Re: [gmx-users] Error: No such moleculetype Protein

Hi Anirban, Probably you have a reference to a group 'Protein' in your .mdp file. Cheers, Tsjerk On Thu, Feb 10, 2011 at 12:01 PM, Anirban Ghosh wrote: > Hi, > I am trying to convert a CG system containing multiple copies of a protein + > lipid + water + ions to an all-atom system using the sp

Re: [gmx-users] doubts on g_confrms output

Hi, The error message says the number of atoms in the first frame is not what was expected. That indicates the reference structure didn't match, which suggests the pdb file with the fitted structures wasn't used as reference. Solution: give the fitted structures both as reference (-s) and as traje

Re: [gmx-users] doubts on g_confrms output

frms output >>> >>> On 12/02/2011 2:55 AM, Kwee Hong wrote: >>>> >>>> Hi Tsjerk, >>>> >>>> Thanks for the help. I got it. >>>> But do you have any idea how to solve this in vmd? >>> >>> Use trjconv -sep on th

Re: [gmx-users] Output of Gromacs Demo

Hi Majid, Check whether you have writing permissions where you're doing the demo. Cheers, Tsjerl On Feb 13, 2011 6:14 AM, "TJ Mustard" wrote: Majid, Can you post the exact executions you did. ie grompp .. mdrun .. This will help alot. On February 12, 2011 at 7:29 PM majid

Re: Fw: [gmx-users] Output of Gromacs Demo

Hi Majid, Maybe it's a good idea to find somebody around that can help you get started with using linux. You should get acquainted with that before trying to use some specialized software. Cheers, Tsjerk On Feb 13, 2011 6:38 PM, "Justin A. Lemkul" wrote: majid hasan wrote: > > I have attached

Re: [gmx-users] visualizing more than 9999 residues....

Hi Anna, The 'problem' is the PDB file format. It is a fixed-width format that does not allow for residue numbers with more than 4 digits. Both VMD and PyMOL do not have problems reading structures with more residues, but they will choke if you renumber the residues, giving numbers with five or mo

Re: [gmx-users] R: visualizing more than 9999 residues...

anks and best regards > Anna > > -- > > Message: 6 > Date: Mon, 14 Feb 2011 16:43:29 +0100 > From: Tsjerk Wassenaar > Subject: Re: [gmx-users] visualizing more than residues > To: Discussion list for GROMACS users > Message-ID: >         > C

Re: [gmx-users] Whereabouts of NDLP???

Hi Ifat, It has: http://haddock.chem.uu.nl/Squeeze/ Cheers, Tsjerk On Tue, Feb 15, 2011 at 12:46 PM, ifat shub wrote: > Hi, > Was this server ever reestablished? > Is there a link which I can use to calculate the optimal box? > Thanks, > Ifat > > > > > Hi Alan, > > Unfortunately there have bee

Re: [gmx-users] Periodic Boundary Conditions g_mindist -pi

Hi Ifat, I guess this is a jump over the periodic boundaries. You should remove jumps from the trajectory (-pbc nojump) before running g_mindist -pi. Cheers, Tsjerk On Wed, Feb 16, 2011 at 10:19 AM, ifat shub wrote: > Hi, > > > > I am running a simulation on the complex 1aik.pdb in 310K. I wan

Re: [gmx-users] g_rmsf reference structure?

Hi, The reference is used for fitting. The RMSF is calculated with respect to the average (fitted) structure, unless you explicitly specify that deviations from the reference should be used. Cheers, Tsjerk On Wed, Feb 16, 2011 at 7:08 AM, Mark Abraham wrote: > On 16/02/2011 3:44 PM, kulleperum

Re: [gmx-users] Re: Periodic Boundary Conditions g_mindist -pi

   0.187   21.99   16.445 16.445 16.445 >> >> 346.1   0.173   21.984 16.445 16.445 16.445 >> >> 346.2   0.181   22.02   16.445 16.445 16.445 >> >> 346.3   10.82   5.984   16.445 16.445 16.445 >> >> 346.4   10.81   6.002   16.445 16.445 16.445 >> >> 346.5  

Re: [gmx-users] g_covar to calculate correlation of motion

Hi Bipin, Try using a .gro or .pdb file as reference structure (-s). Only .tpr files are version specific. Cheers, Tsjerk On Feb 21, 2011 8:05 AM, "bipin singh" wrote: Dear GMX users, I want to calculate the correlated motion between atoms during the md simulation for that purpose I am using

