Re: [gmx-users] x,y and z components of rmsf?

Hi Patrick, You can extract the diagonal from the covariance matrix generated with g_covar (-ascii). That is equal to the RMSF per atom-coordinate. Cheers, Tsjerk On Wed, Mar 28, 2012 at 10:32 PM, patrick wintrode wrote: > Does some one know of a way to get g_rms or g_rmsf to write out the x,

Re: [gmx-users] x,y and z components of rmsf?

Please start a new thread for a new topic. T. On Thu, Mar 29, 2012 at 12:39 AM, Asaf Farhi wrote: > Dear GMCS users > > Hi. Does anyone know if MD at 2K is feasible? > > Thanks, > Best regards, > Asaf > -- > *From:* gmx-users-boun...@gromacs.org [gmx-users-bou

Re: [gmx-users] 200 CPU, 3ns/day for 80,000 atoms !!!!

Hi Albert, You are doing neighboursearching every step! So every step all 200 CPUs need to know the how and what of all the other 199. Imagine the communication overhead. Furthermore, you have 400 atoms per CPU (neglecting the PME dedication). That will also make communication a bottle neck. Which

Re: [gmx-users] Principal Components Analysis in Gromacs

Hi Thomas, > Thanks for all the clarifications about PCA you make on the mailing list! Thank you for the appreciation :) > I have a question about the commandlines you wrote. Why do you use the .tpr > file with the "-s" flag? Is it because you want to compare the > mass-wheighted covariance matr

Re: [gmx-users] Principal Components Analysis in Gromacs

Hi James, > 1- I want to increase amplitude of the motions seen on the selected PCs but > I can't found scalling factor option for that. The analysis gives you the amplitudes that are in your trajectory. Why do you want to amplify them to something probably non-physical? > > 2- I have calculated

Re: [gmx-users] grompp is adding a bond in my model that should not be there

Hey, The problem is likely that pdb2gmx created the bond. It will have given a long bond warning. You can add a ter statement in the pdb file at the break. Cheers, Tsjerk On Mar 26, 2012 5:49 AM, "Mark Abraham" wrote: On 26/03/2012 12:20 PM, Jackson Chief wrote: > > I made a model of a recept

Re: [gmx-users] Box Size in MD

Hi Lara, The cut-offs are pretty much part of the force field. One rule is that the distance between periodic images should be larger than the cutoff. For protein/solute simulations that translates in a minimal distance between the solute and the wall of half the cutoff used. Another rule is based

Re: [gmx-users] pdb2gmx input file error

Hi Acoot, What do you mean with 'not at all'? What is the output of pdb2gmx? Did you check what is in those pdb files? Cheers, Tsjerk On Mar 22, 2012 5:06 AM, "Acoot Brett" wrote: Dear All, I find some pdb files downloaded from RCSB cannot be recognized by pdb2gmx at all. Is any server whic

Re: [gmx-users] Re: g_msd with input by trjconv -pbc nojump:a concern

Hi Ioannis, Coordinates are wrapped during the simulation because of efficiency. There is no track kept of crossings of the boundaries. trjconv can infer such crossings from sudden changes in the coordinates, larger than half a box dimension. That means that for studying diffusion, you have to mak

Re: [gmx-users] Trjconv PDB files define solvent as "ATOM"?

Hi John, Maybe it was laziness, maybe it was the realization that the distinction between atom and hetatm is a bit awkward that caused the developers not to bother with it. It also doesn't relate to your problem, probably. There are non-standard residues and covalently bound ligands that are happi

Re: [gmx-users] Help regarding running DSSP in gmx

Hi Chandran, What did you try, and what error did it come up with? What platform are you using, and which version of DSSP? The latest version of DSSP won't work with Gromacs yet. Cheers, Tsjerk On Mon, Mar 19, 2012 at 2:39 PM, chandran karunakaran wrote: > Dear ALL, > >     We could not r

Re: [gmx-users] on -t nvt.cpt in the Justine Lemkul tutorial

Hi Acoot, It's correct. Checkpoint files (.cpt) were not available in versions <4. Just like the v-rescale thermostat was not available. For many purposes the checkpoint file can be regarded similar to a trajectory though, so replacing nvt.cpt by nvt.trr works properly for version 3.3.3. Cheers,

