Re: [gmx-users] Major code reorganization in git coming up

Hi Erik, Happy New Year! Last year (:p) I rewrote the routine from Andrea Amadei for application of rotational constraints in a statistical mechanical consistent manner. It's completely parallellelellized and consistent with pd/dd as well as application every so many steps. The tests seem good, a

Re: [gmx-users] g-dist

Hi Mohsen, I think you'll have to get a bit creative with g_traj to get the COMs, followed by either some simple scripting or nifty usage of paste and awk (something like: paste com1.xvg com2.xvg | awk '/^...@#;]/{print $2-$6, $3-$7, $4-$8}'). Hope it helps, Tsjerk On Dec 25, 2010 2:40 PM, "moh

Re: [gmx-users] using recolor.sh to color the xpm matrix files produced by r_rms and g_mdmat

Hi Hassan, It seems the scripting language of the Gimp has changed a bit since the version I used at the time of writing that script. The Gimp is also only used for conversion of the xpm to png, which it did better than convert. The important parts for recoloring are the lines using convert, first

Re: [gmx-users] Extreme

Hi Pawan, I can add two things. First of all, the score is simply the projection of a point (conformation) onto the eigenvector. Second, extreme scores/projections, be it positive or negative, are usually most unlikely, thus corresponding to highest energy. For the lowest energies, you'd be looki

Re: [gmx-users] g_anaeig

Hi Pawan, No, there are scores and times, no energies. Cheers, Tsjerk On Fri, Dec 10, 2010 at 6:39 AM, pawan raghav wrote: > Dear justin, > Thanks for your useful suggestions but not the right way to post these > things. Anyway Dear I have already read the link mentioned by you and know > very

Re: [gmx-users] .pqr to .pdb

Hey, For this particular conversion you can also usually use 'mv': mv file.pqr file.pdb Btw, many of these file types are human readable. It usually helps quite a bit to look at the files and get acquainted with the file formats. Cheers, Tsjerk On Nov 22, 2010 12:42 PM, "Mark Abraham" wrote:

Re: [gmx-users] RMSD and Resolution

Hi Ahmet, I'm not sure whether it's been checked. It has been found that NMR structures tend to yield larger deviations than crystal structures. If you're going to try, due make sure to compensate for other potential influences, such as the size and sphericity of the proteins. Cheers, Tsjerk 20

Re: [gmx-users] find the relevant structure out

Hi, > Visualization software can sometimes assign the secondary structure > incorrectly. There has been an interesting discussion on this on the Pymol user list years ago (http://www.mail-archive.com/pymol-us...@lists.sourceforge.net/msg01574.html). Secondary structure assignment is foremost hu

Re: [gmx-users] error found in gmx

Hi Ithayaraja, That's not an error in pdb2gmx. It's an error in your input file. One of your residues (H341) is not complete. This is the first thing to check when going for a simulation. You'll have model the missing atoms in before you can proceed. Cheers, Tsjerk On Wed, Nov 24, 2010 at 5:09

Re: [gmx-users] on calculation of the atomic covariance

Hi Vignesh, If your covariances show different ranges, isn't that a difference between your systems, wild-type and mutated? Then again, there's also noise in the covariances (noise in the fluctuations, ergo noise in the noise ;)). The rest might be comparable, making scaling based on the extremes

Re: [gmx-users] Re: genbox generating acetonitrile box with holes

the box doesn't have the right shape and of pbc issues, but it seems to me that the holes are present in this box, i.e. I don't think they are an artifact of trjconv. Thanks for the help Diana On Sat, Nov 6, 2010 at 8:08 PM, Tsjerk Wassenaar wrote: > > Hi Diana, > > Yeah.

Re: [gmx-users] Re: genbox generating acetonitrile box with holes

Lousa" wrote: Hello, No, the hole don't correspond to parts of the protein sticking out on the other side. The protein is in the center of the box and the holes are not due to pbc issues. Diana On Fri, Nov 5, 2010 at 10:10 PM, Tsjerk Wassenaar wrote: > > > Hey, > > D

Re: [gmx-users] Re: genbox generating acetonitrile box with holes

Hey, Do the holes match the parts of the protein sticking out on the other side? Tsjerk On Nov 5, 2010 8:14 PM, "Vitaly Chaban" wrote: On Fri, Nov 5, 2010 at 3:03 PM, vedat durmaz wrote: > hi vitaly, > > the only acetonitrile boxe that i was able to find is the one provided by > christoph fre

