Re: [gmx-users] RMSF reference state?

Hi, Actually, Justin is completely right (and I should've checked g_rmsf -h). -od calculates the RMSD from the structure in the frame against the structure in the topology file. This does not nullify the statements regarding references for fitting and references for deviations though :p Cheers,

Re: Re: [gmx-users] RMSF reference state?

Hi Pan Wu, There are two things to distinguish: 1. The reference structure used to remove translational and rotational degrees of freedom 2. The reference against which the deviations (on a per atom base) are calculated that are then squared, averaged and taken the root of (root mean square fluct

Re: [gmx-users] run g_cover in parallel

Hi, >> I wonder if there a way to run g_cover in paralel in order to make >> things run faster? > > No. Obviously you can use -dt to reduce the number of frames you analyze. In most cases it's not the reading of frames, but the diagonalization of the covariance matrix that consumes most of the ti

Re: [gmx-users] forcefield

Hi Lalitha, Zebularine is beyond the trivial. You may be able to derive something reasonable from the other bases using 'chemical intuition' (cytidine, thymidine, uracil), but it's likely that the electronic structure of the ring is too different to justify an approach like that. Likely you should

Re: [gmx-users] Advantage of NPT over NVT?

Hi, In addition to the remarks of Ran and Mark, also note that with NVT the density of your system may change significantly and artificially, relating to changes in your protein. This in turn affects the dynamics of your protein, which should be considered an artefact of NVT simulations. Cheers,

Re: [gmx-users] Question about genion, error happens

Hi Pan Wu, You use -pname to specify that the added sodium ions should have the name 'Na'. Accordingly, at the end of your .top file genion writes a line under [ System ] specifying the number of 'Na' molecules. But that requires that 'Na' is defined, which is not the case, given the error. The co

Re: [gmx-users] pdb2gmx problem

Hi Abhijit, I think the Zinc ion goes with chain B and uses the same identifier. Given the fact that you didn't quite understand the error, and found it necessary to post a question, this raises another question: should you be wanting to simulate a protein with a zinc ion? (http://www.gromacs.org/

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

Cool. You can also write a python script to generate and execute your C-code, which you then wrap with Java to be executed through Ruby... etc. Erik, can you maybe give the assembly solution? :p Tsjerk On Mon, Oct 5, 2009 at 10:15 AM, Alexander Bujotzek wrote: > I once wrote some lines of adven

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

Hi, > Is trjconv parallelizable?  This is nowhere in the documentation, but if it > is, that would be very interesting... Well, the most interesting part in that regard is probably the I/O. But that's the hardest bit to parallelize. >> How to pass the choice 0 in the script Just as you would on

Re: [gmx-users] Re: a naive question on restraints and constraints

Hi, It's actually a bit more nuanced and the use of these idioms is not really backed by a semantic distinction: In Gromacs, a constraint fixes some property to a value, whereas a restraint penalizes deviation of a property from a certain value. Cheers, Tsjerk On Wed, Sep 30, 2009 at 2:03 AM, J

Re: [gmx-users] water molecule cannot be settled

Hi Carla, You may have a water molecule trapped inside your protein. Check the water molecule with the given atom number in a viewer, together with your structure. If it is inside, you can try to remove it manually from the system, editing the structure file and decreasing the amount of solvent li

Re: [gmx-users] Trjconv trouble

Hi Guy, Which version are you using? It may be there's a flaw in the code. If you want the forces in human readable format, you can also try converting the .trr to .g96 Hope it helps, Tsjerk On Mon, Sep 28, 2009 at 9:59 PM, Vigers, Guy wrote: > Dear Gromacs users, > > > >     I seem to be havi

Re: [gmx-users] Generating a .gro file from .pdb file

Hi, > No, that procedure generates a topology file, it is not the correct tool for > a change of coordinate format (which is almost never needed anyway). As a > side effect, it regularizes an input coordinate file which might have been > in one of various formats, and outputs a coordinate file who

Re: [gmx-users] Probelm of g_rms

Hi Nikhil, Try extracting the frame just before and just after the jump and view them in pymol/vmd/rasmol/... to check for a possible cause. Cheers, Tsjerk On Fri, Sep 25, 2009 at 5:50 AM, nikhil damle wrote: > Yes. I am correcting the trajectory for periodicity > > Regards, > Nikhil > > _

Re: [gmx-users] editconf and g_rmsdist

Hi Soren, >  Why I am seeing this difference? Is it due to round-off’s after the > transformation to center the molecule in the box? Or am I using g_rmsdist > wrongly? It's a bit weird indeed. You might be right that it's due to round-off errors. You can try to copy the original gro file and repl

Re: [gmx-users] Can Gromacs produce the data from NMR?