Re: [gmx-users] on "tcoupl= V-rescale"

you. > > Cheers, > > Acoot > > From: Tsjerk Wassenaar > To: Acoot Brett ; Discussion list for GROMACS users > > Sent: Monday, 19 March 2012 7:17 PM > Subject: Re: [gmx-users] on "tcoupl= V-rescale" > > Hey Acoot, > Hy not try the latest versio

Re: [gmx-users] on "tcoupl= V-rescale"

Why.., not Hy, sorry :p On Mon, Mar 19, 2012 at 10:17 AM, Tsjerk Wassenaar wrote: > Hey Acoot, > > Hy not try the latest version, or at least the version the tutorial was made > for? > > Cheers, > > Tsjerk > > On Mar 19, 2012 10:13 AM, "Acoot Brett"

Re: [gmx-users] on "tcoupl= V-rescale"

Hey Acoot, Hy not try the latest version, or at least the version the tutorial was made for? Cheers, Tsjerk On Mar 19, 2012 10:13 AM, "Acoot Brett" wrote: Dear All, I am using the GROMACS 3.3.3 to practice the lysozyme tutorial of Justin Lemkul http://www.bevanlab.biochem.vt.edu/Pages/Person

Re: Fw: [gmx-users] number of coordinates in coordinate file does not match topology

Hi Acoot, Read the tutorial. It's explained there... Mind that that tutorial was written for an earlier version of Gromacs and some things have changed. The names of ions, for instance. Cheers, Tsjerk On Mar 19, 2012 6:40 AM, "Acoot Brett" wrote: Dear All, The problem really occurs in the io

Re: [gmx-users] grompp warning with SHAKE, but ok with LINCS

Hi D_Roy, The warning message is quite self-explanatory. Do read beyond the word WARNING. As for the other question, the constraint algorithm stands apart from the forcefield, unlike many other options. You can safely use Lincs with G536. Cheers, Tsjerk On Mar 17, 2012 10:31 AM, "D_Roy" wrote:

Re: [gmx-users] Equilibriation nvt.mdp error

Hi Wholly, It would be better to install a more recent version of gromacs. The tutorial should state which version it is written for. Cheers, Tsjerk On Mar 17, 2012 9:01 AM, "Wholly Peach" wrote: Dear All, I am running the on-line tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/ju

Re: [gmx-users] center the system on specific atoms type

eave comm_grps =  System... > But, could you spare some comments how to center it afterwards? I dont know > why but the fullerene like to spend a lot of time in the boundary (i.e. > divided in two, where it is difficult to see). > Best regards: R > > > On 15-03-12, Tsjerk Wassenaar

Re: [gmx-users] center the system on specific atoms type

Hey :) Why would you want to keep it constant? It's asking for trouble. The fluctuations in a small part of the system like a fullerene molecule can be pretty large. If you try to correct the VCM of that bit only, you make it constantly bump into your solvent molecules. Especially if you have nstc

Re: [gmx-users] RMSD sudden jump

Hi Davide, If you've checked the trajectory, and you've assured that there are no atoms wrapping over the periodic boundaries, and you've noticed a sudden change in conformation, then probably that's what it is: a sudden change in conformation. That does agree with the plot. After a rather station

Re: [gmx-users] Ques

Hi Xianwei Wang, According to the information in your mail (the comments from the mdp file), it's just the other way around: phi is the amplitude and a is the phase. Cheers, Tsjerk On Mar 13, 2012 3:11 AM, "Xianwei Wang" wrote: *Dear gmx users: **I would like to apply electric fie

Re: [gmx-users] Re: questions about Principal Component Analysis

Hi Thomas, Whether or not it makes sense to do PCA on the domain only depends on the question you ask. It may well make sense if you aim at characterizing the intra-domain motions. But be aware that you will view those motions within the context of the rest of the protein. It is quite likely that