Re: [gmx-users] editconf

Hi Mustafa, Check the section on periodic boundary conditions in the manual. Also be sure to use 'show cell' in Pymol to display the triclinic unit cell. That will show you the differences. Besides that, do a direct comparison of the lines encoding the boxes; either the last line of a .gro fil, or

Re: [gmx-users] Re: pressure of the liquid in NPT and NVT

Hi :) I suspect the volume fluctuations are not symmetric around the idealized volume at 1 bar. I think that would mean that the average volume does not correspond to the idealized volume, as you assumed. Cheers, Tsjerk On Wed, Nov 3, 2010 at 12:19 AM, Dallas Warren wrote: > What is the volum

Re: [gmx-users] High Temperature 498 K, NVT or NTP ?

Hi Lin, Not really surprising that water, even SPC, evaporates at 498K and 1 bar, right? (Assuming you performed the simulation at 1 bar). The expansion of the system with NVT seems unlikely, as the volume is fixed. If it really expands, you have pressure coupling turned on, and should double chec

Re: [gmx-users] Reg: NPT Equilibration of water

Hey, There's quite a number of people that should be rereading their statistics... :p First of all, there are instantaneous measurements, averages and fluctuations. If the statistics (mean/fluctuation) are 7 +/- 500, then that doesn't mean that the average of 7 is an estimate that may be off by 5

[gmx-users] Fwd: RMSF => still confused ?

is answers your questions. Cheers, Tsjerk -- Forwarded message -- From: Chih-Ying Lin Date: Thu, Oct 28, 2010 at 8:28 AM Subject: RMSF => still confused ? To: Tsjerk Wassenaar Hi Tsjerk: Well i am still confused about the RMSF. 1. Consider a particle, it has

Re: [gmx-users] Fwd: -pbc nojump

Right :) On Wed, Oct 27, 2010 at 2:27 PM, leila karami wrote: > Dear Tsjerk > > Thus, as you said, Xtc file obtained from trjconv –pbc nojump only concerns > visualization. Thus, can I use old xtc file (with out –pbc nojump) for > analysis such as interfacial waters and water mediated hydrogen bo

Re: [gmx-users] Fwd: -pbc nojump

Hi Leila, 2.xtc should contain all that you want. My point was that you shouldn't need to separate protein/dna and solvent into two trajectories to be combined later. Note that this only concerns visualization. You can do distance and H-bond calculations on the original trajectory, as the relevant

Re: [gmx-users] Fwd: -pbc nojump

Hi Leila, Maybe you're better off trying: 1. trjconv -pbc nojump # choose system for output 2. trjconv -center -pbc mol # choose protein/dna for centering, system for output Centering is done before removing PBC, so you should be safe with two passes. You might also want to play with -ur t

Re: [gmx-users] mirror reflection

editconf -scale -1 -1 -1 On Tue, Oct 26, 2010 at 12:56 PM, Erik Marklund wrote: > #ZHAO LINA# skrev 2010-10-26 11.46: > >  Hi, > > which can help to get the mirror reflection of a known protein? > > Thanks, > > lina > > If it's just one conformation, then I'd just write a script that multiplies >

Re: [gmx-users] g_rmsf => average over # of time frames ???

Hi, Lin, please think your questions over thoroughly in stead of flushing every thought right to the mailing list. It also helps to stick to a certain subject (reply) to make sure everything ends up in the same thread. Maybe it's not a bad idea to read over http://www.catb.org/esr/faqs/smart-quest

Re: [gmx-users] problem with g_density

Hi, > You're not > seeing complete mixing of your two species, but there is some diffusion > between the phases, otherwise both of your particles should drop to exactly > zero density on either side of the box middle, wouldn't they? No, not if there are undulations of the interface. Cheers, Tsj

Re: [gmx-users] g_rmsf -res => average over time for each residue?

