Re: [gmx-users] question about solvating

Please start new emails for new discussion topics. That way you increase the chance that people with the interest and expertise can use their time efficiently, and that you get an answer. Also, archives work better if you separate topics. > Please Let me ask two more simple questions about solv

Re: [gmx-users] energy contributions

- Original Message - From: jojo J Date: Thursday, July 8, 2010 13:17 Subject: [gmx-users] energy contributions / question about solvating To: gmx-users@gromacs.org > Hello everyone, > > I have a question on LJ and coulomb 1-4 energy terms. These are considered as > intramolecular inte

[gmx-users] energy contributions / question about solvating

Hello everyone, I have a question on LJ and coulomb 1-4 energy terms. These are considered as intramolecular interactions and LJ and coulomb SR as intermolecular. If nrexcl in top file is 3, this means we obtain 1-4 energies, 1-5, 1-6, Now what we calculate as intermolecular (SR) contributions

Re: [gmx-users] Capping residues

Sai Pooja wrote: Hi Justin, I do not have the problem of extra hydrogens or a net charge on the NAC group. The net charge is not on NAC, it's on the entire peptide. If you're not seeing it, that makes the bug even more troubling, since it's sporadic. Are you using the latest git versi

Re: [gmx-users] Nitrile_Butadiene_Rubber simulation using Gromos96

- Original Message - From: "C. Batistakis" Date: Wednesday, July 7, 2010 23:19 Subject: [gmx-users] Nitrile_Butadiene_Rubber simulation using Gromos96 To: gromacs --- | - - - > Dear all > I am trying to simulate Nitri

Re: [gmx-users] No such moleculetype SOL

- Original Message - From: nanogroup Date: Wednesday, July 7, 2010 21:51 Subject: [gmx-users] No such moleculetype SOL To: gmx-users@gromacs.org Cc: mark.abra...@anu.edu.au --- | > Dear Mark, > > Many thanks for your e-mail. >

Re: [gmx-users] Capping residues

As a follow-up, it appears that there are several problems with the CHARMM implementation. I will file a bugzilla with a few other things I found. There are a number of errors in the aminoacids.rtp file that cause problems. Most of all, I can't even get pdb2gmx to generate a CHARMM topology

Re: [gmx-users] Capping residues

Sai Pooja wrote: This probably is my ignorance but the error and the "bug" goes when I replaced CBX with NAC everywhere. I would suggest filing a bugzilla. I was able to reproduce your problem. If nothing else, pdb2gmx should not be name-specific. Something very weird is going on. Mo

[gmx-users] Compiling problems on MacOS X 10.6.4

Hi I m trying to compile the gmx development version (from git) on MacOX (Darwin kernel) The configure is successful but after I enter make and after lots of output I get the following: ld: warning: in /opt/local/lib/libxml2.a, file was built for unsupported file format which is not the arch

Re: [gmx-users] Capping residues

This probably is my ignorance but the error and the "bug" goes when I replaced CBX with NAC everywhere. On Wed, Jul 7, 2010 at 4:47 PM, Justin A. Lemkul wrote: > > > Sai Pooja wrote: > >> I checked again and the error does not go. Please read the steps below. >> >> The pdb file I started off wit

Re: [gmx-users] Capping residues

Sai Pooja wrote: I checked again and the error does not go. Please read the steps below. The pdb file I started off with did not have any hydrogens. However, the way I had specified the capping residues in the .rtp file (SEE MARK'S MAIL), I had to specify hydrogens in the pdb file for the ca

Re: [gmx-users] Capping residues

I checked again and the error does not go. Please read the steps below. The pdb file I started off with did not have any hydrogens. However, the way I had specified the capping residues in the .rtp file (SEE MARK'S MAIL), I had to specify hydrogens in the pdb file for the capping residues. So I us

Re: [gmx-users] wrong charge assignment(?) on ATP in rtp file

Hi, The parameters for ATP (and several other building blocks and molecules) in the GROMOS 53a5 and 53a6 force fields are, AFAIK, inherited from the older versions, albeit with some modifications to bring them in line with the rest of the force field. So they weren't reparameterized and thus do no

[gmx-users] Parameters for selenium

I don't have the parameters. You could possibly fudge it by extrapolating out from SER->CYS->Se_CYS based scaled by electronegativities of O,S,Se. I'm not saying that this is rigorous, just that its possible to do. My main point here, though, is to ask if you *really* need to bother with th

[gmx-users] parallel run with integrator=nm ?