Re: [gmx-users] Charge delocalization fullerene

Your statement of regret contradicts with the consciousness behind your action, which is actually underlined by that statement... Besides, maybe noone knew a good answer to your question. Try to elaborate on it and add what you could find yourself in the time since your previous post. Cheers, Ts

Re: [gmx-users] g_select problem (Invalid command line argument:)

Hi Leila, You didn't enclose your selection string, you enclosed some words in your selection string. > g_select -f com_ta_full_3.xtc -s com_ta_full.tpr -n index.ndx -oi -select > "Close to Protein" 'resname' 'SOL' and within 0.25 of group 'Protein' g_select -f com_ta_full_3.xtc -s com_ta_full.t

Re: [gmx-users] one ligand in ATB

Hey Ahmet, The conformation is not important. What is important is that the number and order of the atoms in you structure match the topology file. If the order is wrong, you can simply swap lines to make them match. If the number of atoms is different, you have to fix your structure to be able to

Re: [gmx-users] Correcting PBC effects

Hi Ariel, If it works, it's good :) It really only affects the visualization... It doesn't change the system. Cheers, Tsjerk On Tue, Feb 21, 2012 at 10:33 AM, Siew Wen Leong wrote: > Dear all, > > Have anyone tried using CHARMM36 equilibrated POPE bilayer by Dr.Klauda > http://terpconnect.umd.

Re: [gmx-users] problems with martinize.py

e through the pdb. Do you know a fastest way to make it >> work? Thanks >> >> However, my Martini account never worked, don't know why, so I cannot >> post it directly. >> >> 2012/2/20 Tsjerk Wassenaar : >>> Hey Francesca, >>> >>>

Re: [gmx-users] problems with martinize.py

15.730  1.00  0.00 > ATOM     24  O1  GLU     3      11.907  16.693  15.192  1.00  0.00 > ATOM     25  O2  GLU     3      10.020  15.787  16.413  1.00  0.00 > TER > > > can you please explain which the problem is to me? > > thanks > > > > 2012/2/20 Tsjerk Wassena

Re: [gmx-users] problems with martinize.py

5]), S(a[5:10]),   I(a[:5]), " ", > 10*F(a[20:28]),10*F(a[28:36]),10*F(a[36:44])) > ValueError: invalid literal for int() with base 10: '2.' > > > > 2012/2/20 Tsjerk Wassenaar : >> Hi Francesca, >> >> The problem is that the second line of your

Re: [gmx-users] problems with martinize.py

0.0307 >    3GLU     CB   22   1.192   1.426   1.757 -0.3397  0.1329  0.0602 >    3GLU      C   23   1.066   1.533   1.572 -0.3117 -0.4554 -0.5274 >    3GLU     O1   24   1.072   1.606   1.471  0.0488  0.2651  0.0047 >    3GLU     O2   25   0.965   1.542   1.646 -0.1745 -0.2606 -0.3621 >  

Re: [gmx-users] problems with martinize.py

Hi Francesca, Is this the latest version (http://md.chem.rug.nl/cgmartini/index.php/downloads/tools/204-martinize)? If it is, please send me the input file and I'll fix the bug. Note that the previous version that was available online was one used in a workshop, while the script was still in beta.

Re: [gmx-users] reverse transformation

Hi Francesca, Can you post your complete workflow? Cheers, Tsjerk On Feb 16, 2012 7:04 PM, "francesca vitalini" < francesca.vitalin...@gmail.com> wrote: Hi all! I'm having some issues with the reverse transformation, so I decided to start from a toy system, alias the 1UBQ present in the martin

Re: [gmx-users] how to create a proper box size for a membrane?

Hi Ricardo, If you've generated your membrane without taking PBC into account, then I'd say measuring the extent and setting the box manually (editconf -box) is the best option you have. Cheers, Tsjerk On Thu, Feb 16, 2012 at 5:44 PM, Ricardo O. S. Soares wrote: > Hello dear users, > > I'm fam

Re: [gmx-users] how to get the block averaged MSD curve ?

