[gmx-users] Unexpected lincs errors for OH groups in protein

alterations to this setup, e.g. rvdw = 1.0, but still no success. Any help coming to grips with the new non-bonded stuff is much welcome. Kind regards, Erik Marklund, PhD Postdoctoral Research Associate Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks

[gmx-users] Forcefield conversion script for POPC lipids

. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Associate Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

Re: [gmx-users] Forcefield conversion script for POPC lipids

and ordered the same) into some united-atom force fields (43A1-S3, Berger, 53A6L and CKP). I can dig it out and send it to you off list, if you are interested? Cheers Tom On 02/06/2014 03:07 PM, Erik Marklund wrote: Hi users, I've searched the web for tools that convert atom names

Re: [gmx-users] Hydrogen bond with chlorine

for atoms other than [ON] to be taken into account, but will omit the angular criterion entirely. Erik Erik Marklund, PhD Postdoctoral Research Associate Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ On 10 Feb 2014

Re: [gmx-users] Hydrogen bond with chlorine

Strange. Could you send the tpr and a short xtc for me to play with? Erik Marklund, PhD Postdoctoral Research Associate Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ On 10 Feb 2014, at 10:11, Dhawal Shah dha

Re: [gmx-users] Water naming

Hi Kavya, Most (all?) gromacs tools ignore the atom indices in the PDB file anyway, so what you intend to do is straightforward. Kind regards, Erik On 13 Feb 2014, at 06:30, Kavyashree M hmkv...@gmail.com wrote: Dear users, I was analysing the hydrogen bonding interaction of proteins and

Re: [gmx-users] Water naming

. Regards kavya On Thu, Feb 13, 2014 at 3:33 PM, Erik Marklund erik.markl...@chem.ox.ac.ukwrote: Hi Kavya, Most (all?) gromacs tools ignore the atom indices in the PDB file anyway, so what you intend to do is straightforward. Kind regards, Erik On 13 Feb 2014, at 06:30, Kavyashree M

Re: [gmx-users] probability density map

Hi, All you need is in the hbm and hbn output. Best regards, Erik Erik Marklund, PhD Postdoctoral Research Associate Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ On 22 Mar 2014, at 07:08, pratibha kapoorpratib

Re: [gmx-users] probability density map

… from g_hbond I mean. On 23 Mar 2014, at 00:04, Erik Marklund erik.markl...@chem.ox.ac.uk wrote: Hi, All you need is in the hbm and hbn output. Best regards, Erik Erik Marklund, PhD Postdoctoral Research Associate Department of Chemistry Physical Theoretical Chemistry

Re: [gmx-users] pdb2gmx, charmm22 and HEME

On 29 Apr 2014, at 23:32, Justin Lemkul jalem...@vt.edu wrote: On 4/29/14, 5:13 PM, Erik Marklund wrote: Dear users, I am trying to preprocess a cytochrome C structure with pdb2gmx and have run into some problems. The forcefield has parameters for the HEME group, but other

Re: [gmx-users] All-atom MD simulation of a protein at 323K and 283K

on the magnitude of this effect however. Yours, Erik Marklund On 8 May 2014, at 07:48, Pappu Kumar papu...@yahoo.com wrote: I am trying to compare the stability of a protein from two organisms which live in the aforesaid temperature. I am wondering it would make sense to run MD simulation

Re: [gmx-users] dssp installation error

Hi, A: Did you set the DSSP environment variable to the dssp executable? B: Does your dssp version match that which is expected by do_dssp? Yours, Erik On 10 May 2014, at 19:39, elham tazikeh elham.tazi...@gmail.com wrote: dear gromacs users when i run do_dssp program 4.5 and 4.6 i saw

Re: [gmx-users] Hydrogen bonds

Hi, You need to inspect the -hbm and -hbn output. It's the complete existence matrix for all h-bonds encountered in the analysis and a list of corresponding acceptor-H-donor triads. Consequently those files are usually rather big, but that's where the information is. Inspect the bonds you find

Re: [gmx-users] Secondary structure not visible afterconverting from .gro to .pdb

Hi, Gromacs sometimes omits chain labels when writing PDBs, so there might actually be something to fix. I don't remember under exactly what circumstances though, and the reason could be perfectly reasonable. Furthermore, in pymol you can assign the secondary structure to a protein in case

Re: [gmx-users] question

Hi, For one ion this would perhaps be possible, but for many ions this becomes a difficult problem. If it's really important I suggest running a simulations where the ions are allowed to equilibrate, possibly with position restraints on any macromolecules you have. It is highly questionable

