Fault using g_cluster

Hi Evelyne, I haven't got a clue... But does it work if you use -settime when concatenating the trajectories, to avoid having frames with the same time index? It shouldn't cause a segfault, but it might. Cheers, Tsjerk On Fri, Sep 6, 2013 at 7:20 AM, deplazes wrote: > Hi guys > > do you have

Re: [gmx-users] Re: Segmentation Fault using g_cluster

ke a new index file that corresponds to the new , > reduced .tpr file > Cheers > E > > Enjoy Ausserberg > > From: "Tsjerk Wassenaar [via GROMACS]" < > ml-node+s5086n5011009...@n6.nabble.com ml-node+s5086n5011009...@n6.nabble.com>> > Date: Fri, 6 Sep 201

Re: [gmx-users] RE: average pressure of a system

Hi Dallas, Justin, e.a., As has been mentioned a number of times 0.9 +- 190 and 2.3 +- 190 are not > statistically different. > This is not true. Whether this is statistically different depends on the number of independent samples. For pressure, the fluctuations are wild, and the autocorrelation

Re: [gmx-users] Re: Seeking solution for the error "Atom OXT in residue TRP 323 was not found in rtp entry TRP with 24 atoms while sorting atoms".

Hi Santhosh, Try renaming the atom (mind the space): sed 's/OXT/O2 /' pdbfile > fixed.pdb And then run pdb2gmx on that. Cheers, Tsjerk On Tue, Sep 17, 2013 at 6:05 AM, Santhosh Kumar Nagarajan < santhoshraja...@gmail.com> wrote: > > This is the command I used > pdb2gmx -f protein.pdb -o pro

Re: [gmx-users] virtual sites in gromacs

Hi Neha, Yes. The MN* particles are the virtual sites. Cheers, Tsjerk On Wed, Sep 18, 2013 at 7:13 AM, Neha Gandhi wrote: > Dear Users, > > I am trying to prepare file using pdb2gmx using Gomos 43a1 ff. I am > using following command. > pdb2gmx -f input.gro -o input1.gro -vsite hydrogens -i

Re: [gmx-users] Re: grompp for minimization: note & warning

Hi Shahab, What did you do exactly? Can you state your complete protocol (1. fetched this structure file there, 2. got the topology from there, 3. did something, 4. ran grompp like this, etc)? Use brief, clear explanations and the command lines as you issued them. Cheers, Tsjerk On Tue, Sep 17

Re: [gmx-users] Re: grompp for minimization: note & warning

Hi Shahab, That site has a lot of structures. It would be better to explicitly state which one you took. However, in this case, the better question is, how did you write the topology, and did you check the correspondence of the order of molecules/atoms in the topology file and the structure file?

Re: [gmx-users] Re: grompp for minimization: note & warning

Hi Shahab, You edited the .gro file, but you made an error. So you have to read the manual to understand the file format and then see where and how your edited file doesn't match. Cheers, Tsjerk On Thu, Sep 19, 2013 at 5:00 PM, shahab shariati wrote: > Dear Tsjerk > > Thanks for your consider

Re: [gmx-users] g_covar average.pdb calculation

Hi Deniz, The option -ref/-noref is not what you think it is. You want to use -nofit. Cheers, Tsjerk On Fri, Sep 20, 2013 at 2:26 PM, Deniz Aydin wrote: > Dear All, > > I would like to get information on how g_covar calculates the average > structure file (average.pdb) > > My aim was actuall

Re: [gmx-users] emstep unit

It's the size of the attempted step in conformational space, the distance from one configuration to the next. Cheers, Tsjerk On Sep 21, 2013 10:11 PM, "Justin Lemkul" wrote: On 9/21/13 2:47 PM, Atila Petrosian wrote: > > Dear Justin > > Thanks for your reply. > > Ok. You ... A quick Google sea

Re: [gmx-users] trjcat after trjconv

Hi Venkat, It depends on what you mean with "removing pbc". Cheers, Tsjerk On Sep 26, 2013 5:21 PM, "Venkat Reddy" wrote: Dear Sir, Thanks for the quick reply. I accidentally lost one of my raw .xtc files. But I have the noPBC xtc file. So, when ever I extend my simulation, first I am removin

Re: [gmx-users] trjcat after trjconv

Hi Venkat, These options are 'frame intrinsic' or 'history independent', unlike -pbc nojump. Cheers, Tsjerk On Sep 26, 2013 6:46 PM, "Venkat Reddy" wrote: Dear Tsjerk sir, I used trjconv -pbc mol -ur compact options. On Thu, Sep 26, 2013 at 9:17 PM, Tsjerk

Re: [gmx-users] Writing periodic image coordinates.