Well, I don't think excel will be a convenient tool for this. Why not try awk for a change? paste msd*.xvg | awk '/^[^@#&;]/{S=0;N=0; for (i=2;i<21; i+=2) {S+=$i;N++}; print S/N}' Otherwise a few lines of python would also do the trick. Cheers, Tsjerk On Thu, Feb 9, 2012 at 1:56 PM, lina wrot

Re: [gmx-users] Problem with simulation of Protein-DNA complex

Hi Rohit, Have you checked the atoms around 3460? It seems there's something wrong with your starting structure. Cheers, Tsjerk On Feb 9, 2012 2:09 PM, wrote: Hi Lina, I am sorry, I think I forgot to mention that I did perform energy minimisation using Steep-Descent for 5000 steps, before NV

Re: [gmx-users] trjconv select group

In bash you can also use 'here-strings': trjconv ... <<< 0 Quite similar to using echo, though. Cheers, Tsjerk On Feb 3, 2012 3:17 PM, "lina" wrote: On Friday 03,February,2012 10:02 PM, francesca vitalini wrote: > > Sure! > My code is > > #!/bin/bas... try touch a file as index.txt and put 0

Re: [gmx-users] chains blowing away during minimization

Hi Priyanka, Are you sure it's not merely due to PBC? Cheers, Tsjerk On Feb 4, 2012 6:29 AM, "Priyanka Shah" wrote: Dear gmx-users, Some residues are missing in my PDB file and during energy minimisation, two of the chains blown away from each other. How to resolve this problem. -- Let spo

Re: [gmx-users] problem with energy minimization

Hi Anushree, You're not using a single cpu, although you probably think you do. Is this em in vacuum or just a small system? Either way, you can enforce running on a single cpu by adding '-nt 1' to the mdrun options. Cheers, Tsjerk On Jan 31, 2012 7:53 AM, "Anushree Tripathi" wrote: I am usin

Re: [gmx-users] root-mean-square distance

om rms distance of the headgroup atoms from > the micelle center of mass. > May I ask you to help me? > > Best Regards > Dina > > > From: Tsjerk Wassenaar > To: dina dusti ; Discussion list for GROMACS users > > Sent: Sunday, Januar

Re: [gmx-users] root-mean-square distance

Hi Dina, g_rms calculates the RMS from pairwise distances after performing a least-squares fit. That's quite different from what you want, and actually is what you get from g_gyrate... Cheers, Tsjerk On Sun, Jan 29, 2012 at 8:09 AM, dina dusti wrote: > Dear Specialists, > > I have a problem ab

Re: [gmx-users] pdb2gmx changes conformation?

Hi Igor, Please look at the contents of the files. Note the order of atoms. Cheers, Tsjerk On Jan 24, 2012 7:31 PM, "192.168.100.1" wrote: ** Hi, I applied *pdb2gmx* to PDB file *A.pdb* with force field *gromos53a5* and water model *spc* and then compared the resulting *A.gro* file with ini

Re: [gmx-users] -fitall option problems

Oh, Justin's right. So I was wrong in my first mail, as well as in my mental picture... So fitting all to all is default... Terribly sorry :$ Tsjerk On Jan 24, 2012 12:05 PM, "Justin A. Lemkul" wrote: Víctor wrote: > > I've having some problems with use of the option '-fitall'. > > The command

Re: [gmx-users] About g_rms and the XPM file format

Hi Victor, By default it does this: > for each frame f in traj1: >   superimpose f with first frame > > for each frame f1 in traj1: >   for each frame f2 in traj2: >     calculateRMSD f1, f2 But there's a hidden option -fitall that gives you the other. Check g_rms -h -hidden > I've also been t

Re: [gmx-users] getting rid of PBC, completely

Hi Chandan, > fr.box[XX][XX], fr.box[YY][YY] and fr.box[ZZ][ZZ] gives me the values > but fr.box[XX][YY], fr.box[XX][ZZ] prints 0. Which seems to me that the > origin of the box is at (0,0,0). Then,  fr.box[XX][XX] is the maximum > X-coordinate, fr.box[YY][YY] is the maximum Y-coordinate,fr.box[ZZ

Re: [gmx-users] getting rid of PBC, completely

Hi Chandan, The box is accessible from the t_trxframe struct. Assuming you have t_trxframe *fr You can access it through fr->box But if you remove jumps first, you're fine anyway. Just don't put things back in the box afterwards. And don't center if your aim is calculating MSDs. Hope it helps