Hi Lin, How many residues do you have and how many points do you get? (Only answer for yourself). We're no substitute for your brain, you know... Cheers, Tsjerk On Oct 25, 2010 7:47 AM, "Chih-Ying Lin" wrote: Hi g_rmsf -f abc.xtc -s abc.tpr -res -o abcrmsf.xvg *-[no]res* bool no Calc

Re: [gmx-users] g_dipole ? => The salt molecule => The discrepancy of dipole moment between my calculation and GROMACS

Hey Lin, Did you consider PBC? Also, I wouldn't include the bromide if I were you, as it just adds noise, because it can move around freely. You seem to be interested in the change in dipole moment in the cation only, anyway. Cheers, Tsjerk On Oct 21, 2010 7:02 AM, "Chih-Ying Lin" wrote: HI

Re: [gmx-users] simulation of a protein including calcium ion

Hi, Do mind that calcium binding may involve (quantum) effects that are ill captured by classical force fields. If the binding site plays a central role in your research question, this may be problematic. Cheers, Tsjerk On Oct 16, 2010 2:34 PM, "Justin A. Lemkul" wrote: leila karami wrote: >

Re: [gmx-users] Re: eigenvectors in readable format

Hi Rama, You can convert the .trr file to readable .gro/.g96 with trjconv. Frames with positive times will correspond to eigenvectors; the time indicates the eigenvector index. Make sure not to use any options like pbc/fitting :p Cheers, Tsjerk On Sat, Oct 16, 2010 at 7:00 AM, Ramachandran G w

Re: [gmx-users] Fw: last frame in trr

Hey Floris, Here's a python script to write out the last frame from a .trr file: # #!/usr/bin/env python import sys # Read a 32 bit unsigned int def i(x): return sum([ord(x[j])<<(24-j*8) for j in range(4)]) # Open the file, find the end and go back f = open(sys.argv[1],'rb') f.seek(0,2) eof =

Re: [gmx-users] numerical matrix from xpm file

Hi Anupam, I recently wrote a small python script to convert gromacs .xpm files to numbers. Maybe it'll be of some use to you: Cheers, Tsjerk ### #!/usr/bin/env python import sys def unquote(s): return s[1+s.find('"'):s.rfind('"')] def uncomment(s): return s[2+s.find('/*'):s.rfind('

Re: [gmx-users] Query regarding protonation and deprotonation of some residues

Hi Sonali, First of all, you'll have to find a force field that supports tyrosinate and serinate. These aren't generally considered titratable and are consequently not in the list for interactive selections with pdb2gmx. Once you've found a suitable force field, you'll have to set the protonation

Re: [gmx-users] D-proline

Hi Stefano, Using C N CA CD instead of C CA N C inverts the improper dihedral. And unlike all atom force fields, you can start from an L-proline :) Cheers, Tsjerk On Sep 24, 2010 10:46 AM, "Stefano Pieraccini" wrote: Dear Gromacs users, I would like to use gromacs to simulate a peptide

[gmx-users] Fwd: Residue 'MOL' not found in residue topology database

Probably I wasn't the only one who got this in a personal mail box, but I'll forward it anyway. And, no, I'm not a private tutor, unless I've explicitly indicated otherwise. Tsjerk -- Forwarded message -- From: AJANI HARESH Date: Thu, Sep 16, 2010 at 2:00 PM Subject: Residue 'MO

Re: [gmx-users] pdb2gmx -chainsep vs -merge

Hey Nahren, > > sed -i '/^ATOM.*O2/d' DIMER.pdb > > Am i going wrong here? You should try :) But it looks quite okay to me ;) Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology / Un

Re: [gmx-users] pdb2gmx -chainsep vs -merge

8 1.00 > 0.00 H > ATOM 2847 H2 LYS B 284 -23.156 109.392 62.730 1.00 > 0.00 H > > > Best, > nahren > > --- On *Tue, 9/7/10, Tsjerk Wassenaar * wrote: > > > From: Tsjerk Wassenaar > Subject: Re: [gmx-users] pdb2gmx -chainsep vs -

Re: [gmx-users] pdb2gmx -chainsep vs -merge

Hi, > One work-around for the -chainsep situation you've observed is to remove or > rename the terminal oxygen atoms (OXT) that pdb2gmx is complaining about when > it tries to merge the chains. It should be taking care of that itself, but > handling it yourself might help. pdb2gmx can probably

Re: [gmx-users] Protein stability using MARTINI

Hey, It might also be related to the PBC, with gromacs not writing whole molecules anymore. Maybe a link to a picture would be good, showing protein beads spheres, together with the (triclinic) unit cell. Cheers, Tsjerk On Mon, Sep 6, 2010 at 12:05 PM, XAvier Periole wrote: > > Dear Itamar, >

Re: [gmx-users] Force Field => Residues PHE, TRP, TYR, HIS ?