Dear all, In an attempt to speed up things, I tried to calculate an hessian matrix in parallel, using two processors and it finished in about half the time when compared to a single-node run. However, the parallel run produces an .mtx file that has about half the size of the one obtained in the

[gmx-users] Re: Parameters for selenium

Em 7 de julho de 2010 11:47, Luis Paulo escreveu: > Please > > Someone know Gromos parameters for selenium. WE need to simulate the > Thioredoxin and we need to simulate a cisteine with a selenium. > > Thanks > regards > > Luis Scott > > -- > Prof. Dr. Luis Paulo Scott > CMCC- Centro de Matemáti

Re: [gmx-users] (no subject)

munu...@yahoo.com wrote: Hi, I am using GROMACS 4.0 for simulating a peptide having 5 residues. I have built the sequence using pymol and capped the peptide with CH3CO and NHCH3 at its N and C terminal respectively and save in pdb file format. The pdb file was used to produce *.gro and *.t

[gmx-users] problems with g_wham

I missed that pull_start = yes, sorry. So Gavin, your run should have stayed around the starting position. Make the histogram directly and you should get a better idea. Chris. -- original message -- To clarify, the tutorial sets "pull_init1 = 0" because it is used in conjunction with "p

[gmx-users] (no subject)

Hi, I am using GROMACS 4.0 for simulating a peptide having 5 residues.  I have built the sequence using pymol and capped the peptide with CH3CO and NHCH3 at its N and C terminal respectively and save in pdb file format.  The pdb file was used to produce *.gro and *.top files using pdb2gmx ff G43

[gmx-users] wrong charge assignment(?) on ATP in rtp file

"It seems that I do not need to care about decimal total group charges as I am planning to use PME." -- well, find it in the literature first! -- original message -- Dear Chris, I really appreciate your comment. Can you provide a reference for the idea that the charge groups must have inte

Re:[gmx-users] wrong charge assignment(?) on ATP in rtp file

Dear Chris, I really appreciate your comment. > Can you provide a reference for the idea that the charge groups must have > integer charge? I actually do not have any critical literature for the idea of “whole number rule”; 1) In the item of “Charge group” of the “GROMACS USER MANUAL, ver.4” i

Re: [gmx-users] problems with g_wham

Gavin Melaugh wrote: Hi Chris Thanks very much for your help. The reason I used pull_init1 = 0 is because this is the value that is used in the tutorial. Maybe I am misinterpreting its meaning. In the tutorial it says that you do not have to specify a value separately for each configuration. I

[gmx-users] problems with g_wham

Gavin, I think it's time for you to read some papers and read the gromacs manual pull COM section. A few days of reading will make all of this clear to you. -- original message -- Hi Chris Thanks very much for your help. The reason I used pull_init1 = 0 is because this is the value that i

Re: [gmx-users] problems with g_wham

Hi Chris Thanks very much for your help. The reason I used pull_init1 = 0 is because this is the value that is used in the tutorial. Maybe I am misinterpreting its meaning. In the tutorial it says that you do not have to specify a value separately for each configuration. I am now thinking that in

[gmx-users] problems with g_wham

Gavin, let's take g_wham out of the picture for now to simplify things. First, you umbrella is pretty strange. You want them to have a distance of 0.0 nm (pull_init1 = 0)??? So let's look at making a histogram from your raw data. 1. cat pullx.xvg |awk '{print sqrt($1,$5*$5+$6*$6+$7*$7)}' > m

[gmx-users] problem with g_clustsize

perhaps that's not standard terminology, sorry. The numbering starts at the headgroup so the distal atom would be the one at the end of the acyl-chain (the one most likely to spend its time in the middle of the cluster. -- original message -- Thanks. Just wondering what is a 'distal atom'