Hi Kavya, genconf -nbox 3 3 3 Cheers, Tsjerk On Thu, Sep 26, 2013 at 6:24 PM, Kavyashree M wrote: > Dear users, > > For some analysis I require the 27 periodic images > of the system I ran the simulation for. Kindly let me > know how can it be written to a pdb file. > > Thanking you > Regard

Re: [gmx-users] per mol of what?

Hi Ángel, kJ per mol of system contained in the unit cell? > > Exactly. As if whatever is in there is one 'molecule' (-nmol 1). Adios! Tsjerk -- Tsjerk A. Wassenaar, Ph.D. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please searc

Re: [gmx-users] trjcat after trjconv

Yes. Cheers, Tsjerk On Fri, Sep 27, 2013 at 7:51 AM, Venkat Reddy wrote: > Thanks for the quick reply sir. > So, does it mean I can apply "trjcat" on the processed xtc files??? > > > On Thu, Sep 26, 2013 at 10:25 PM, Tsjerk Wassenaar >wrote: > > > Hi Ven

Re: [gmx-users] principal component analysis

Hi Pratibha, The table is all garbled, and your description insufficiently clear for us to form a mental picture of what you want, what you've tried to get that, where it goes wrong, or where you get stuck, and how we can help you on the right track again. Cheers, Tsjerk On Fri, Sep 27, 2013 a

Re: [gmx-users] principal component analysis

Hi Prathiba, I think you should have a look at the "Functional Mode Analysis" method from Bert de Groot's lab. Cheers, Tsjerk On Sat, Sep 28, 2013 at 8:13 AM, pratibha kapoor wrote: > Dear all users > > I would like to calculate pc loadings for various integrated factors in the > form of foll

[gmx-users] Re: questions

Dear Dwey, Please direct questions like this to the gromacs user list, after asserting that the answer has not already been given. In addition, please read http://md.chem.rug.nl/~mdcourse/molmod2012/md.html Regards, Tsjerk On Tue, Oct 8, 2013 at 5:35 PM, Dwey wrote: > Dear Tsjerk, > >I s

Re: [gmx-users] Is Gromos force field 45a3 out of dated?

Hi Lin, I would say that it is not correct to call 45a3 deprecated. Like other force fields, GROMOS 45a3 is also the result of careful parameterization. The later GROMOS forcefields 53a5, 53a6, 54a7 and 54a8, took of a completely different approach in parameterization, and are in that respect not

Re: [gmx-users] Adding proton using genion to study proton transfer reaction

Hi DeepaK, You should be aware that excess protons are not floating around freely among a bunch of H2O. Whatever reasoning along this line is physically meaningless (including thinking of a mixture of H3O+, H2O, OH-). This is the realm of QM. Cheers, Tsjerk On Thu, Oct 10, 2013 at 8:05 AM, De

[gmx-users] Molecular dynamics with LEGO?

Hi :) Apologies if this seems inappropriate, but I would like to ask as many people as I can to give support for the molecular modeling LEGO project at http://lego.cuusoo.com/ideas/view/51273. With 10 000 votes, LEGO will consider producing the bricks required for such models, and we can add cool

Re: [gmx-users] Molecular dynamics with LEGO?

Hi James, There are models, yes. But if a manufacturer like LEGO is taking this up, it can make the models much cheaper and more easily available. In addition, the LEGO models would allow more flexibility in building and handling. And you can combine it with your other LEGO ;) And, yes, bendy pie

Re: [gmx-users] Minimum distance between periodic images

Hi Nidhi, These are periodicity artifacts. Make sure that you remove jumps over PBC from your trajectory by using trjconv -pbc nojump. Cheers, Tsjerk On Tue, Oct 22, 2013 at 11:14 AM, Nidhi Katyal wrote: > Dear all users > > I have simulated a protein with two chains (153 residues each) for >

Re: [gmx-users] pbc problem

Hi Shahab, What about running trjconv -pbc mol with a .tpr as input file? Cheers, Tsjerk On Sun, Oct 27, 2013 at 3:24 PM, shahab shariati wrote: > Dear Justin > > I attached images related to before (em2.gro) and after equilibration. > > > https://www.dropbox.com/s/yjkyj5ycshvp20u/images.docx