Re: [gmx-users] dssp

Hi, dssp.exe? Are you sure that's the name of the file? Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Associate Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ On 5 Jun 2014, at 10:40, Uma Devi renuma

Re: [gmx-users] Hbonds per residue

Hi Natalia, It's a feature that has been requested a number of times, but has not been implemented yet unfortunately. Erik On 12 Jun 2014, at 00:50, Natalia Alveal F. nalv...@bio.puc.cl wrote: Dear gromacs users, I have used g_hbond with -hbn option to generate a .ndx file. There is a

Re: [gmx-users] Hydrogen bond existence map

Hi Nidhi, Only with post processing of named files I'm afraid. Kind regards, Erik On 19 Jun 2014, at 10:48, Nidhi Katyal nidhikatyal1...@gmail.com wrote: Hi all I would like to create hydrogen bond existence map for interaction of each residue with my ligand. I am aware that -hbm and -hbn

Re: [gmx-users] simulation at acid medium

Hi Chris, This very much depends on what system you are studying and what properties you aim to look at. Could you provide more detail please. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Associate Department of Chemistry Physical Theoretical Chemistry Laboratory University

Re: [gmx-users] simulation at acid medium

Chris I do not known if it is another different way to do the medium Erik Marklund erik.markl...@chem.ox.ac.uk ha escrito: Hi Chris, This very much depends on what system you are studying and what properties you aim to look at. Could you provide more detail please. Kind regards

Re: [gmx-users] g_hbond

Hi, I think this may actually be a bug. g_hbond reports zero contacts in cases where I know there are many. Will examine this more thoroughly and file a redmine issue. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Associate Department of Chemistry Physical Theoretical

Re: [gmx-users] g_hbond

No. Strike that. The number of contacts is just reported the wrong way. It says Average number of contacts per timeframe 0.000… in the terminal but hbnum.xvg says different. Not sure if this applies to your problem. Erik Erik Marklund, PhD Postdoctoral Research Associate Department

Re: [gmx-users] treatment of electrostatics in vaccum

Hi, Cut-offs can also be more efficient, depending on the size and charge of your molecule. A periodic box that is large enough to keep periodicity artefacts negligible in vacuo may involve a huge PME grid. Kind regards, Erik On 5 Aug 2014, at 18:17, Justin Lemkul jalem...@vt.edu wrote:

Re: [gmx-users] g_mindist for hydrophobic interactions

Another option is g_hbond -contact. On 8 Sep 2014, at 09:25, Ca C. devi...@hotmail.com wrote: Dear All, I have to verify if some hydrophobic residues, during the simulation, conserve their interactions and make a cross talk for receptor's transactivation. Is g_mindist a good tool for this

Re: [gmx-users] Temperature coupling of two-phase system

Dear Jason, MD thermostats are in some sense unrealistic to begin with, considering how energy is transferred to and from the atoms. Alas, that seems to be unavoidable for microscopic emulation of the macroscopic case. For systems where some degrees of freedom are very loosely coupled to

Re: [gmx-users] umbrella sampling

Hi, Three coordinates and a reference make a three dimensional distance, which is your reaction coordinate. Simple as that. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Associate Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks

Re: [gmx-users] (no subject)

, Erik Erik Marklund, PhD Postdoctoral Research Associate Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ On 24 Sep 2014, at 08:38, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: Hi GMX users what command should I use

Re: [gmx-users] How can I select a group number automatically

Or redirected input: g_msd -s topol.tpr -f traj.xtc EOF 0 EOF Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Associate Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ On 24 Sep 2014, at 05:14, Chandan

Re: [gmx-users] atoms over 100,000

Hi, Atom indices in gro files aren't actually used by the gromacs tools. Hence going over 100,000 is not a problem. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow, JRF Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road

Re: [gmx-users] atoms over 100,000

? thanks again Albert On 10/09/2014 04:45 PM, Erik Marklund wrote: Hi, Atom indices in gro files aren't actually used by the gromacs tools. Hence going over 100,000 is not a problem. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow, JRF Department

Re: [gmx-users] binding Free energy

Dear Urszula, Apologies for the self promotion, but we've made some attempts to do that for a TF-DNA complex: http://www.pnas.org/content/110/49/19796. Note that the rotational degrees of freedom are hard to sample and you may need some further assumptions about mesoscopic scales for the