Re: [gmx-users] getting rid of PBC, completely

Hi Chadan, You should stop after your second step, removing jumps. Don't center. And definitely don't put the system in the box, as that exactly undoes removal of jumps. Cheers, Tsjerk On Thu, Jan 19, 2012 at 7:39 AM, Chandan Choudhury wrote: > > Dear gmx-users, > > I have a simulated a system

Re: [gmx-users] questions on distance restraints

Hi Huiwen, Your approach seems good. Information about the distance restraints will be printed in the log file from mdrun, or can be extracted from the .edr file. You can also work your way through the information in the .tpr file given by gmxdump to see if they are indeed properly defined. Cheer

Re: Fw: [gmx-users] trjconv in martini

ut my problem, please? > > Best Regards > Sara > > > > rom: Tsjerk Wassenaar > To: mohammad agha ; Discussion list for GROMACS users > > Sent: Wednesday, January 11, 2012 1:38 PM > > Subject: Re: Fw: [gmx-users] trjconv

Re: Fw: [gmx-users] trjconv in martini

>     o = open(sys.argv[2],"w") > IndexError: list index out of range > > May I ask you to help me, please? > > Best Regards > Sara > > From: Tsjerk Wassenaar > To: mohammad agha ; Discussion list for GROMACS users > >

Re: Fw: [gmx-users] trjconv in martini

)<<(24-j*8) for j in range(4)]) > IndexError: string index out of range > > I know that j is out of range but I don't know that what should I do > exactly? > May I ask you to help me, Please? > > Best Regards > Sara > > From:

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.

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] 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] 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] 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] 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] 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: Fw: [gmx-users] trjconv in martini

Hi Sara, > # Extract the first part of the trajectory > trjconv -s md.tpr -f md.trr -n index.ndx -o 1a.xtc -e 1 That should be -e 19 :) But you can also use -e 20. Probably that is better. I first thought it'd be better to avoid a double frame, but since trjcat is used to combine the

Re: Fw: [gmx-users] trjconv in martini

rs, Tsjerk On Sat, Dec 31, 2011 at 10:29 AM, mohammad agha wrote: > Hi Tsjerk, > > Thanks for your reply, yes, I did this, too! but my problem wasn't solved! > > Best Regards > Sara > > ________ > From: Tsjerk Wassenaar > To: mohammad

Re: Fw: [gmx-users] trjconv in martini

n > May I ask you to help me? > > Best Regards > Sara > > ________ > From: Tsjerk Wassenaar > To: mohammad agha ; Discussion list for GROMACS users > > Sent: Friday, December 30, 2011 8:06 PM > Subject: Re: Fw: [gmx-users] trjconv in martini

Re: Fw: [gmx-users] trjconv in martini

Hi Sara, Make sure the first line of the script is: #!/usr/bin/env python Cheers, Tsjerk On Dec 30, 2011 1:25 PM, "mohammad agha" wrote: - Forwarded Message - From: mohammad agha To: Tsjerk Wassenaar http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the

Re: [gmx-users] trjconv in martini

Hi Sara, Assuming you have saved the script xtcrev.py: # Get a clustered reference frame trjconv -s md.tpr -f md.trr -o cluster.gro -pbc cluster -dump 20 # Extract the first part of the trajectory trjconv -s md.tpr -f md.trr -n index.ndx -o 1a.xtc -e 1 # Reverse it ./xtcrev.py 1a.xtc >

Re: [gmx-users] how to obtain error bar for plotting?

Hey :) Just some side notes. Make sure to distinguish between 'statistical error' or 'standard error of the mean', which is a measure of how 'correct' your estimate of the average is, and the standard deviation or the variance, which is a measure of the natural spread. The latter is not an error!