Re: [gmx-users] Re: gmx-users Digest, Vol 82, Issue 150

Hi Evelyne, > 1) trjconv  -f trajout_dt2000.xtc -s topol.tpr -pbc mol -o trajout_mol.xtc The option -pbc mol IIRC relates to the option for the unit cell representation (-ur). To unbreak molecules using trjconv, you need to have .tpr file and use the option -pbc whole. > 2) trjconv  -f trajout_m

Re: [gmx-users] g_covar to calculate correlation of motion

( THR) has   141 elements > Group    20 ( SOL) has 27882 elements > Group    21 (  CL) has 5 elements > > > On Mon, Feb 21, 2011 at 12:44, Tsjerk Wassenaar wrote: >> >> Hi Bipin, >> >> Try using a .gro or .pdb file as reference

Re: [gmx-users] Interatomic distance matrices

Hi Nathan, g_rmsdist gives full matrices, and in .xpm format for which you'd need to do more scripting than for your original problem :) But you might find genrestr useful. It can generate constraints for all distances in a selection, which means you get a half matrix with the distances. They're n

Re: [gmx-users] negative steps from tpbconv

Hi Jesper, Using a .cpt file will also work with the modified .tpr file. Maybe it is also worth considering using the -maxh option to mdrun, with nsteps in the .mdp file set to -1 (run infinitely). That avoids the hassle with extensions. Cheers, Tsjerk 2011/2/24 Jesper Sørensen : > Hi Xavier, >

Re: [gmx-users] negative steps from tpbconv

> > On Feb 24, 2011, at 1:01 PM, Tsjerk Wassenaar wrote: > >> Hi Jesper, >> >> Using a .cpt file will also work with the modified .tpr file. >> Maybe it is also worth considering using the -maxh option to mdrun, >> with nsteps in the .mdp file set to -1 (r

Re: [gmx-users] trjconv problem

Hi Алексей, We have no use for your PDB files anyway :) In order not to loose the phospho from your tyrosine, you want to start out with trjconv -pbc whole. To obtain what you desire, you probably want to give the following a good read: http://www.gromacs.org/Documentation/Terminology/Periodic_Bou

Re: [gmx-users] Vectors in non-cubic box

Hi Afsaneh, The PBC and the .gro file format are explained in the manual, chapter 3. The last line of the .gro file has the box stored as XX YY ZZ XY XZ YX YZ ZX ZY Cheers, Tsjerk On Mar 5, 2011 6:03 AM, "afsaneh maleki" wrote: Hi, I want to create *.gro file with simulation box size as fo

Re: [gmx-users] Vectors in non-cubic box

Hi Afsaneh, Sorry for missing out on that one. Yes, all tools properly deal with tric. cells. Cheers, Tsjerk On Mar 5, 2011 7:24 AM, "afsaneh maleki" wrote: Thanks Dear Tsjerk g_hbond has the compatibility with non-cubic (or parallelpiped) cells? Best wishes, Afsaneh -- gmx-users mailing li

Re: [gmx-users] Replacing a residue and continuing a simulation run

Hi :) I'd say that if the changes are small you should be able to get away with it. You might want to start off the second part of the run with a smaller time step to relax, though. If the change is from TRP to TRP*, you only need to have a modified topology, without touching the coordinates. You

Re: [gmx-users] g_rms & g-rmsd

Hi Mohsen. These programs calculate quite different things. Please read their manpages. Read them better if you already read them once ;) Cheers, Tsjerk On Mar 19, 2011 12:16 PM, "mohsen ramezanpour" wrote: Dear All I have a trajectory(.xtc) and its corresponding .tpr file: I used the follow

Re: [gmx-users] Simulation of slow folding proteins

Hi Bharat, In addition to the good comments from Chris, mind that to understand the molecular nature of experimental observations like yours requires quite a bit of statistics. With just two cases - wild type and insertion - there is too much uncertainty to claim that possible differences you obse

Re: [gmx-users] question about g_tcaf

Hi Muhammad, It's 'just' a fit/proportionality parameter relating the viscosity for a k-vector to the length of the vector and the viscosity proper (eta0). From the equation you can work out that the unit is nm^-2. Hope it helps, Tsjerk On Thu, Mar 24, 2011 at 10:27 AM, Alif M Latif wrote: >