Hi Lin, You should check the manual, check the literature on cross validation of MD/NMR, and note that the tutorial you've been following has two items related to it, namely distance analysis, including NOE back calculation, and calculation of order parameters. Hope it helps, Tsjerk On Fri, S

Re: [gmx-users] Periodic Boundary Conditions & Location of Atoms Near Box Edges

Hi Darrell, No, you just have to make sure that the bond lengths are correct in the periodic system. The PBC are invariant under translation. Cheers, Tsjerk On 9/17/09, Darrell Koskinen wrote: > Dear GROMACS Gurus, > In order to correctly model an infinite graphene sheet using periodic > boun

Re: [gmx-users] Re: System has non-zero total charge: 2.570000e+00

Hi, On Sun, Sep 13, 2009 at 8:55 AM, Vitaly V. Chaban wrote: >> before energy minimization step , I performed the preprosessing step using >> grompp  . However, there’s a note that : System has non-zero total charge: >> 2.57e+00 “. >> why the total charge of system is not an integer? > > Th

Re: [gmx-users] bypassing pdb2gmx

Hi Amit, You don't need to convert the .pdb file. Gromacs can handle several file formats, including .pdb. If you have a topology that matches the .pdb in terms of atoms, then you can simply proceed with the subsequent steps. pdb2gmx is not exactly meant to convert the structure file to another fi

Re: [gmx-users] how to use a new force field

Hi, Well, to *add* a new force field, summerizing and extending the replies given earlier, you edit the file FF.dat in the directory $GMXPATH/share/gromacs/top.This file looks like 11 ffG43a1 GROMOS96 43a1 force field ffG43b1 GROMOS96 43b1 vacuum force field ffG43a2 GROMOS96 43a2 force field (

Re: [gmx-users] How to select Force field

Hey :) What did grompp say (and why -maxwarn 3)? And what did the previous steps give? Did you check the convergence of the potential energy during energy minimization? Was there anything odd running pdb2gmx? Oh, and why would you waste resources using a cubic box? Tsjerk On Sun, Aug 30, 2009 at

Re: [gmx-users] LINCS

Hi, .snip... > No, because that's not a well-defined proposition. You could generate a > small box with one solute +solvent, and then use *genbox* to replicate it. genconf, rather than genbox: genconf -f in.gro -o out.gro -nbox nx ny nz with suitable nx, ny and nz for nx*ny*nz copies. Unfortun

Re: [gmx-users] grompp.mdp

Hi kayal, Well, given that it reads "Fatal error" your final question seems a bit odd, doesn't it? How did you obtain the topology? Apparently, there's a bit more specified in it than a single butane! Besides, I notice that you use the GROMOS force field, which is a united atom force field. That m

Re: [gmx-users] cluster graph

Hey, According to the urban dictionary: II. Defining 'Noob' Contrary to the belief of many, a noob/n00b and a newbie/newb are not the same thing. Newbs are those who are new to some task* and are very beginner at it, possibly a little overconfident about it, but they are willing to learn and fix

Re: [gmx-users] Control Atoms for Hydroxide ?

Hi, Well, who'd need control atoms? You'd just need to position it at a certain distance along a random vector. If you're talking about it as part of a water cluster or something, technically speaking it's not a hydroxide anymore :) On another note, as I mentioned before, the proton has an intrins

Re: [gmx-users] How to start the Normal Modes Analysis?