Re: [gmx-users] -pbc nojump

Hi Sara, Please keep discussions on the list. I'm not your private tutor. Whether you can do your analysis depends on the analysis you want to do. But if your aim is analyzing the formation of the micelle, you're probably better of reversing the trajectory. > 1- trjconv -f md.trr -o md1.xtc -n i

Re: [gmx-users] -pbc nojump

Hi Sara, The problem is that your micelle is formed at the end of the trajectory. To get what you want, you need to mirror the trajectory, follow the procedure you followed, and mirror the resulting trajectory. I posted a piece of python code for mirroring a trajectory a while back: http://lists.g

Re: [gmx-users] dodecahedron box

Hi Zahra, You could first create rectangular boxes for each of the two, using -d 0.5 Then translate one over the first box vector length of the other (along x: editconf -translate). Put the two coordinate sets together and generate a rhombic dodecahedron for the combined set. Cheers, Tsjerk On

Re: [gmx-users] calculation of concentration

Hi Sara, 1 M = 1 mole / dm^3 = 6.022e23 molecules / dm^3 (6.53 nm)^3 = 6.53e-8^3 nm^3 Concentration: 60 / 6.022e23 / 6.53e-8^3 = 0.3578 Alternatively, you can work with the number of solvent molecules 1L H2O = ~55.4 mole 1M = 1 molecule / 55.4 molecules H2O Concentration = 60/(7579./55.4) = 0.43

Re: [gmx-users] discrepancy between ED motions and the MD motion

Hi Vijayan R., Eigenvectors are specific up to a sign. So it's not said the start will end up as the negative extreme. It seems your interpolation just shows what happens in reverse. As a sidenote, do check whether it is a biologically relevant motion, or merely relaxation. Cheers, Tsjerk On De

Re: [gmx-users] a doubt about pbc nojump or mol or whole

Hi Anna, Jumps like that are a consequence of PBC. Nothing wrong. Removing jumps like you did is the proper treatment. Cheers, Tsjerk On Dec 20, 2011 9:27 PM, "Anna Marabotti" wrote: ** Dear gmx-users, I've just finished several simulations of 4 single point mutants of my dimeric protein in r

Re: [gmx-users] calculation of density for martini coarse-grained

Hi Sara, For calculation of the density you need the masses. Neither editconf nor genbox uses real masses. They approximate the mass based on a list of atom names and associated masses, which is quite crude and fails if the atoms are not listed. Martini beads are not listed... To get the density y

Re: [gmx-users] Re: Eigenvalue values from PCA (a general question)

Hi Michiel, You're right there. The OP may have assumed that the numbers were percentages, whereas they are the eigenvalues, which remain to be divided by the total variance to get the cumulative fraction of variance explained. The variance explained by the first ten pc's in this case is approxima

Re: [gmx-users] Re: Eigenvalue values from PCA (a general question)

Hi Michiel, I disagree, and so does semantics. The cumulative variance of a pc is the variance of it plus the sum of the preceding ones. You're talking about the cumulative fraction of the total variance. Cheers, Tajerk On Dec 16, 2011 12:07 AM, "Niesen, Michiel" wrote: >Date: Thu, 15 Dec 201

Re: [gmx-users] Eigenvalue values from PCA (a general question)

.R > > On Thu, Dec 15, 2011 at 3:39 PM, Tsjerk Wassenaar wrote: >> >> Hi Vijayan R., >> >> > What i infer from this is that the cumulative variance experienced by >> > the >> > top 10 PC is  hardly ~ 30 %. >> >> Not experienced...; It&

Re: [gmx-users] Eigenvalue values from PCA (a general question)

Hi Vijayan R., > What i infer from this is that the cumulative variance experienced by  the > top 10 PC is  hardly ~ 30 %. Not experienced...; It's the variance captured by the first ten PC's. > a) does this imply inadequate sampling by MD or a limited conformational > change happening  in the s

Re: [gmx-users] Help with g_rmsf

Hi Carla, > during my simulation, the dimer I'm simulating changed a lot. > So when I calculate with g_rms, the RMSD between my initial and my final > structure (choosing "Protein-H"), I get a value of 10 angstroms. Have you made sure there are no atoms jumping across the boundaries? > g_rmsf -s

Re: [gmx-users] Cosine content

Hey :) This is pretty incorrect... A high cosine content is an indicator of unidirectional motion in phase space. I've elaborated on that on this list some while ago. > Regarding your case, this means that, even if the RMSD is stable starting > from 5ns, the protein still experiences "random" mot