Re: [gmx-users] pdb2gmx conversion

Hi Musyoka, I would guess that that is related to the input coordinates. A bit of EM should fix it. Cheers, Tsjerk On Mon, Oct 28, 2013 at 11:20 AM, MUSYOKA THOMMAS < mutemibiochemis...@gmail.com> wrote: > Dear Users, > > Whenever i convert a protein.pdb file using the following command (pdb2

Re: [gmx-users] how to get Eigenvectors

Hi Nahren, You can try the .g96 format for this, which has high precision. To understand the format, convert something to .g96 and replace the coordinates with the eigenvectors. Hope it helps, Tsjerk On Fri, Nov 1, 2013 at 4:10 AM, nahren manuel wrote: > Dear GMX Users, > > I performed an AN

Re: [gmx-users] trjconv for pbc

Hi Blake, Centering on the solute should help. Cheers, Tsjerk On Sat, Nov 2, 2013 at 3:55 PM, rankinb wrote: > Hi all, > > I am trying to use trjconv to remove PBC. More specifically, I would like > to extract the coordinates of all the water molecules within a certain > distance of a singl

Re: [gmx-users] Diffusion/PBC

Hi Debashis, Makes sure that the anion and receptor are together in the reference structure you use for trjconv -pbc nojump Cheers, Tsjerk On Tue, Nov 5, 2013 at 8:12 AM, Debashis Sahu wrote: > Dear All, > I have an problem related to jumping trajectory. In my MD > run, there is

Re: [gmx-users] Re: Bilayer COM removal issue: Large VCM

Hi Rajat, If you remove comm on the bilayer, there may be relative comm between leaflets. If that relative motion is significant and you switch to removing comm per leaflet, the program suddenly finds itself resetting the com over a large distance. About equilibration, you equilibrated with comm_g

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] 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] 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 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] 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] 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] 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] -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] about the bond connection between different groups

am not sure about that. Can you give me much more information about > that? > > Thank you very much. > > Yang > > From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf > Of Tsjerk Wassenaar [tsje...@gm

[gmx-users] Inclusion of position_restraints

Hi Nitu, >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of gmx-users digest..." Please!... And don't include the whole digest. > > Dear Mark > Thanks for your reply. as u ask- how many atoms is--Protein A- 5244 > > protein B- 4658 >        

Re: [gmx-users] g_sas

Hi, Of course you can. But if part of Protein A is buried in an interface, doing the SAS calculation over A only will also include the surface interface; it will give the total surface of A. That may actually be handy if you want to determine what the buried surface is. You calculate the total sur

[gmx-users] Re: Questions

Hi Lin, I bounce this mail to the gromacs user list as the issues are well off to be archived. > I have two stupid questions here. Well, that's up to us to decide ;) > 1. I want to get the proper structure of lysozyme. > > From your tutorials, 1LW9.pdb file is used. Potassium (K), chloride (CL)

[gmx-users] Re: Questions

Hi Lin, > 1. Although you have explained the differece between HOH, AHOH and > BHOH, I do not fully understand.     => Can I delete all of atoms, > HOH, AHOH and BHOH ? You can delete one of them, either A or B, if you want to include the water in your model. It may be that pdb2gmx discards the B

Re: [gmx-users] Conjugate Gradient - Equations

Hi Una, Maybe this answers your question? http://en.wikipedia.org/wiki/Conjugate_gradient_method Cheers, Tsjerk On Thu, Apr 30, 2009 at 5:00 PM, Una Bjarnadottir wrote: > Hi everyone, > > In the gromacs manual the equations regarding the conjugate gradient are not > shown. > > Is there anybod

Re: [gmx-users] P-coupling in vacuum, inflexibility

Hi Pavel, It seems that your molecules are broken over the periodic boundaries. Make sure that you set up your coordinates and topology file correctly. Cheers, Tsjerk 2009/5/6 Pavel Semenyuk : > Dear colleagues, > > I want to put in my cell a lot of molecules (f.e., 32 lipids), and I make for

Re: [gmx-users] Are Gromos 45a3 and GROMOS 53a6 compatible?

Hi Lin, Well, actually G53a6 is heavily reparameterized... partly. So your observation that large portions of the force fields are equal is correct. That also makes the question of whether or not to mix them more difficult. It seems implicitly assumed by the authors that the parts of the force fie

Re: [gmx-users] Where are the good tutorials?

Casey, Could you expand your criticism? You must have found the tutorials section on the wiki. Then please note the specific points you dislike about the tutorials there (especially the beginners) and provide some ideas you would think improve them. To my opinion, a beginners tutorial provides a

Re: [gmx-users] How can i know if the protein swell during the MD simulation?