Hi, Start out with reading and only stop reading when you grasp what it is, what it does, what it can do and what it can't do. Tsjerk On Thu, Aug 13, 2009 at 10:37 PM, Justin A. Lemkul wrote: > > > Chih-Ying Lin wrote: >> >> >> Hi >> I read the Manual and still have no idea about the Normal Mode

[gmx-users] Re: solvation

Hi, Right, but genbox puts things inside the rectangular brick corresponding to the unit cell, starting at the origin. That means that if the solute is on one end, then placing something close to the part that sticks out will actually be put on the other side of the box. But maybe I just want to m

Re: [gmx-users] Re: solvation

Hi, > Thanks for the answer. When I said far away means my pore was in one corner > of vmd window and the water molecules in opposite corner (almost). Did I miss something or did neither Vitaly nor Justin reply "Are you perhaps seeing the effect of periodic boundary conditions?". Tsjerk -- Tsj

Re: [gmx-users] minimization

Hi Morteza, I think it will be best for all of us if you can provide the exact command lines you are using, and the output of pdb2gmx for the well-performing and an ill-performing force field. Otherwise I'm afraid that we will not be able to get any further than making guesses. Cheers, Tsjerk 2

Re: [gmx-users] minimization

Hmm, was the OPLSAA run following the GMX one on the dimer or also performed on the monomers? If you feed a multimeric protein without chain identifiers (like in a .gro file) to pdb2gmx, it will bind the different chains together. That would be a good cause for a crash. So I'd say check that first,

Re: [gmx-users] minimization

Hi Morteza, How did you obtain these structures? If they were modeled, maybe in part, check for knots and chain overlaps. Also check whether you're using PBC and if so, whether the box is large enough or you may have overlapping periodic images. Cheers, Tsjerk 2009/8/13 Mark Abraham : > Morteza

Re: [gmx-users] A question regarding single sum virial

Hi Lanyuan Lu, It's described in detail in Chapter 2 of Henk Bekkers PhD thesis, available at: http://dissertations.ub.rug.nl/faculties/science/1996/h.bekker/ Cheers, Tsjerk 2009/8/12 LuLanyuan : > Hello all, > I got a question when I read the the manual chapter for the single sum > virial (p19

Re: [gmx-users] copper cluster bond to histidines

Hi Andrea, You're probably best off 'fixing' the copper to the protein, meaning introducing bonds at least (harmonic, type 6?). With these bonds you can to some degree account for the effects of polarization and such on the interatomic distances, which are likely more difficult to model reparamete

Re: [gmx-users] Improper Dihedrals

Hi, If you turn all bonds to constraints, and your system is infinitely periodic, you probably don't even need impropers. The bond lengths can only be satisfied in the plane. Adding impropers, straining your molecule further into the configuration you think is proper, adds forces that inevitable c

Re: [gmx-users] energy minimization

Hi, On Wed, Aug 12, 2009 at 3:06 AM, Mark Abraham wrote: > Jamie Seyed wrote: >> >> Dear all, >> I performed an md simulation but it crashed at the beginning because >> according to it "system was exploding". Also when I tried to see the >> system >> by ngmx, there was no water anymore and it was

Re: [gmx-users] Supercomputing Center

Hi Negar Ashari Astani, There are plenty supercomputing facilities, probably even in your country, but they're not 'free'. You'll have to request time, most likely through writing an application. Your institute should have some information about contacts with (inter)national supercomputing facilit

[gmx-users] Fwd: Error in PDB2GMX

Sunny, It is improper to send (un)personal mails like this, targeted to several people, just changing the addressing. Basically you qualify for straightforward neglect. Do you really think the user list is only kept for fun? And I'm not even sure I ever answered one mail related to CG simulations!

Re: [gmx-users] Protein Activity

Hi Lin, Start with defining "Protein activity". Tsjerk On Tue, Aug 4, 2009 at 8:11 PM, Chih-Ying Lin wrote: > > > > Hi > How can I analyze / describe Protein Activity after MD simulation? > > > Thank you > Lin > > > > > > > ___ > gmx-users mailing list

[gmx-users] Fwd: help-how to define a new residue in gromacs ?

This is what the GMX user list is for. Please post such requests there. Tsjerk -- Forwarded message -- From: 郭建路 Date: 2009/8/4 Subject: help-how to define a new residue in gromacs ? To: tsjerkw HI Tsjerk: can you help me ? My problem is How to define new residue in GROMACS?

Re: [gmx-users] Hg2+ ions in ion.itp

Hi Anirban, I wouldn't try it if I were you. Hg is a classical example of an exotic species: http://oldwiki.gromacs.org/index.php/Exotic_Species. It has everything: non-standard (linear) coordination, charge transfer, etc. But, it may well be that the ions were only used for phasing the crystals.