Re: [gmx-users] Re: Force field for polymer molecule - tips (Mark Abraham)

Hi Jernej, You can copy the charmm27.ff directory to your working directory and make changes locally. Cheers, Tsjerk On Dec 14, 2011 2:54 AM, "Jernej Zidar" wrote: Hi Mark. >> How will pdb2gmx "know" it has to parse the monomeres.rtp file? >It can't. You must add to an existing .rtp file. Th

Re: [gmx-users] How to neutralize 0.748e system charge

Hi Sundar, Just add 0.748 Cl- But you might want to go back through your workflow and the topology resulting from it, to see how you ended up with a non-integer charge. It is sort of unphysical. Cheers, Tsjerk On Tue, Dec 13, 2011 at 11:59 AM, Sundargenesan wrote: > Dear GROMACS users, > > >

Re: [gmx-users] No such moleculetype Na

Hi Setare, That tutorial is made for later gromacs versions, as stated at the beginning. The naming of ions has changed since 4.0.*. Cheers, Tsjerk On Dec 10, 2011 1:00 PM, "Setare Jiji" wrote: Hi, I am running Tutorial 1: Lysozyme in Water

Re: [gmx-users] Newbie: How to modify the topology file after adding ions?

Hi Jose, The references to NA+ and CL- have been changed, you can reload the page in your browser if you care to continue. Now I still think your statement was rather rude and showing disrespect to the time I put in the tutorial. Apart from the reference to NA/CL you're also factually incorrect in

Re: [gmx-users] Newbie: How to modify the topology file after adding ions?

Hi Jose, You're not the first one to follow the tutorial, it does state which version to use (4.5, see introduction), and it does state how to fix the topology: editing the file, adding the lines, using the appropriate names. This tutorial is made to be read and to be thought over. Of course time

Re: [gmx-users] box vectors

Hey, On a general note, assuming the frame is read in as a t_trxframe structure called frame, the box is accessible as frame.box and is a matrix instance, which means it's a 3x3 array, containing the triclinic box as a lower triangular matrix. If the code says t_trxframe *frame somewhere, rather t

Re: [gmx-users] g_msd and pbc

Hi Chandan, Pretty simple; you just take the smallest distance between the time points in the periodic system. Cheers, Tsjerk On Wed, Dec 7, 2011 at 6:44 PM, Chandan Choudhury wrote: > > Dear gmx_users, > > I was just wondering how the g_msd (of gmx 4.0.7) code, takes care of the > PBC. e.g. I

Re: [gmx-users] box vectors

#!/usr/bin/env python # Python compliant email -- Just save the content :) """ Hey :) The neatest way is using python to extract them from the XTC file :) """ from struct import unpack import sys import os def i(x): return sum([ord(x[j])<<(24-j*8) for j in range(4)]) def strseek(stream,s

Re: [gmx-users] RMDS calculation

Hi Valerio, Check the help for both tools. That explains it all. Oh, and you're not correct ;) Cheers, Tsjerk On Mon, Dec 5, 2011 at 4:42 PM, wrote: > Dear all, > > I need to calculate the RMSD of a protein during time. So that I've > calculated the trajectory; for the calculation which tool

Re: [gmx-users] Analysis of Protein Complex

Hi Saba, You can use g_mdmat or run g_rmsdist for different time windows. It's also a good idea to have a look at all the analysis tools and think of how they may suit your purpose. Cheers, Tsjerk On Thu, Dec 1, 2011 at 5:43 AM, Saba Ferdous wrote: > Dear Sir, > I am studying a protein complex

Re: [gmx-users] Spherical Position Restrain from the center of the Box

Hi Ricardo, Unfortunately that is not possible. What you can do is rearrange the water in the structure and use two water moleculetypes, one with and one without position restraints. It might be nice to have something like global_position_restraints, added under [ system ], but that needs to be im