Hi, Well, I think 'swelling' is unambiguously, though roughly, defined as 'growing larger', which suggests that you'd have to look for an increase in volume. But how to do that, how to define the volume of the protein is still a matter of setting your criteria and finding the right tools to assess

Re: [gmx-users] How can i know if the protein swell during the MD simulation?

stretching != swelling, e.g. On Mon, May 18, 2009 at 10:46 AM, Bhanu wrote: > How about checking radius of gyration??? > > 2009/5/18 Tsjerk Wassenaar >> >> Hi, >> >> Well, I think 'swelling' is unambiguously, though roughly, defined as >> 'g

Re: [gmx-users] Hello: Forcefield and potentials for DNA-zinc finger complex

Hi, Have a look at http://wiki.gromacs.org/index.php/Parameterization and http://wiki.gromacs.org/index.php/Exotic_Species Next to that, also consider that you are talking about a site with -2 formal charge (ZnS4)2-. How likely is that? From QM studies, it seems much more likely that there are 1

Re: [gmx-users] How can i know if the protein swell during the MD simulation?

Well, why didn't I think of that? Maybe because flattening will also increase the SAS, or (partial) unfolding, or opening of two domains... :) Tsjerk On Tue, May 19, 2009 at 6:10 PM, Marius Retegan wrote: > sovent accesible surface area? > > On Mon, May 18, 2009 at 11:09 AM, Ts

Re: [gmx-users] Selection of force field

Hi Anindita, Proper carbohydrate parameters were introduced in G45a3. But you're not easily satisfied, wanting proteins carbohydrates and lipids to work together! You're short of wanting to include nucleic acids :) Anyway, the lipids are a bit problematic. There are parameters for some lipids for

Re: [gmx-users] gromacs on glacier.westgrid.ca

Hi Payman, That is probably not the only grid facility on which Gromacs may be run and it would be helpful if you could give specifications of it (WMS software e.g.), which could give you more response. Also, it would be helpful if you'd be able to give more information regarding the output. Then

Re: [gmx-users] Selection of force fields

Hi Anindita, I was sort of afraid you might be dealing with glycosphingolipids. The Gromos force fields do not have properly behaving models for sphingolipids yet. I'm not sure whether other force fields do much better. There's some serious parameterization to do here. If you have experimenal data

Re: Hi: Re: [gmx-users] Hello: Forcefield and potentials for DNA-zinc finger complex

Hi Nehme, I've did simulations on TRAIL, which also contains a zinc-finger domain, involving three cysteines and a chloride ion. But it's not so simple. Luckily the exact parameters seemed not that vital, as the zinc apparently functions to keep the three subunits together and was in any case not

Re: [gmx-users] Re: question about force field parameter

Hi Johnny, If for a dihedral the definition only lists two atoms, these signify the central atoms with any possible substituents. I think this is explained in Chapter 5 of the manual. Cheers, Tsjerk On Sun, May 24, 2009 at 5:58 PM, Zhanglin Ni wrote: > The reason I asked the question was becua

Re: [gmx-users] The default pH =7.0 ??? and the protonation state after pdb2gmx

Hi Lin, Please follow the advice to do more background reading on both biochemistry and molecular dynamics if you aren't doing so already. The charge is not related to the pH. pH is related to the concentration of H+ in the solution, but you don't have H+ (H3O+/OH-) in your solution. The charge i

Re: [gmx-users] Dynamics with DNA

> Nearly all the force fields that can be used with Gromacs have > nucleic acids represented as fundamental building blocks. That may be true, but does not mean that in all these force fields the parameters are good enough to assess 'real' behaviour of nucleic acids. E.g. the older GROMOS force fi

Re: Hi: Re: [gmx-users] Hello: Forcefield and potentials for DNA-zinc finger complex

Hi Nehme, > Also, in our zinc finger models, the zinc plays a structural role and it is > not implicated in DNA recognition. Furthermore, I will read your paper and > the references. I looked in the Literature and from NMR studies/X-ray and MD > done on zinc fingers containing a zinc ion coordinat

Re: [gmx-users] Extend water layer along negative Z-direction

Hi, > The first thing that you need to do is to use editconf to increase your box > z and then genbox to add more solvent. My script (and C-program) do not do > this, they focus only on removing waters that are placed within your > bilayer. Of course it is also trivial to edit the .gro file and c

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