Re: [gmx-users] Hydroxide Ion

Hi, Well, it's not just a matter of topology. This is only true if the basic assumption holds, that the particles behave approximately classical. This is definitely not the case for species such as hydroxide and hydronium. Cheers, Tsjerk On Thu, Jul 16, 2009 at 4:13 AM, Justin A. Lemkul wrote:

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

Think outside of the box when using Periodic Boundary Conditions. :p Tsjerk On Wed, Jul 15, 2009 at 9:14 AM, Mark Abraham wrote: > nikhil damle wrote: >> >> Hello, >> >> When I am running energy minimisation of protein-peptide complex, >> minimised structure shows a space for the protein in wate

Re: [gmx-users] about do_dssp

Hi hazizian, That information is stored in the file you get with the option -sc. To get percentages you have to use awk or something along thos lines. Cheers, Tsjerk On Tue, Jul 14, 2009 at 5:47 AM, hazizian wrote: > > Hi > I have a question about do_dssp program.is it posible to define the amo

Re: [gmx-users] Different RMSD of the same system

Hi Dechang Li, If your simulations are different, the results will be different. It's chaos! Cheers, Tsjerk 2009/7/13 Dechang Li : > Dear all, > >        I have did a simulation with explict water model using Gromacs-3.3.3. > To save the hard disk space, I didn't collect the coordinates of wate

Re: [gmx-users] Water clustering

Hi Taka, I'd say you need to add some more water :) But in addition to that, you definitely should run with pressure coupling in stead of at constant volume. Cheers, Tsjerk 2009/7/10 H T : > Hi, I am trying to calculate micelle formation with SDS molecules for > all-atom simulation. > 49 SDS mo

Re: [gmx-users] global rmsf fraction to each eigenvector

Hi Fabricio, With total RMSF, do you mean over all atoms or total per atom? The former is simply the eigenvalue divided by the sum of all eigenvalues. For the latter, check g_anaeig. Cheers, Tsjerk On Fri, Jul 10, 2009 at 7:01 PM, Ragnarok sdf wrote: > Once I have the eigenvalue.xvg, how do I c

Re: [gmx-users] Can I change xtc-groups while continuing a simulation?

Hi Michael, > My only idea so far sounds pretty hacky: use the original coordinates and > mdp file to make a phony "initial.tpr" with the new xtc-groups and pass this > phony file on to tpbconv. I'm hesitant to do this because I don't actually > know what all is in a .tpr file and whether this wou

Re: [gmx-users] Regarding numbering

Dear P.R.Anand Narayanan, > 1. how did the number of atoms and residues change. Hydrogen atoms were added to your structure, which accounts for the increase in number of atoms. The number of residues should not have changed. Probably there is a discrepancy between the number of residues you have

Re: [gmx-users] Fatal error

Hi, Probably you don't have write permissions in that folder. Cheers, Tsjerk On Wed, Jul 8, 2009 at 1:07 AM, s lal badshah wrote: > Hi Gromacs user, > > I changed the version and this time it gave the following error > s...@linux-g1cj:~/Desktop/283> g_energy -f md283.edr -o md283-TE.xvg >  

Re: [gmx-users] Why is triclinic geometry not retained in confout.gro?

Hi Jenny, Check chapter 3 of the manual regarding PBC. There is no box in PBC (a box defines PBC, but PBC does not define a box). The rectangular brick is just one of the ways to represent the unit cell. If you insist in seeing a triclinic unit cell, use trjconv -ur triclinic -pbc inbox. Cheers,

Re: [gmx-users] using editconf to duplicate membrane

Hi Bing, You do want to use genconf for that (the way you use it, editconf scales the coordinates). genconf -f xxx.pdb -nbox 2 2 1 -o zzz.pdb The thing to make sure is that all molecules are whole before processing them with genconf. The other possibility is to use editconf to translate a few co

Re: [gmx-users] .mdp => Dihedral Angles conflict Bond Constraints ?