Re: [gmx-users] COM distances

Hi Chris Sorry I sent my e-mail just prior to receiving yours? Is it any clearer? Gavin chris.ne...@utoronto.ca wrote: > The pullx file should contain everything that you need. dX,dY,dZ *are* > the components of the distances between the two groups. > > I still don't understand your question (per

Re: [gmx-users] problem with g_clustsize

Thanks. Just wondering what is a 'distal atom' as you mentioned.   I am creating a new subject on g_clustsize.  --- On Wed, 7/7/10, chris.ne...@utoronto.ca wrote: From: chris.ne...@utoronto.ca Subject: [gmx-users] problem with trjconv -pbc cluster To: gmx-users@gromacs.org Date: Wednesday, 7 Ju

[gmx-users] problems with g_wham

Hi Guys I am having great difficulty generating a histogram of the correct shape from g_wham. I am running umbrella sampling on one configuration fo two molecules at a fixed distance using the following pull parameters. ( I am just running one configuration to begin with so that can make sure that

[gmx-users] COM distances

The pullx file should contain everything that you need. dX,dY,dZ *are* the components of the distances between the two groups. I still don't understand your question (perhaps you could give us a worked example with real data?), but if you just want the COM distance, then try this: cat pul

Re: [gmx-users] Fatal error:

Nilesh Dhumal wrote: Hello, I am trying to equilibrate my system, ionic liquids. Simulations stops with following error Fatal error: 1 of the 43778 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.32754 nm) or

[gmx-users] Fatal error:

Hello, I am trying to equilibrate my system, ionic liquids. Simulations stops with following error Fatal error: 1 of the 43778 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.32754 nm) or the two-body cut-off dist

[gmx-users] problem with trjconv -pbc cluster

I wrote my own program to do this and so I never tried that one. We did find that clustering based on a dingle atom in the chain was a very good idea. So take your distal carbon in the surfactant and make in index group of it and cluster it (with a larger cutoff) with g_clustsize. Obvious

[gmx-users] how gromacs calculate center of mass for broken molecules?

That depends. mdrun pull code does it smartly via pull_pbcatom (assuming that you have chosen pull_pbcatom and your box size smartly), while g_dist is not smart about it at all. Can you be more specific about what you want to do? -- original message -- Hi everyone: How gromacs calculate c

Re: [gmx-users] problem with trjconv -pbc cluster

Hi Chris,  Thanks a lot for your responses. I will surely try them. But, before I go to trjconv -pbc cluster, I had one more problem to sort out. This has to do with quantifying the cluster-size distribution from the trajectory. As I mentioned, if I visualize the trajectory in VMD, I see that st

[gmx-users] wrong charge assignment(?) on ATP in rtp file

Dear Shuntaro: If you're using PME then there is no need to have unit charge in charge groups. I can't comment on any other errors that may or may not be in that topology as I have never simulated ATP. Also, if you're not using PME, then I can not advise you if it is ok to have non-integer

[gmx-users] wrong charge assignment(?) on ATP in rtp file

Dear gmxusers, I am going to carry out an MD simulation using G53a6 FF, whose system contains some ATP molecules. In order to know whether the calculation is possible or not, I looked for a topology of ATP in ffG53a6.rtp. Although the topology exists, each total charge of charge group 9, 10 a

[gmx-users] Frozen N2 in a very long tube; was "help: gromacs mistake"

Dear shuai shuai: Please use a descriptive title. I renamed it. You must describe your problem more. e.g. is the problem that you get a frozen cluster in some simulations, or that you don't get this in other simulations? What, exactly, is a small cluster of frozen molecules? You must als

[gmx-users] help: gromacs mistake

Dear all, Recently I met a strong error from gromacs. Therefore I would like to know whether you have experienced the same thing or what is the reason for that. The system I simulated is nvt MD for N2 (with partial charge) diffusion in a long tube (100x2.5x2.5 nm^3) at 300k. The problem is that o

[gmx-users] problem with trjconv -pbc cluster

PS: you realize that trjconv -pbc cluster is never going to work unless you actually have a cluster, right? So you can't start this procedure near your initial dispersed state. You need to start at some time T where you actually do have a cluster. Then you can try -dump T, -dump (T+X), -d

[gmx-users] problem with trjconv -pbc cluster

Dear Jagannath: There is, as far as I know, no way to fix this. Here's what you should do. 1. Let the space between your timesteps be X ps. 2. Use trjconv -pbc cluster -dump X -o out.gro 2b. if that doesn't work, try trjconv -pbc cluster -dump (X*2) -o out.gro 2c. if that doesn't work, try trjco

[gmx-users] how gromacs calculate center of mass for broken molecules?