Re: [gmx-users] g_tcaf reference

Hi Florian, It should be Phys. Rev. E i.s.o. JCP. Cheers, Tsjerk On Thu, Mar 24, 2011 at 12:49 PM, Dommert Florian wrote: > Hello, > > g_tcaf gives a reference for the method to calculate \eta. However I can > not find the Palmer JCP 49 (1994), either in a database nor on the JCP > page. As I

Re: [gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral

Hi Maria, The CHARMM force field is an all-atom one. That means it does not require improper dihedrals to maintain chirality. If you have a D-ASP in your structure file, you can rename it to ASP and just run pdb2gmx. Mind not to regenerate hydrogens in that case, or make sure to modify the hydroge

Re: [gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral

fact have an L-ASP which i want to convert to D. So > the question is simply how to set the proper chirality to a D-amino acid in > CHARMM. > > > Maria > On Fri, Mar 25, 2011 at 11:49 AM, Tsjerk Wassenaar > wrote: >> >> Hi Maria, >> >> The CHARMM force

Re: [gmx-users] RMSD Calculation

Hey :) You probably want to fit on the protein and calculate the RMSD on the ligand. You may need to specify these groups in an index file. Hope it helps, Tsjerk On Mar 27, 2011 3:28 AM, "Justin A. Lemkul" wrote: Nancy wrote: > > Hi All, > > I need to determine the RMSD of a small molecule co

Re: [gmx-users] oligoglycines

Hi Nisha, For building you can also use pymol if you have it installed. On the command line you can issue: pymol -qcd 'editor.build_peptide("GGG");cmd.save("triglycine.pdb","not hydro")' Hope it helps, Tsjerk On Mon, Mar 28, 2011 at 6:05 PM, wrote: > Hello, > >   I want to simulate n-glycine

Re: [gmx-users] Re: Which structure to be used during covariance analysis

Hi Bipin, That won't really matter. The reference is just for fitting. Cheers, Tsjerk On Mar 29, 2011 3:51 PM, "bipin singh" wrote: > > Hello, > I just want to know which structure to be used during covariance analysis with g_cov... -- gmx-users mailing listgmx-users@gromacs.org http://l

Re: [gmx-users] the total charge of system is not an integer

Hi Ahmet, As suggested, it's better to break up your molecule into smaller charge groups. Note that charge groups don't need to have zero charge, nor integer charge. In your case, I'd suggest two COH groups for EDO, which will have zero net charge each, and for TRS I'd take the COH groups as separ

Re: [gmx-users] the total charge of system is not an integer

Hi Ahmet, Why would I get angry? :) Sending a reply to the list will not usually be taken as asking for private tutoring... As Mark pointed out, you need to get familiar with the format of the files. That's the first thing you should do if you get to the point of needing to use non standard topol

Re: [gmx-users] adding a new residue in the ff

Hi, > It would probably be easier, faster, and more accurate to just use most of > the parameters for Cys rather than try to have PRODRG re-create a > (potentially flawed) model of your compound.  The only new parameters are > related to SO3, so the rest should be identical to the Cys residue. Th

Re: [gmx-users] FW: protein split over boundary

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -TAW On Fri, Apr 1, 2011 at 10:53 AM, anahita wrote: > > > > > From: anahita [mailto:ana_j0...@yahoo.com] > Sent: Friday, April 01, 2011 1:13 PM > To: 'gmx-users-requ...@gromacs.org' > Subject: protein split over bound

Re: [gmx-users] how to simulate crystals in Gromacs

Hi, When building crystals, you first have to generate all symmetry mates for a single unit cell. This may involve both rotations and translations, and the information should be present in the structure file. The unit cell can then be used to build a larger crystal with genconf. With Pymol you can

Re: [gmx-users] membedded.gro from g_membed has broken molecules (fix periodicity?)