Re: [gmx-users] Very large Max Force [Energy minimisation] in water with ions

sites no longer conform to the constraint. So, I am guessing whether the extremely large Max Force originates from the force constants in the hydroxide topology? Thank you for your time and assistance! -Kester - 원본 메일 - 보낸사람 : Erik Marklund erik.markl

Re: [gmx-users] Problem - How to center a protein in a CG simulation

, adding restraints can affect the dynamics and you can often use trjconv -nojump followed by trjconv -fit to get your protein sit steadily in the middle of your box, assuming the protein was where you wanted it to be in the first place. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research

Re: [gmx-users] Flat-bottomed position restraint set

. Note that gromacs can be told to keep the neighbour list from the first frame, which would speed up things a bit. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow, Fulford JRF Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road

Re: [gmx-users] g_hbond tool question

Dear Carlos, You get a double contribution from MainChain and SideChain in this way, don't you? Kind regards, Erik On 19 Nov 2014, at 03:00, Carlos Navarro Retamal cnava...@utalca.cl wrote: Dear gromacs users, I’m studying the hydrogen bond interaction between a protein and different

Re: [gmx-users] Structure downloads

. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow, Fulford JRF Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ On 5 Dec 2014, at 18:32, Norman, Lucy lucy.norman...@ucl.ac.ukmailto:lucy.norman

Re: [gmx-users] PMF and RDF

Dear Sujith, Umbrella sampling does exactly that, but adds a biasing potential to sample high-energy regions of the reaction coordinate in separate simulations. The -px output when you do umbrella sampling with mdrun is indeed a sampling of distances along the reaction coordinate, which if you

Re: [gmx-users] PMF and RDF

On 9 Dec 2014, at 11:00, Erik Marklund erik.markl...@chem.ox.ac.uk wrote: Dear Sujith, Umbrella sampling does exactly that, but adds a biasing potential to sample high-energy regions of the reaction coordinate in separate simulations. The -px output when you do umbrella sampling

Re: [gmx-users] Protein distance with respect to box walls

Hi, The location of the box boundary is irrelevant in virtually all cases, unlike the distance to the periodic image. Why do you need to know the distance to the box? Note that regardless of box angles the simulation cell will be represented as a cuboid within mdrun anyway. Erik On 9 Dec

Re: [gmx-users] Steered molecular dynamics

Dear Priya, Scheck out the pull code in the Gromacs manual. Kind regards, Erik Marklund Erik Marklund, PhD Postdoctoral Research Fellow, Fulford JRF Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ On 16 Dec 2014, at 06

Re: [gmx-users] g_hbond not running

Hi Toni, Have you tried with -nthreads 1, which effectively turns off the parallel grid search? Never seen/heard of this problem before. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow, Fulford JRF Department of Chemistry Physical Theoretical Chemistry Laboratory

Re: [gmx-users] g_hbond not running

search? Never seen/heard of this problem before. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow, Fulford JRF Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ On 16 Dec 2014, at 14:11, antoni borysik

Re: [gmx-users] Implicit and explicit solvation

Dear Neha, Wikipedia (or any simulation textbook) can! http://en.wikipedia.org/wiki/Implicit_solvation Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow, Fulford JRF Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road

Re: [gmx-users] coordinates file format

and the program both! So if I get this right you want to change the spacing between xn yn zn and xn+1 yn+1 zn+1. It will take you 5 min to write a python script to do that. And I can’t see why the current output format would be “confusing” for a program. Kind regards, Erik Erik Marklund, PhD

Re: [gmx-users] g_hbond not running

Hi, There’s an issue with g_hbond assuming periodic boundary conditions. I will try to fix this. Kind regards, Erik On 17 Dec 2014, at 12:05, Erik Marklund erik.markl...@chem.ox.ac.uk wrote: Hi Toni, Or better still, you can file a redmine issue and upload the files there: http

Re: [gmx-users] g_rms with two trajectories

Dear Julian, Use the -m flag. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow, Fulford JRF Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ On 9 Feb 2015, at 12:20, Julian julim...@gmail.commailto:julim

Re: [gmx-users] g_rms with two trajectories

, Julian Message: 5 Date: Mon, 9 Feb 2015 12:28:04 + From: Erik Marklund erik.markl...@chem.ox.ac.ukmailto:erik.markl...@chem.ox.ac.uk To: gmx-us...@gromacs.orgmailto:gmx-us...@gromacs.org gmx-us...@gromacs.orgmailto:gmx-us...@gromacs.org Subject: Re: [gmx-users] g_rms with two trajectories