Hi Chih-Ying Lin, There's no such thing as a pi bond in a classical force field, bonds are merely connections with a certain distance based potential. Gromacs doesn't deal with polarity, the distribution of charges, etc. is part of the force field. Better check the papers relating to the force fi

Re: [gmx-users] (no subject)

Hi Prabha, Why did you choose that force field, and what CA atom type? Tsjerk On Thu, Sep 2, 2010 at 1:30 PM, praba vathy wrote: > Dear Sir, > > We have chosen force field Gromos96 53A6 parameter set. > In that forcefield, how we add this CA atom type. > > > Prabha > -- > gmx-users mailing list

Re: [gmx-users] Please solve this

Pawan, What are you trying to do? Tsjerk On Fri, Aug 27, 2010 at 9:16 AM, pawan raghav wrote: > I am posting this question second time so please tell me, where I was wrong? > > In manual g_analyze reads an ascii file and analyzes data sets, in which > input file was graph.xvg. To generate eigen

Re: [gmx-users] g_sas => protein interface => HALF of ( A+B-AB) ?

Hi, >> the interface is now A + B - AB" >> WHy not HALF of (A+B-AB)  ? > > You are right. A + B - AB gives the Buried Surface Area, which is the amount of surface that gets excluded from the solvent by complexation (and consequently is twice the size of the interface). :) Tsjerk -- Tsjerk A.

Re: [gmx-users] minima

Hi Pawan, These are the maximum and minimum projections on the eigenvectors. They are very unlikely to correspond to energy minima, as minima will be modal. Think of a pendulum, projecting the position on the floor. The extreme projections actually correspond to states of higher (potential) energy

Re: [gmx-users] pbc atom

Hey, > directly. I think you want this (assuming that cols 5,6,7 give you the > dx,dy,dz, which I believe that they do): > > cat pullx.xvg | grep -v '[#|@]' | awk '{print $1,sqrt($5*$5+$6*$6+$7*$7)}' > > my.data Nothing directly harmful of course, but why using three programs for this? awk will d

Re: [gmx-users] essential dynamics

Hi Pawan, This goes beyond a few lines of explanation. Move away from the tools g_covar and g_anaeig slowly ;) and do some more background reading on principal component analysis. I've tried to explain it in my tutorial at http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis1.html (which will prob

Re: [gmx-users] g_rms question

Hi Udi, Square the numbers... It's Root Mean Square Deviation, right? But roots don't add up like that. Cheers, Tsjerk On Aug 12, 2010 12:02 AM, "udi" wrote: Hi gromacs users, I’m simulating a protein that consists of 5 domains. I have calculated the whole protein’s backbone RMSD by enterin

Re: [gmx-users] mean square displacement frequency

Hi Greg, So you want a distribution of MSD, right? > I have trajectories which has been obtained from simulating 20,000 atoms in > NVT simulation for 25ns.  I recorded the trajectory every 3ps which means > that I have 60,000 data points per atom. 25000/3 = 8333 Where do these 60k per atom come

Re: [gmx-users] g_rmsf

Hi Pooja, Try to get a grip on the file types and what they contain. A .cpt file is a checkpoint file containing a single configuration. Not much fluctuation to expect there. This sort of analysis only makes sense for a trajectory, or at least an ensemble of structures. Try the .xtc or the .trr fi

Re: [gmx-users] to visualise protein conformation after every 1ns

Sonali, Why wouldn't it be correct if you did just what David told you to do? And how would you be able to check yourself whether you were correct? We can't hold your hand here for every step you make. Have you already gone through the tutorial material linked on the Gromacs website? If not, pleas

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

Re: [gmx-users] how to strip velocities out of a .gro file

Hi Chris, That was indeed what happened with the first version. The '$q' bails out at the last line without editing. Of course it's also easy to write a python script doing it, combined with find -exec. Cheers, Tsjerk On Jul 5, 2010 11:57 PM, "Chris Neale" wrote: Shay: that's a better idea th

Re: [gmx-users] how to strip velocities out of a .gro file

Hi Chris, What about: find . -name "*.gro" -exec sed -i -e '$q' -e '3,$s/^\(.\{44\}.\).*$/\1/' {} \; Assuming using a format %8.3f for coordinates and a single frame in the .gro file. Otherwise things will get more complicated. Cheers, Tsjerk On Sun, Jul 4, 2010 at 12:45 AM, wrote: > How ab