Hi Lin, > lincs-warnangle       =       30 > this allows each covalent bond to rotate at most 30 degrees This line says to issue a warning when a bond rotates more than 30 degrees. It doesn't say lincs-maxangle or something along those lines, indicating prohibiting such rotations. Tsjerk --

Re: [gmx-users] changing pdb file residue name

Hi Rukmani Sridharan, It's not a matter of name. Gromacs is unlikely to have a topological description of the molecule and you have to provide that. See http://oldwiki.gromacs.org/index.php/Parameterization Cheers, Tsjerk On Mon, Jul 6, 2009 at 6:06 AM, Rukmani Sridharan wrote: > Hi, > I am a

Re: [gmx-users] protein covalently bond to ligand

Hi haziz...@razi.tums.ac.ir, I think it's better to only use PRODRG for the pyridoxal phosphate part. Then you can process the rest of the protein as usual, preserving the parameters for lysine backbone and side chain. The PLP part you can renumber and merge with the protein topology, adding bond,

Re: [gmx-users] problem during simulation of dna-protein complex

Hi Nitu, Energy minimization is only to remove some strain from your system. You probably don't want to include position restraints there. After energy minimization you typically run a short MD run in which you use position restraints such that the protein/DNA doesn't move to much, but the water c

Re: [gmx-users] problem in simulation of dna-protein complex

Hi Nitu, Check the atoms and their order in the pdb and the rtp file and try to find out which match and which miss. >     C2    amber99_2 0.56770    25 > O    amber99_41   -0.58810    26 I place my bet on this one. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) B

Re: [gmx-users] How to avoid generating wrong dihedrals?

Hi Chaofu Wu, Indeed it seems improper to have a dihedral with C-N-H-H. So it's an improper dihedral! :p The problem might arise from the addition of hydrogens. Could you give more information? Which force field did you use? what residue was causing the problem? Can you reproduce the problem start

Re: [gmx-users] Non-bonded Copper

Hi Matthew, On top of the advice of Mark, consider that Copper has a rather peculiar electronic structure, which may make it difficult to model using only a Lennard-Jones potential for the non-bonded interactions. And then it will also matter whether it's Cu(I) or Cu(II). Are you sure that the sim

Re: [gmx-users] stopping and restarting a simulations after adding more constraints

Hi Jayant, On Sun, Jun 28, 2009 at 8:23 PM, jayant james wrote: > Hi! > I have been performing a distance restrained simulation for 7ns and now I > feel that its time to throw in a few more distance restraints. So this is > what I am planning to to > > 1. Stop the simulation .The command would be,

Re: [gmx-users] 45a4 force field files to nucleic acids simulations

Hi Guilherme, These parameters are kept in the later series 53a5 and 53a6. Cheers, Tsjerk On Fri, Jun 26, 2009 at 7:19 PM, Guilherme Menegon Giesel wrote: > Hello folks!!! > > I'm trying make simulations with nucleic acids with GROMOS. I know that was > published the article " An improved nucle

Re: [gmx-users] Re: Re: problems with some calculated trajectories

Hi Bernhard, The images, are they taken from exactly the same angle? If so, there's some change in orientation that is just impossible in such a short time. You didn't happen to fit your structure to a reference prior to removal of jumps, did you? Fitting messes up PBC and garbles results from -pb

Re: [gmx-users] Problem wih Fe-S cluster

Hi Subarna, If you just want to retain the structure of the cluster it doesn't matter too much. It may be good to average values from different structures, though. HOWEVER, an FeS cluster is a catalytic site, which probably has fancy electronic properties, which may well affect the behaviour of th

Re: [gmx-users] Parameters for -Si-Si- chains?

Hi Semen, When confronted with Si-Si-Si and radicals in the same sentence, I don't get comforted and definitely wouldn't characterize it as 'rather simmple' ;) There seem to be quite a number of publications referring to MD of Si-Si systems though. Try googling a bit, or try Web of Science; gives

Re: [gmx-users] non squares box

Right, there was no reference whatsoever to MD. The first sentence, preluding the problem, mentioned editconf. The second, mentioned trjconv. No grompp/mdrun etc in between. Anyway, also to check the periodicity in your output (note how flexibly I adapt it to the current situation): genconf -f con

Re: [gmx-users] non squares box

Hi Omer, To check your periodicity use genconf: genconf -f in.pdb -o out.pdb -nbox 2 2 2 Cheers, Tsjerk On Sun, Jun 21, 2009 at 11:23 AM, Omer Markovitch wrote: > Dear All, > I would like to ask your help on the following - I want my simulation to > include a surface, and have PBC. > The surfa

Re: [gmx-users] g_energy => the reasonable range of RMSD or Fluctuation ?