Hi everyone: How gromacs calculate center of mass for broken molecules? If the molecule is broken due to the pbc, where will the center of mass be? Thanks, Kun -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] Nitrile_Butadiene_Rubber simulation using Gromos96

Dear all   I am trying to simulate Nitrile-Butadiene-Rubber, using the Gromos96 force field. I have difficulties in finding the correct parameters from the bon.itp file , in order to define the polymer in the .rtp file.   Can someone suggest which parameters I shall choose in the followin

Re: [gmx-users] COM distances

Hi all In hindsight I think the question I posted yesterday may have been a little naive. To rephrase it - If the pullx.xvg files contain X Y Z dX dY dZ, (because pull_dim = Y Y Y), does the g_wham programme calculate the centre of mass distances to use in the histogram i.e. Will the first column

Re: [gmx-users] No such moleculetype SOL

nanogroup wrote: Dear Mark, Many thanks for your e-mail. I checked the TOP file, the SOL is diefined there and numbers of solvent moelcules are presented. If this were true, you wouldn't have gotten the error you did. The best information you can provide is the relevant section of .t

[gmx-users] No such moleculetype SOL

Dear Mark,   Many thanks for your e-mail.   I checked the TOP file, the SOL is diefined there and numbers of solvent moelcules are presented.   I solved the sample by genbox command and selected spc216.gro   I am looking forward to reading from you.   Bests, Mahmoud -- gmx-users mailing l

Re: [gmx-users] g_anaeig & pymol

Hi, you probably did the covariance analysis on the backbone atoms of your system. However, for the calculation of the secondary structure PyMOL needs at least the MainChain part of your molecule. So the easiest thing would be repeat your analysis with the MainChain group instead of backone.

Re: [gmx-users] No such moleculetype SOL

- Original Message - From: nanogroup Date: Wednesday, July 7, 2010 18:16 Subject: [gmx-users] No such moleculetype SOL To: gmx-users-requ...@gromacs.org Cc: gmx-users@gromacs.org --- | > Dear GMX Users, > > I solve sample in the w

[gmx-users] g_anaeig & pymol

Hi everyone, I did a covariance analysis by following this link: http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis1.html Now I want to visualize the differences between the extreme structures by doing this: pymol ev?.pdb Split the models in the pdb files and delete the originals. split_state

[gmx-users] No such moleculetype SOL

Dear GMX Users, I solve sample in the water, but when I run GROMPP, this error appeares: Fatal error: No such moleculetype SOL Without water, the grompp was done. Thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please sear

Re: [gmx-users] problem with trjconv -pbc cluster

Thanks for the reply. I used following command to extract first frame that has all the surfectants ( as suggested by first step for characterizing micelle clustering).    trjconv -f a.xtc -o a_cluster.gro -dump 0 -pbc cluster Here is the output I got:COM:    0.000     0.000    19.999  iter = 195

[gmx-users] Release of the R.E.D.-III.4 tools

Dear All, I am pleased to announce the release of the program RESP ESP charge Derive version III.4 (or R.E.D. III.4) and its related tools (Ante_R.E.D.-1.4 and X R.E.D. III.4) available @ http://q4md-forcefieldtools.org/RED/. New features available: - Bug corrections and code cleaning in

Re: [gmx-users] problem while simulating metal ions

- Original Message - From: Kwee Hong Date: Wednesday, July 7, 2010 11:36 Subject: [gmx-users] problem while simulating metal ions To: gmx-users@gromacs.org --- | > > Hi. > > I'm trying to subject a metalloprotein bound to cad