Hi Peter, No, you don't need to fix molecules prior to MD. Fixing them is also not that hard. Build the .tpr, just using the structure with molecules broken, and then use it as reference structure to trjconv, with -pbc mol. That will fix the molecules based on the distances between bonded atoms, w

Re: [gmx-users] orientational relaxation

Hi Daniel, If you want to fix the com position, specify the molecule as comm-grps. If you really don't want movement of the com, and use pressure coupling, first put the molecule at the origin. Hope it helps, Tsjerk On Apr 12, 2011 7:28 AM, "Mark Abraham" wrote: > yes , position restraints of

[gmx-users] Re: EDO and TRS ligand

Ahmet, Please refrain from sending personal e-mails, unless you're invited to do so. > I am working on the EDO and TRS ligands for 2/3 weeks.But I dont solved it. > Please help me. This is what supervisors are for. I assume you have one. > I am using the wavefunction spartan 8 program to calcul

Re: [gmx-users] micelles and trjconv -pbc cluster

Hi George, Recently I wrote an alternative, non-iterative clustering routine, that does not suffer from convergence failures. If you want, I can send you the modified trjconv source code. Note that it does not bother about the center of mass of the cluster, but just builds a network of neighbours,

Re: [gmx-users] micelles and trjconv -pbc cluster

2c1061,1062 < if (0 == top.mols.nr && (bCluster || bPBCcomMol)) --- > /*if (0 == top.mols.nr && (bCluster || bPBCcomMol))*/ > if (0 == top.mols.nr && bPBCcomMol) 1197c1327,1328 < --- > taw_pbc_cluster(ifit,&top,

Re: [gmx-users] Adding water to protein to start the simulation process

Hey :) I see that I never stated to run the production run... But at that point in the tutorial there have been several equilibration runs already, so it should be trivial to figure it out. Yet I'll add a small paragraph at the end of the production run section. Thanks for the interest in the tuto

Re: [gmx-users] erorr while using grep command

Hi Sajad, The error seems quite explicit. The input file to grep does not exist. Are you in the right directory? Are you mixing op O and 0? Also, please note that this has nothing to do with gromacs. This is just your basic linux and this mailing list is the wrong place for such questions. Furthe

Re: [gmx-users] ask for help on connection to vpn from two computers

Hi Delara, This isn't really the place for these kind of questions, is it? Why not ask the system admins of your network? Cheers, Tsjerk On Apr 18, 2011 9:11 AM, "delara aghaie" wrote: Dear gromacs users I connect via vpn to the university which I run my jobs using gromacs on its HPC system.

Re: [gmx-users] fetal erorr while running" pdb2gmx" command

Hey Sajad, That sounds quite serious, having a fetal error (http://www.thefreedictionary.com/fetal)! But it seems you just have a missing atom, as is indicated in the output. Check the structure before trying to convert it. In particular, read the sections in the PDB file starting with 'REMARK 46

Re: [gmx-users] saving coordinates

Hey :) With domain decomposition the particles are saved with the coordinates corresponding to the position in the rectangular brick with sides equal to the diagonal elements of your unit cell. With particle decomposition the positions are taken for which holds that the first atom of the molecule

Re: [gmx-users] Coarse-grained force field

Hi Ksenie, I don't think you'll be able to find a proper atomistic force field description for lanthanide either. Check http://www.gromacs.org/Documentation/How-tos/Parameterization. But in general, no, you can't mix force fields, and definitely not ones of different resolution. In addition, thin

Re: 答复: [gmx-users] any software which could convert a polypeptidesequence to a pdb file?

Hi, Pymol is sort of semi commercial. You can install it easily on Ubuntu, using apt-get install pymol (free!), you can install from source (also free!). You can obtain an educational build (also free!, though requiring registration). Any will do for the building of sequences, which on linux is as

Re: [gmx-users] trjcat eneconv time continuation

Hi David, You should have as many lines with a 'c' as you have trajectories. Cheers, Tsjerk On Apr 25, 2011 3:51 PM, "David Rodríguez" wrote: 2011/4/25 Mark Abraham > > On 4/25/2011 8:42 PM, David Rodríguez wrote: >>... Sorry that my query wasn't detailed enough. Trjcat yields a Fatal err

Re: [gmx-users] trjcat eneconv time continuation

Hi David, Sorry for reading half... 'echo c c | trjcat ... ' should work. Cheers, Tsjerk On Apr 25, 2011 6:02 PM, "David Rodríguez" wrote: 2011/4/25 Tsjerk Wassenaar > > Hi David, > > You should have as many lines with ... Sure Tsjerk! Now options 2 an

Re: [gmx-users] g_rmsf

Hi Efrat, 2011/5/3 Efrat Noy : > Hi, > > I have 2 questions regarding root mean square fluctuation calculations: > > 1. what exactly is the difference between the values in the rmsf.xvg file > and the values in the rmsdev.xvg file (obtained with the -od option)? Are > the rmsf.xvg values are stand