Hi Lin, That depends on the size of your system. Maybe add a book about statistical mechanics and thermodynamics to your reading list... Cheers, Tsjerk On Fri, Jun 19, 2009 at 8:00 PM, Chih-Ying Lin wrote: > HI > Once the system reaches the equilibrium, the thermal properties still > fluctuate

Re: [gmx-users] g_energy => RMSD = Standard Deviation?

Hi, It also doesn't hurt to read up more about statistics. The standard deviation is the square root of the second central moment of a distribution, so it's the expectation value for the average deviation found in a set of mutually indepent data points. Root mean square deviation does not imply mu

Re: [gmx-users] problem fitting trajectory

Hi, It is better to do PBC options first and fitting options after, with separate calls to trjconv. Fitting and PBC don't go well together, This has been elaborately discussed on the mailing list before. Cheers, Tsjerk On Wed, Jun 10, 2009 at 8:59 PM, Justin A. Lemkul wrote: > > I have found th

Re: [gmx-users] units of eigenvalues of mass-weighted covariance matrix

Hi, Well, as has been pointed out before nm\S2\N stands for nm superscript 2 normal. That is correct for non mass-weigthed covariance analysis. It's just fluctuation. Why would it be kg/m2 (kg/nm2) for mass weighted? Look at the equations in the manual. It's sqrt(mass)*sqrt(mass)*nm*nm, which make

Re: [gmx-users] non-standard residues in pdb2gmx

Hi, > What might be even easier is to create an .itp file for myristic acid, so > you can #include "myristic.itp" in any topology that needs it.  That way you > don't have to mess with .rtp files, or run pdb2gmx for every system that > contains myristic acid. But this doesn't help when it has to

Re: [gmx-users] Reg. g_density

ide a tpr file right... is there a way of doing it without the tpr... > and also from where are the radii of the atoms read for calculation of the > volume... or is the volume calculated differently... > thanks in advance > > Regards, > Jagan > > On Sat, Jun 6, 2009 at 3:10

Re: [gmx-users] Reg. g_density

Hi Jagan, If you provide a .tpr file, the masses will be read from there. Otherwise, when providing a .gro/.pdb file or so, masses will be read from the file atommass.dat in the GMX library directory. Cheers, Tsjerk On Sat, Jun 6, 2009 at 11:25 AM, Jagan Mohan wrote: > Hey everyone, > I would l

Re: [gmx-users] Re: Extending water in negative Z direction

Anirban, Please, many of us have years of experience with MD and this type of systems. If you had considered that, rather than assuming that we still don't understand what you mean, you would have been on the right track to fix an apparent caveat in your knowledge regarding MD simulations, and not

Re: [gmx-users] Entending water in negative Z direction

Hi, What is the difference between increasing in the positive z direction and the negative z direction? Tsjerk On Thu, Jun 4, 2009 at 4:31 PM, Anirban Ghosh wrote: > Hi ALL, > > In previous posts I mentioned the problem I am facing: a portion of my > protein (GPCR in a POPC bilayer) in extendin

[gmx-users] Fwd: problem with FES4 cluster

Subarna, I am not a helpdesk or mailing list, if I had had the answer, I would have replied on the mailing list already. Then, if you feel it is appropriate to send a mail to someone you don't know, at least take the effort to write a complete message. Tsjerk -- Forwarded message --

Re: [gmx-users] gromacs invsqrt() overlaps with icc invsqrt()

wing procedure: >> >> # >> #!/bin/bash >> for i in `find ./gromacs-4.0.4`; do >>  sed 's/invsqrt/invSAFEsqrt/g' "$i" > tmp; >>  mv tmp "$i"; >> done >> chmod +x ./gromacs-4.0.4/configure > > Using sed -i is a bit more elegant and keeps the permissions, IIRC. > Correct. You

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

Hi Anirban, You have to get a grip on PBC. What you're suggesting is like extending the earth only westward, but not eastward as something is sticking out in only one direction. It's impossible! The system is periodic.The box vectors are direction vectors, indicating the periodicity. Moreover, you

Re: [gmx-users] essential dynamics analysis

Hi JJ, > 1) Should ED analysis be performed only on the segment of trajectory wherein > the protein's RMSD has equilibrated, am I right?  Because I have the notion > that harmonic analysis of a trajectory can only be performed when the > protein is undergoing fluctuations about a minimum. In other

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

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] 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: [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] 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: 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] 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: [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 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] 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] 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?

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] 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] 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] 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] 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] 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

[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

[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)

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] 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] 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

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