Re: [gmx-users] B-factor

Hi, >> ATOM 12 CA SER 2 23.444 51.157 35.390 1.00257.41 > > The last column is the occupancy (1.00) and temperature factor numbers > concatenated. You can fix the symptoms by editing the file by hand so that > these numbers occupy the right columns - see the PDB format. > > This illustrates buggy

Re: [gmx-users] Re: Re: Re:Chain Terminus

Hi Stephan, > I did this from the biggening, it's strait forward as you said.  The problems > with the tutorials is they already work, and are missing a shlew of problems > one may incounter when doing more complicated things, etc... It must have been a disappointment while going for your dri

Re: [gmx-users] FWSpider Tutorial

Hi Nayef, >> grompp –f em.mdp –c fws_b4em.gro –p fws.top –o fws_em.tpr >> genion –s fws_em.tpr –o fws_ion.gro –nname CL- –nn 2 –g fws_ion.log >> [select Group 12: SOL] >> pico fws.top [reduce number of SOL by two and add 2 CL- at the end of the >> file] This is all fine. You take the structure be

Re: [gmx-users] g_rama / mult

Hi Shahab, The dihedral definitions should be in the .top file. But you don't give any clue to what you've done or what you're doing, so there's nothing more for us to say to try and help you. > ok. [ g_rama -f *.xtc -s *.tpr -o rama.xvg ]  is my actual command line. So you're actually using wil

Re: [gmx-users] Dimer g_rms

Hi, > Not necessary! > If the dimer separates across the boundaries you have > a problem of fitting the two together while they are separated. > This is only if you use the dimer. The monomers would be fine. That was the case before gromacs 4. But the current versions don't keep molecules whole.

Re: [gmx-users] g_rama / mult

Hi Shahab, > I used  [ g_rama -f *.xtc -s *.tpr -o rama.xvg ] command for analysis of Was that your actual command line? If you used a .tpr, why didn't it have all the dihedrals defined then? How did you get it? Anyway, you should be able to assert that the dihedrals mentioned are in fact your ph

Re: [gmx-users] -dt

Hi, In the mathematical sense, gromacs will only use the frames in the trajectory for which time modulus dt equals 0 (time % dt == 0). Cheers, Tsjerk On Wed, Jun 30, 2010 at 11:47 AM, XAvier Periole wrote: > -dt will define the frequency of analysis that a program will do. > > In the cases you

Re: [gmx-users] automating analysis using shell scripting

Hi Hassan, If you have an index file with all the groups, you can use something like: #!/bin/bash groups=`grep "^\[" index.ndx | wc -l` for ((i=0; i<$groups; i++)) do echo $((i++)) $i | g_dist ... done This will take groups 0 and 1, 2 and 3, etc, passing the selections to g_dist. If you want

Re: [gmx-users] g_rdf has a huge memory leak.

Hi Kun, Can you tell more about what you are doing? What are you analyzing? How large is the system? Which groups do you use for analysis. Etc., etc. Now, you might be right, but you might as well be jumping to conclusions. Cheers, Tsjerk On Tue, Jun 29, 2010 at 4:12 PM, Kun Huang wrote: > Hi

Re: [gmx-users] g_anaeig -proj

Hi Chris, Carla, Sorry I didn't reply before. To understand the projections, first consider the following. Take a single atom with three coordinates (x,y,z). These coordinates are the projections onto a set of (three, Cartesian) axes. If you consider, e.g., the projection of the coordinates onto t

Re: [gmx-users] Problem on forming bonds

Ni hao Kwee Hong, These special links should be defined in the file specbond.dat. That file you can find in the gromacs topology data directory. Have a look at the linkage of iron, e.g.. Also check the manual/wiki/mailinglist on 'specbond.dat' for more information. Hope it helps, Tsjerk On Thu,

Re: [gmx-users] Energy miscalculation

Hi Thanasis, Chris, I read the first while there was only one :p I agree that most people (including me) will not readily go through eight lengthy posts as an introduction to an issue. But the issue raised does seem in need of attention. Not mine though :p Also, the stream-of-consciousness approac