Re: [gmx-users] trjconv center on protein

Hey :) Option -center shifts the system, which will show up as a component in the displacement. Cheers, Tsjerk On May 6, 2011 5:39 PM, "Justin A. Lemkul" wrote: Tomek Wlodarski wrote: > > Dear Justin, > > Thanks, sure I will give more details. > > This comman... Are all the measurements being

Re: [gmx-users] g_sas query

Hey Anirban, I would consider the ions part of the solvent. But the procedure is right. Cheers, Tsjerk On May 7, 2011 7:35 AM, "Anirban Ghosh" wrote: Hi ALL, I want to calculate the SASA of a protein embedded in a bilayer along with water and ions. So while using g_sas I understand that I ne

Re: [gmx-users] How to recenter solvent around solute

Hi, Justin is very right to point at the workflow. In your case, the points 5 and 6 apply: centering, and putting things in some box. Maybe that doesn't work in one pass and you'll have to use trjconv twice. >> This does not work. Neither is the solute always surrounded by solvent for >> every fr

Re: [gmx-users] problem in multichain protein solvation

Hi, > I tried to solvate an assembly of amyliod peptides (16 peptide), using > editconf and genbox respectively as follow, > editconf -f rotated.gro  -box  76 6 6 -center 0 0 0  -o rotated-box > > Nothing here does any rotation. Well, it seems something that was rotated goes in... that seems fine

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

Hi Nilesh, You don't state the size of your system and the length of your simulations, which are highly relevant in relation to your observations. In any case, you should consider that your simulation is but a single sample, drawn from a distribution of possible paths, and it is probably quite rea

Re: [gmx-users] R: gmx-users Digest, Vol 85, Issue 101

Hi Anna, You can also renumber the xvg file: awk 'BEGIN{N=1}/^[^@#]/{print N++, $2}' file.xvg > renum.xvg Hope it helps, Tsjerk On May 13, 2011 3:51 PM, "Anna Marabotti" wrote: Dear Mark, thank you also for your suggestion, indeed using the nvt.gro file with the sequential numbering I was a

[gmx-users] Fwd: Question => g_anaeig -first -last

es of freedom you remove by fitting the trajectory. Due to limited numerical precision, these may turn out slightly negative. Cheers, Tsjerk -- Forwarded message -- From: Chih-Ying Lin Date: Mon, May 16, 2011 at 4:33 AM Subject: Question => g_anaeig -first -last To: Tsjerk W

Re: [gmx-users] "Command Not Found"

Hi Natalie, You're in the wrong place, and probably trying the wrong thing. The FDAtools are not part of Gromacs and if you encounter issues with them you should raise it with the authors. They may have a user list too. Aside from that, the FDAtools seem to be an R package. That means that they w

Re: [gmx-users] mirroring a trajectorie

#!/usr/bin/env python # Python compliant e-mail # Save it as xtcrev.py # Hi Thomas, # Here's a piece of python code that reverses a trajectory. ### xtcrev.py: ### #!/usr/bin/env python # Reverse an XTC trajectory # # (c)2011 Tsjerk A. Wassenaar # University of Groningen # from struct impor

Re: [gmx-users] average trajectory

Hey, If you can sum them, the only thing needed afterwards is updating the color labels. Like per awk (dividing by two): awk -F\" '/#/{$4=$4/2}1' file.xpm Cheers, Tsjerk On Thu, May 19, 2011 at 2:43 PM, Erik Marklund wrote: > Justin A. Lemkul skrev 2011-05-19 14.30: >> >> >> Yulian Gavrilov

Re: [gmx-users] Domain Motion => How do get the rotational axis from eigenvectors ?

Hi Lin, You don't get such axes directly from covariance analysis. If you want to know which rotations are associated with a certain eigenvector, you have to run a routine like dyndom (http://fizz.cmp.uea.ac.uk/dyndom/) on the extreme projections of your trajectory onto an eigenvector. Cheers, T

Re: [gmx-users] Minimum periodic distance

Hi Kavya, > "shortest periodic distance is 1.39714 (nm) at time 21824 (ps), > between atoms 2062 and 3688" > where 2062 is a protein atom and 21824 is a water molecule. 21824 is the time in ps at which the two atoms indicated, 2062 and 3688, are at the short distance given. You can dump the frame

Re: [gmx-users] is it possible to convert NAMD psf file to gromacas format?