Re: [gmx-users] regarding Contact Existence Map

Each row corresponds to the existence of a hydrogen bond over time for a specific donor-(hydrogen-)acceptor pair (triad). Which pair (triad) is shown on which row is found in the index file produced with the -hbn flag. Erik On 3 Jan 2015, at 02:56, Nizar Masbukhin nizar.fku...@gmail.com

Re: [gmx-users] Calculating h-bonds frequency along the simulation

On 7 Jan 2015, at 16:08, Vered Kunik ve...@ofranlab.org wrote: Dear gromacs users, I am rather new to gromacs and would very much appreciate your help. I have several MD runs of an ATP binding protein (WT versus several mutants). I would like to calculate the frequency of H-bonds between

Re: [gmx-users] DNA-protein complex distorted in vacuum simulation

On 25 Mar 2015, at 11:43, rahul dhakne rahuldhakn...@gmail.commailto:rahuldhakn...@gmail.com wrote: NOTE 1 [file topol.top, line 44]: System has non-zero total charge: -163.00 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic

Re: [gmx-users] end to end normalized vector

Hi, I suggest running g_traj to get the cartesian coordinates of the termini, from which you can easily calculate the projection onto some other vector, autocorrelation, or other projections. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow, Fulford JRF Department

Re: [gmx-users] error while executing do_dssp program

Hi, I just tried do_dssp with a freshly installed gromacs 5.0.4 and dssp 2.0.4. Worked like a charm. Kind regards, Erik On 15 Apr 2015, at 13:35, sam samuel.mo...@vub.ac.be wrote: Hi, With Gromacs version 5.0.4 I get the same error message as Nizar. However, with version 4.6.5

Re: [gmx-users] Checking the existence of a hydrogen bond network

Dear Max, You will need to use the -hbm and -hbn options to generate the existance function for all hydrogen bonds over time. Parsing those files requires a bit of work, but is certainly doable. Kind regards, Erik On 16 Apr 2015, at 12:59, Ebert Maximilian m.eb...@umontreal.ca wrote: Dear

Re: [gmx-users] Protein-DNA simulation LINKS error

: Erik Marklund erik.markl...@chem.ox.ac.uk To: gmx-us...@gromacs.org gmx-us...@gromacs.org Subject: Re: [gmx-users] Protein-DNA simulation LINKS error Message-ID: 61edbf38-6d1f-4089-8ebe-03caaaff6...@chem.ox.ac.uk Content-Type: text/plain; charset=us-ascii The vsite parameters

Re: [gmx-users] Protein-DNA simulation LINKS error

On 24 Jun 2015, at 10:58, Justin Lemkul jalem...@vt.edu wrote: On 6/24/15 5:20 AM, Erik Marklund wrote: Hi Timofey, If I recall correctly, there is no constrainttype defined for the pair MCH3 CT in ffbonded.itp, which is needed for making a 4out virtual site for the methyl group

Re: [gmx-users] calculation of total no of hydrogen bond present in the system

Dear Rahman, I replied to this question yesterday. Please check the archives. Kind regards, Erik On 24 Jun 2015, at 11:13, MOHD HOMAIDUR RAHMAN rahman...@gmail.com wrote: Dear All Gromacs users I am try to calculate total no of hydrogen bond present in a system. For that I am using

Re: [gmx-users] calculation of total no of hydrogen bond present in the system

Dear Rahman, The donors are not the hydrogens, but the oxygens to which they are bonded. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow Fulford JRF, Somerville College Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road

Re: [gmx-users] Protein-DNA simulation LINKS error

The vsite parameters are not complete for DNA/RNA. Perhaps you have faster oscillations in your system than you intended to have. Erik On 23 Jun 2015, at 21:15, Justin Lemkul jalem...@vt.edu wrote: On 6/23/15 7:13 AM, Timofey Tyugashev wrote: I'm trying a few simulations of a

Re: [gmx-users] Volume of active site

of while using the tool... I am just wonder what you had mentioned as clever use of the tool gmx sasa ? Could you please little more explicit in the usage of the tool for volume prediction . Regards, Raja On Jun 1, 2015 8:42 PM, Erik Marklund erik.markl...@chem.ox.ac.uk wrote: Dear Raja

Re: [gmx-users] Volume of active site

Dear Raja, Depending on how you define that volume, you may achieve what you want through clever use of g_sas -tv (gmx sas nowadays). Kind regards, Erik On 1 Jun 2015, at 15:19, Raj D gromacs.fo...@gmail.com wrote: Dear user, I have completed a set of MD simulations of mutants and wild