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

tude of programs. > > Thanks for your interest in the tutorial. > > Cheers, > > Tsjerk > > On Fri, Feb 26, 2010 at 1:27 PM, Anna Duncan > wrote: >> >> Hi, >> >> I've been trying to go through the 'Introduction to Molecular Dynamics &

Re: [gmx-users] Re: His protonation

> There are no protons in crystal structures. http://www.rcsb.org/pdb/explore/explore.do?structureId=2VB1 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- g

Re: [gmx-users] convert traj file between diff gromacs versions

Hi Alcides, The .xtc format hasn't changed, so no need for conversion. Cheers, Tsjerk On Tue, Jun 15, 2010 at 4:44 PM, Alcides Nicastro < alcides_nicas...@yahoo.com.ar> wrote: > Users: How I can convert one xtc file created by gromacs_4.0.5 in a xtc > gromacs_3.x.x file? > Best regards, > Alci

Re: [gmx-users] the box lengths

Hi, Which version of gromacs was this again? There have been issues with pdb files being written without box (CRYST1) records, recorded in the archive. Check the output .pdb files, especially after calling genbox (grep "^CRYST1" file.pdb). Also, try the sequence always writing .gro files as output

Re: [gmx-users] No Energy Conservation in NVE simulation of liquid mixtures

Hey :) Errm, you subtract the overall linear momentum. That affects the kinetic energy, decreasing it, doesn't it? Tsjerk On Mon, Jun 14, 2010 at 10:59 AM, Berk Hess wrote: > Hi, > > Why not? > > Berk > >> Date: Mon, 14 Jun 2010 08:19:30 +0200 >> Subject: Re: [gmx-users] No Energy Conservation

Re: [gmx-users] No Energy Conservation in NVE simulation of liquid mixtures

Hi Godwin, I noticed you're removing center of mass motion, which you shouldn't for NVE. Cheers, Tsjerk On Mon, Jun 14, 2010 at 4:09 AM, Godwin Kanu wrote: > > Hi GMX Users, > > I am having difficulties getting gromacs to conserve energy (I experience a > directional drift) when I do an NVE si

Re: [gmx-users] g_rmsf -res

Hi Carla, On Thu, Jun 10, 2010 at 12:03 PM, Carla Jamous wrote: > Hi Everyone, > > please I have a question concerning g_rmsf. > I need to compare the RMSF from my initial structure to the RMSF of my > average structure. Single structures (initial c.q. average) do not have an RMSF. > When I did

Re: Re[4]: [gmx-users] Non-conservation of total energy while using structure file to resume the simulation

Hi Dmitri, Try editconf -f your_run_input_file.tpr -o test.gro to see if the box is stored correctly in the .tpr. Alternatively, you can do gmxdump -s your_run_input_file.tpr, and browse for the box in the output. Then, see if you can reproduce the problem with the last frame of the .trr file ex

Re: [gmx-users] I know about improper dihedrals (i.e. gi_1) , etc. Is there a way to keep phenyl rings absolutely flat.

Hi, Mind not to set force constants too high, as they will introduce high frequency motions, high speeds, and decreased stability. Indeed, absolute flatness need not be required. Phenyl rings naturally come with out of plane motions. Is there reason to believe that the extent of the deformations i

Re: [gmx-users] g_covar

Hi, Fitting is commonly done mass weighted if the reference file contains masses, like a run input file. But covariance analysis is only performed mass weighted if explicitly requested (and masses are available). If mass-weighted analysis is not requested, the masses for the fit will all be set to

Re: [gmx-users] template.c

Hi Chandan, The problem is that with floating points the equality in >  if (fr.time == (4000.000 + (50.0 * inc))) is very unlikely to be satisfied at any time. To compare floating point numbers, you'll have to check whether the value is within a certain interval. But Jussi's approach is far more

Re: [gmx-users] PCA

Hi Pawan, You may want to read up on PCA in some elementary multivariate statistics textbook to get a better grasp on what it does and how it's done. > I have a little concept problem regarding principal component analysis. So > my question is about ED sampling are as follows: > > 1. I have read

Re: [gmx-users] Re: Re: energy decreasing in NVE simulation

Hi Yun-an Yan, In addition to the other things, COMM removal is also a source of energy drift. It is better to center your solute afterwards. Cheers, Tsjerk On Thu, May 20, 2010 at 1:05 PM, Yan Yun-an wrote: > Dear Erik, > > Thank you so much for your prompt reply. I appreciate it. > > Yun-an