Hey, >> If a rename atom A into B, it will mix the old atom B which already there >> before A renamed into B. However, if the old atom B also need to be renamed >> into C. Here is the problem , command cannot recognize this atom B is the >> new generated or the old atom B. Of course, those atom B

Re: [gmx-users] GTG to GAG with amber FF99SB force field

Hi Lishan, Your mail would be a bit more readable with more structure... Anyway, it says in the manual you can't do perturbation on the multiplicity. That makes sense, because interpolation from 1 to 3 goes through a whole series of rational numbers, but you can't have non-integer periods... If y

Re: [gmx-users] Minimum periodic distance

on cell for simulation. I have run >> the simulation for 100ns, did you man I have to restart the >> simulation again? >> >> Thanking you >> Kavya >> >> On Sun, May 29, 2011 at 5:40 PM, Tsjerk Wassenaar >> wrote: >>> >>> Hi Kavya, >>

Re: [gmx-users] flexibility

Hi, The usual (statistical) way to compare fluctuations (variances) is by taking the ratio (i.e. of the MSFs, not the RMSFs). Maragliano e.a. (BiophysJ 2004) wrote on such comparison of fluctuations, using a variance ratio test. In your case, you'd have to combine it with a structure alignment to

Re: [gmx-users] g_covar

Hi Kavya, Each atom has three coordinates; 3*3740=11220 coordinates, yielding as many eigenvalues and -vectors. Cheers, Tsjerk On Wed, Jun 1, 2011 at 2:44 PM, Kavyashree M wrote: > Dear users, > > I was using g_covar (gmx 4.5.3) to find the eigenvalue and > eigenvectors. When I used f

Re: [gmx-users] Solvating dodecahedron

Hi Justin, > Note that the pseudo-sphere representation is for visualization > purposes only; the triclinic cell should be the input for any simulation. This not true. It doesn't matter which representation you use as input. Molecules may be broken over PBC, but the topological information is tak

Re: [gmx-users] Essential dynamics - concepts

Hi Kavya, On Sat, Jun 4, 2011 at 8:18 AM, Kavyashree M wrote: > Dear Gromacs users, > >  I am new to essential dynamics, I have gone through > some fundamentals in PCS, the mailing list related to ED > and few publications by - > Amadei (Proteins, 17, 412-425, 1993), > a. Amadei (journal of biomo

Re: [gmx-users] Essential dynamics - concepts

Hi Kavya, > Its g_covar contributed by Dr. Rossen apostolov if I am right.  Here it > states that those which are having correlation coefficient better than 0.5 > will be reported, so covariance gives those which have correlation > coefficient > less than 0.5? I don't know the modified version. B

Re: [gmx-users] Essential dynamics - concepts

Hi Kavya, > Thanks sir. I will go through them. However I have referred - > "A Tutorial on Principle component Analysis" by  Lindsay I Smith. > Which gave a good understanding about the concepts. Still I > have some doubts regarding eigen values, as you have told > I will think over them again. I

Re: [gmx-users] ED-analysis

Hi Kavya, > 1.  Can the .xtc file from MD be used directly for analysis > without applying -pbc nojump or mol option? [I had > asked the same question before but was not clear > with the answer. It is absolutely necessary that the molecules be whole, and in the case of multimers, c

Re: [gmx-users] ED-analysis

Hi Kavya, >> It is absolutely necessary that the molecules be whole, and in the >> case of multimers, correctly assembled. > > But if there is only one polymer (protein) with water in the system > then also is it necessary to use nojump or mol in trjconv?because > in one of the mails - > > http://

Re: [gmx-users] standard deviation about rmsd and rmsf values

Hey, The rmsf and rmsd are themselves sort of standard deviations. They are chi distributed, and the confidence intervals are generally not characterized by a standard deviation, which would be a standard deviation of a standard deviation :p Cheers, Tsjerk On Jun 18, 2011 1:21 PM, "Francesco Ot

Re: [gmx-users] cross correlations

Hey, The method from Lange is quite a different thing. It includes non-linear correlations, which is interesting to look at for overall correlation between atoms. If the ultimate goal is to do PCA on it, then it will give you awkward components that will give you a hard time trying to interpret.