Re: [gmx-users] DNA virtual site with Charmm force field

Hi Terry, Correct. The forcefields provided with gromacs do not have a complete set of parameters for making vsites for nucleotides. You can work them out from geometry and mass moments however. Kind regards, Erik On 1 Jul 2015, at 10:23, Terry terrence...@gmail.com wrote: Hi all, I'm

Re: [gmx-users] HBlife time

Dear Nilesh, If memory serves me right, it computes the HB autocorrelation function based on all individual HBs, then fits Luzar and Chandler’s kinetic model to that (for now). Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow Fulford JRF, Somerville College Department

Re: [gmx-users] Vector calculation of COM of a molecule

Hi, gmx traj seems like the tool for you. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow Fulford JRF, Somerville College Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ On 3 Jul 2015, at 15:55, Him

Re: [gmx-users] Energy contribution of individual residues

, individual residues. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow Fulford JRF, Somerville College Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ On 3 Jul 2015, at 05:50, Dr. Seema Mishra seema_...@yahoo.com

Re: [gmx-users] Regarding PMF profile in umbrella samplling

Dear Sathish, Do you actually pull it 20 nm from the DNA, or is your plot showing the wrong units? If that is correct, you have very long-reaching effective interactions in your system. How big is your nanoparticle? Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow Fulford

Re: [gmx-users] Regarding PMF profile in umbrella samplling

. I pull the RNA from one end of the strand away from nanoparticle. Nanoparticle contains 200 atoms. The distance between center of mass of nanoparticle and RNA in last window is 20 nm only. Best sathish On Fri, Jul 3, 2015 at 1:25 AM, Erik Marklund erik.markl...@chem.ox.ac.ukmailto:erik.markl

Re: [gmx-users] Regarding PMF profile in umbrella samplling

On 3 Jul 2015, at 11:31, Erik Marklund erik.markl...@chem.ox.ac.uk wrote: Hi, What is your pull geometry, and is your RNA periodic or somehow kept aligned with the x or z axes? … and is your nanoparticle charged? Erik Erik On 3 Jul 2015, at 09:50, Sathish Kumar sathishk

Re: [gmx-users] pairwise h-bonds

Dear Morpheus, Try the -hbn and -hbm options. The latter generates a similar matrix and the former is essentially a dictionary to that matrix. Kind regards, Erik On 21 Aug 2015, at 12:45, bernhard morpheus.sommer2...@gmail.com wrote: Dear Gromacs users, I was wondering about the best

Re: [gmx-users] pH

that the pKa of a group might be shifted somewhat by the environment, so this is not entirely straightforward. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow Fulford JRF, Somerville College Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford

Re: [gmx-users] Surface roughness

Hi, How do you define surface roughness to begin with? Fractal dimension has been used in the past to look at the “crumpledness” of biopolymers. Several runs of gmx sasa can be used for that. Kind regards, Erik On 10 Aug 2015, at 18:09, gozde ergin gozdeeer...@gmail.com wrote: Hi all,

Re: [gmx-users] magnetic field - segmentation fault

Dear Maryam, I usually like to keep it simple and use gdb. That said, clang+lldb is a great compiler+debugger combo. Valgrind may also be helpful. Kind regards, Erik On 24 Jul 2015, at 18:02, Maryam Kowsar maryam.kow...@gmail.com wrote: Dear Erik, Thank you! My sleeves are rolled up

Re: [gmx-users] magnetic field - segmentation fault

Dear Maryam, We can’t possibly say why your modified source core generates a segfault. You need to roll up your sleeves and run it through a debugger. Kind regards, Erik On 23 Jul 2015, at 11:52, Maryam Kowsar maryam.kow...@gmail.com wrote: Dear users, Iam trying to add magnetic field

Re: [gmx-users] Radius of Gyration

Depending on exactly what you want to measure, gmx clustsize might be useful for you. Erik Erik Marklund, PhD Postdoctoral Research Fellow Fulford JRF, Somerville College Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ

Re: [gmx-users] g_hbond : normalization autocorrelation function.