Re: [gmx-users] Unit of r in radial distribution function

Hi Bipin, Gromacs uses nm. Cheers, Tsjerk On Wed, Nov 30, 2011 at 3:32 PM, bipin singh wrote: > Hello, > > Please let me know what is the unit of r (nm or A) in the radial > distribution function > output(rdf.xvg) of the program g_rdf in gromacs. As the output shows no units. > > -- >

Re: [gmx-users] Suppress writing step*.pdb files

Thanks guys! I see I'm using an outdated manual... Tsjerk On Wed, Nov 30, 2011 at 1:28 PM, Justin A. Lemkul wrote: > > > Mark Abraham wrote: >> >> On 30/11/2011 9:56 PM, Tsjerk Wassenaar wrote: >>> >>> Hey :) >>> >>> I think I recal

[gmx-users] Suppress writing step*.pdb files

Hey :) I think I recall there was a way to suppress writing step*.pdb files, but I couldn't find it. Anyone know from the top of his/her head? Otherwise I'll go and check the source... Oh, trust me... I know what I'm doing ;) Even though it's insane... :D Groetjes, Tsjerk -- Tsjerk A. Wassenaa

Re: [gmx-users] frames in 2 trajectory files

trjcat Cheers, Tsjerk On Nov 30, 2011 6:11 AM, "Saba Ferdous" wrote: Dear Gromacs group, I was running simulation of protein complex, due to power outage, my simulation got interrupted. I resumed it by the mdrun command provided. it got resumed starting from the frame, it stopped. Now simula

Re: [gmx-users] .top to .itp file conversion

Hi, You can print the moleculetype definition, up to the system tag using sed: sed -n -e '/^\s*\[\s*system\s*\]\s*$/q' -e '/^\s*\[\s*moleculetype\s*\]\s*$/,$p' TOP > ITP First expression: quit at [ system ], allowing spaces before, in between and after Second expression: print everything from [

Re: [gmx-users] to gro or not to gro

pdb file by converting it to 0.417 nm in the gro file. What > is the point in dropping useful "2" by introducing useless "0"? > > On Sun, Nov 27, 2011 at 10:30 AM, Tsjerk Wassenaar > wrote: >> >> My my. Why is it a fault to adhere to ISO units (nm) ove

Re: [gmx-users] to gro or not to gro

My my. Why is it a fault to adhere to ISO units (nm) over non-standard (A)? It's a choice, but a choice is not faulty. The consequences may be undesirable. But shouldn't a user, certainly a computation scientist, understand the file formats, as an experimentalist should know its solvent? And know t

Re: [gmx-users] Pressure stabilization during NPT phase

.rfind(X[:8]):]' > last.xtc Cheers, Tsjerk On Fri, Nov 25, 2011 at 10:01 AM, Tsjerk Wassenaar wrote: > Hey, > > You don't actually need to copy the trajectory. trjconv and other > tools are comfortable operating on an unfinished trajectory. They'll > just bail o

Re: [gmx-users] multiple molecules simulations

Hi Gloria, It think it's pretty obvious that loose pieces will see one another across periodic boundaries diffusing around the place. Whether it's a good model of reality is something for you to verify. A priori, the approach seems fine. Cheers, Tsjerk On Fri, Nov 25, 2011 at 8:46 AM, Gloria Sa

Re: [gmx-users] Pressure stabilization during NPT phase

)  ? >> >> Choose a length of time in advance that you are happy to risk being >> wasted. Run that length of time, make a backup, check whatever you want to >> check, then continue the simulation. As you acquire confidence, you will >> want to increase that time

Re: [gmx-users] Pressure stabilization during NPT phase

Hi James, There have been extensive discussions about this on the list. Check the archives. In short, smaller systems give larger fluctuations, and shorter simulations give larger deviations from the expected average. Cheers, Tsjerk On Nov 25, 2011 7:23 AM, "James Starlight" wrote: Dear Groma

Re: [gmx-users] about relaxation protocol

Hi Albert, You can use the free energy perturbation stuff. Check the manual. Cheers, Tsjerk On Nov 25, 2011 7:43 AM, "Albert" wrote: Dear all: I am a new Gromacs user and I would like to relax my membrane system by linear force constant: NPT with protein and ligand heavy atoms annealing,

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