Re: [gmx-users] cross correlations

mputing > > C_ij = / sqrt ( x_i ^2 * x_j^2 ) assuming that x_i and x_j is > vectors > > > [1] > http://omrb.pnpi.spb.ru/gitweb/?p=gromacs/gromacs.git;a=shortlog;h=refs/heads/alexxy/g_correl > On Sun, 19 Jun 2011 12:27:53 +0200, Tsjerk Wassenaar wrote: >> >> He

Re: [gmx-users] radius of gyration - compactness

Hey Shahab, What's the contradiction? > [ Furthermore, INT–DBD appears less compact in the complex, as far as the > radius of gyration increases and more molecular surface is exposed to the > solvent (Table 1). ] larger radius of gyration, less compact, more surface > [ Furthermore, according t

Re: [gmx-users] adius of gyration - compactness

Hi Shahab, > I want to know exactly how do radius of gyration of protein from free state > to complex state change . > Rg increased od decreased? That depends on the protein. Some will, e.g., close or fold upon binding, while others may open up, or unfold. > I want to know my data [ In my simula

Re: [gmx-users] radius of gyration - compactness - accessible surface area

Hi Shahab, When comparing two variables, they have to share an axis. Time for instance... Cheers, Tsjerk On Tue, Jun 21, 2011 at 6:36 AM, shahab shariati wrote: > Dear Tsjerk > > thanks for your attention. > > larger radius of gyration, more surface. and smaller radius of > gyration, less sur

Re: [gmx-users] radius of gyration - compactness - accessible surface area

You understand correctly. On Tue, Jun 21, 2011 at 11:35 AM, shahab shariati wrote: > Dear Tsjerk > > very thanks for your useful guidance. > > I now know that I should compare output of g_gyrate (containing Rg vs time) > by area.xvg output file of g_sas (containing area vs time). > > In area.xvg

Re: [gmx-users] Re: Trajectory and ED - (not old question again)

trjconv -fit rot+trans Cheers, Tsjerk On Jun 23, 2011 8:12 AM, "Kavyashree M" wrote: Dear Users, Are there any tool for superposing the trajectory structures form MD. Please correct me if I am asking any illogical question. My previous question was regarding the trjconv output pdb trajectory,

Re: [gmx-users] Re: Trajectory and ED - (not old question again)

anding the concept wrong. > > Thanking you > With regards > M. Kavyashree > > > On Thu, Jun 23, 2011 at 11:56 AM, Kavyashree M wrote: >> >> Thank you Sir! >> >> With regards >> M. Kavyashree >> >> On Thu, Jun 23, 2011 at 11:50 AM, Tsjerk Wa

Re: [gmx-users] Re: Trajectory and ED - (not old question again)

ree that > trajectory > along one eigenvector might not give movements of all the regions that is > observed > in superposed trajectory but whichever region it shows movements is > extremely less > compared to that when viewed from superposed structures in trajectory. > >

Re: [gmx-users] cross correlations

3 columns, but I am not able to get what are these column contains,I mean how to change it to the format in which I can directly plot the data to get DCCM map... For e.g in this form Res1 Res2 Correlation coefficient x yz On Sun, Jun 19, 2011 at 16:16, Tsjerk Wassenaar wrote: >

Re: [gmx-users] ED - Projecting on an eigenvector

Did you make the molecules whole and removed jumps (in case of a multimer) prior to filtering? Cheers, Tsjerk On Jun 24, 2011 8:10 PM, "Kavyashree M" wrote: Dear user, When projection of a trajectory (50ns) on an eigen vector was visualised in pymol, there was broken chains, but when I projec

Re: [gmx-users] cross correlations

of 537X537,instead of179X179.Please suggest me how to get correlation between the C-alpha atoms only. On Fri, Jun 24, 2011 at 22:54, Tsjerk Wassenaar wrote: > > Hi Bipin, > > Read... -- --- *Regards,* Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org ht

Re: [gmx-users] Periodic Images - clarification

Hey, Maybe I missed this, but what type of unit cell did you use? You should use a rhombic dodecahedron. Then, I would argue that it isn't necessarily so problematic as the others put it when you have transient contacts. For the greater part of the simulation the distances in the periodic system