Re: [gmx-users] asking help for simulation of protein in 8M urea

Hi Caty, In addition to Luca's comments, also consider what you mean with 8M. Molarity is defined as mole per liter, but the addition of urea may have an effect on the volume, such that adding a volume x urea to a volume y water does not yield a volume x+y. Especially with such high concentrations

Re: [gmx-users] RMSIP

Hi, The answer is given by g_anaeig (-h): When -v, -eig, -v2 and -eig2 are given, a single number for the overlap between the covariance matrices is generated. The formulas are: difference = sqrt(tr((sqrt(M1) - sqrt(M2))^2)) normalized overlap = 1 - difference/sqrt(tr(M1) + tr(M2)) s

Re: [gmx-users] RE: .rtp libraries

Hi Stephen, > I am particularly interested in lipid .rtp libraries hopefully for something > that has all-atom force fields, as I personally believe simulations should be > as real as possible, and also believe non-polar hydrogens still illicite some > force in the overall scheme of the molecul

Re: [gmx-users] Wrapping molecules for octahedron box

Hi, You might want to have a look at the pbc routines in src/gmxlib/pbc.c in the gromacs source code. You'll have to translate it to Fortran yourself though. Maybe Appendix C of http://dissertations.ub.rug.nl/FILES/faculties/science/2006/t.a.wassenaar/03_c3.pdf is also useful. Cheers, Tsjerk On

Re: [gmx-users] Trj conversion: ABCXYZ to AXBYCZ

the problem was not with GROMACS. I have one structure as a X-ray and > the other i created by homology modeling based on this structure. So the > difference arose because my starting structures themselves were different. > > I did try trjconv with an index file , but it did not work out fine.

Re: [gmx-users] Trj conversion: ABCXYZ to AXBYCZ

Hi Nahren, You can do that using trjconv and an index file with the atom indices as they are in the order as they have to be. But is that really your problem? To understand what happened, it would help if you gave the series of commands that led to these results. Cheers, Tsjerk On Mon, May 10,

Re: [gmx-users] PCA component

Hi, Of course you can filter along one eigenvector. My guess is that the option for 3d projection was also selected (-3d)... Cheers, Tsjerk On May 8, 2010 10:08 AM, "David van der Spoel" wrote: On 2010-05-08 08.45, Anirban Ghosh wrote: > > Hi ALL, > > I am trying to do a PCA for my simulatio

Re: [gmx-users] Magic error xtc?

Hey, Otherwise it's also still possible to do old style continuation with a frame from the .trr/.edr file, provided you have those... Cheers, Tsjerk On Thu, Apr 22, 2010 at 7:55 PM, Justin A. Lemkul wrote: > > > nishap.pa...@utoronto.ca wrote: >> >> Hi Justin, >> >>    Well the way I continued

Re: [gmx-users] Finishing time donot showing

Hi Bharath, It means updating the neighbor lists every 10 steps. You might want to check the manual on those options. Also, you're writing full precision coordinates and velocities very often, and you're writing coordinates to the .xtc file as often as to the .trr file, which is redundant anyhow.

Re: [gmx-users] Trehalose RTP file trouble

Hi, The sugars were improved in 45a3. The parameters haven't changed for the later versions. Cheers, Tsjerk On Tue, Apr 13, 2010 at 12:24 AM, Justin A. Lemkul wrote: > > > Michael McGovern wrote: >> >> Hi everyone.  I'm doing some simulations involving the sugar trehalose, >> with the 53a6 for

Re: [gmx-users] Joining two peptide chains

Hi Anirban, If you have the two chains in one file, with identical chain identifiers and no TER statement in case it's a PDB file, then running pdb2gmx will actually create the bond between them (no matter how far away the termini are). Cheers, Tsjerk On Fri, Apr 9, 2010 at 9:37 AM, Anirban Gh

Re: [gmx-users] g_sas => protein and ligand aggregate interface area ?

Hey Lin, > Is it the same step as calculation of protein A and B interface, which David > mentioned above? > But replacing protein B to Ligand aggregate (small micelle of ligand) ? > g_sas -n ligand-micelle-index.ndx ? Of course. > Is my idea correct? Is it necessary to always question

[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] 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

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] 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] 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] 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] 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] 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] 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] 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, 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, 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

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