Re: [gmx-users] Periodic Images - clarification

Hi Kavya, > I did use dodecahedron cell.  but how does using a dodecahedron cell > be advantageous than any other cell when minimum image violation > has occurred? This is just my inquisitiveness. In a rectangular cell, such interactions may occur merely by reorientation of the solute. In that ca

Re: [gmx-users] g_msd bug

Hi Slawomir, That's quite a usage of memory! Can you provide more information? Like the number of frames in the trajectory, the command line you used, and the system you ran on? Cheers, Tsjerk 2011/6/27 Sławomir Stachura : > Hi GMX Users, > I am writting this email, beacause I think the g_msd p

Re: [gmx-users] about periodic images violation

Hi Anna, The spikes you see occur because the protein is broken over the periodic boundaries. Not hard to see that a broken molecule will have a minimal minimal distance. The other problem may well occur due to rotation of your molecule. Since you set -bt tric, you just get a rectangular unit cel

Re: [gmx-users] micelle clustering

Hi Sulatha, Did you install gromacs yourself or are you using a system wide installation? A. I installed myself In that case you go into the directory where you have put the gromacs source code and put the modified version of gmx_trjconv.c in the subdirectory src/tools. Then you go into that dir

Re: [gmx-users] pdb2gmx

Hi Simon, pdb2gmx takesthe first structure. Taking an average would ba awkward, as it is unlikely to correspond to a real structure. Cheers, Tsjerk On Jun 30, 2011 6:02 PM, "simon sham" wrote: Hi, I have a question about pdb2gmx. If a pdb file contains a multiple structures, will it average t

Re: [gmx-users] micelle clustering

Hi Sulatha, With my clustering algorithm there can be no infinite loop :) By the way, sorry for the error messages you ran into with compiling 4.0.7. It had escaped me that these changes were made after that version. Cheers, Tsjerk On Fri, Jul 1, 2011 at 8:29 AM, sulatha M. S wrote: > Thanks M

Re: [gmx-users] trjconv keeps asking for tpr

Hi Peter, The .tpr file is needed for the atom and residue names and numbers. Coordinates are read from the trajectory. Cheers, Tsjerk On Fri, Jan 6, 2012 at 9:13 AM, Peter C. Lai wrote: > > On 2012-01-06 02:10:49AM -0600, Peter C. Lai wrote: >> In gromacs 4.5.4, trjconv keeps asking for a .tp

Re: [gmx-users] regarding rmsd and md

Hi Priya, Inspect your trajectory visually and you'll probably see the cause of the high RMSD. Also check the mailing list on the topic. Whether you'll see micelle formation depends on many factors. The time scale, for example. Cheers, Tsjerk On Jan 7, 2012 7:02 AM, "priya thiyagarajan" wrote

Re: [gmx-users] regarding NVT

Hi Priya, Does it help if you set tcoupl = v-rescale Please read the manual, follow a tutorial properly, and think about what you're doing and what you get out. Cheers, Tsjerk On Jan 7, 2012 8:54 AM, "priya thiyagarajan" wrote: hello sir, i followed lysozyme tutorial to do dynamics for my

Re: [gmx-users] how to calculate position displacements ??

Hi Kiwoong Kim, Check out g_traj Cheers, Tsjerk On Tue, Jan 10, 2012 at 8:09 AM, Kiwoong Kim wrote: > Hi. > > I have questions about calculating the position change of each particles. > > Consider there are 4 atoms diffuses into some channel. > > Hence, the aim is to calculate position change

Re: [gmx-users] multi file input for index files

Hey, In cases where you do end up with two index files, like resulting from a script or so, you can also simply combine them by concatenation: cat A.ndx B.ndx > C.ndx Of course you'll have to make sure that the group names are unique ;) Cheers, Tsjerk 2012/1/10 ahmet yıldırım : > Thanks Mark

Re: [gmx-users] Coupling groups - Thermostat

Hey, In addition to the foregoing... The separate coupling is to prevent draining energy from one part to the other. It is pretty unlikely that either protein or tube will drain the other one. Water is always a different story. You can check the setup you choose afterwards, like after a short run,

Re: [gmx-users] Coupling groups - Thermostat

rk Abraham wrote: > On 11/01/2012 4:23 PM, Tsjerk Wassenaar wrote: > > Hey, > > In addition to the foregoing... > The separate coupling is to prevent draining energy from one part to the > other. It is pretty unlikely that either protein or tube will drain the > other one.

  1   2   3   4   5   6   7   8   9   10   >