Hi Nilesh, I’m not sure what you mean. Both Ac_finSys and Ac are 1 at t=0. What normalisation do you expect? Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow Fulford JRF, Somerville College Department of Chemistry Physical Theoretical Chemistry Laboratory University

Re: [gmx-users] Problem with GROMACS simulation

Hi, I don’t think attachments are accepted on the mailing list. Kind regards, Erik > On 14 Nov 2015, at 15:32, Shantanu Singh wrote: > > Hello! > > I am a Senior undergraduate at IIT delhi, India. I have trying to simulate > a system of alkanes in water with the

Re: [gmx-users] using charmm36 force field with gromacs

Use constraints = h-bonds You'll get incorrect balance of 1-4 interactions if you constrain all bonds with CHARMM. Interesting. Can you please elaborate Justin? Kind regards, Erik lincs_iter= 1; accuracy of LINCS lincs_order= 4; also

Re: [gmx-users] using charmm36 force field with gromacs

On 3 Nov 2015, at 23:02, Justin Lemkul <jalem...@vt.edu<mailto:jalem...@vt.edu>> wrote: On 11/3/15 5:53 PM, Erik Marklund wrote: Use constraints = h-bonds You'll get incorrect balance of 1-4 interactions if you constrain all bonds with CHARMM. Interesting. Can you plea

Re: [gmx-users] using charmm36 force field with gromacs

On 3 Nov 2015, at 23:51, Justin Lemkul <jalem...@vt.edu<mailto:jalem...@vt.edu>> wrote: On 11/3/15 6:45 PM, Erik Marklund wrote: On 3 Nov 2015, at 23:02, Justin Lemkul <jalem...@vt.edu<mailto:jalem...@vt.edu><mailto:jalem...@vt.edu>> wrote: On 11/3/1

Re: [gmx-users] [gmx-developers] DNA is one moltype or two moltype?

Hi, This is a user question, not a developer question, so I reply too the user list. Normally, they do not have bonded interactions between them. And unless they have identical sequence, they are two molecule types. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow Fulford

Re: [gmx-users] Virtual sites error

Unfortunately, the parameters required for certain virtual sites in nucleic acids are not define in the force field files that are shipped with Gromacs. Erik Marklund, PhD Postdoctoral Research Fellow Fulford JRF, Somerville College Department of Chemistry Physical & Theoretical Chemi

Re: [gmx-users] Virtual sites error

s > Is there any way to remedy this without significant hassle? What things are > exactly lacking? >> -- >> >> Message: 4 >> Date: Thu, 8 Oct 2015 11:15:17 + >> From: Erik Marklund <erik.markl...@chem.ox.ac.uk> >> To: "

Re: [gmx-users] g_hbond

Hi Nilesh, You could try gmx hbond -noda -r 0.25 -num hb.xvg, which should get the contacts in the last column of hb.xvg. Kind regards, Erik On 10 Jul 2015, at 15:58, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: I don't understand why am I not getting hydrogen bond,if I use cufoff 0.25nm?

Re: [gmx-users] g_hbond

But without contact you will need a full donor-hydrogen-acceptor triad for it to be registered, which is not what you want as far as I can tell. Erik On 10 Jul 2015, at 15:17, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: This is index file [ O8-H18-1 ] 8 18 [ O8-H18-2 ] 4032

Re: [gmx-users] g_hbond

Hi Nilesh, Am not sure it accepts hydrogens as donors/acceptors even with -contact. How many donors and acceptors are found? Kind regards, Erik On 10 Jul 2015, at 14:37, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: I calculated number of hydrogen bond with cutoff 0.25 nm (Distance between

Re: [gmx-users] pairwise h-bonds

Hi, Note however that each line is a specific donor-acceptor pair. All the information you need is in that matrix and the corresponding index file. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow Fulford JRF, Somerville College Department of Chemistry Physical Theoretical

Re: [gmx-users] vacuum simulation vs specific solvent simulation

Dear Tasneem, You need to reduce the time step. You are doing NVE simulations, where energy conservation is a bit tricky. You are also not using constraints, which also implies you need to reduce time step. Probably below 0.5 fs. Or you can turn on constraints. We have successfully used LINCS

Re: [gmx-users] RMSD comparison to a different reference structure.

Hi, How about comparing only C-alphas? As long as you have the same number of residues, that should work. You need to make reduced versions of your tpr and trajectory files. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow Fulford JRF, Somerville College Department

Re: [gmx-users] H-bond calculation

Dear RJ, I don’t remember exactly how the groups are treated internally, but I think you might need to include the hydrogen in the donor group. Kind regards, Erik > On 16 Sep 2015, at 07:39, RJ wrote: > > Dear gmx, > > > I would like to calculate the H-bond occupancy

Re: [gmx-users] Accelerating data analysis.

.trr -n index.ndx -o >>> rmsd-protein.xvg >>> >>> and g_rmsd still starts from 0 and it says "Skipping frame..." and it >> seems >>> it will skip all frames (as it would read it) until 0.9 us. >>> Is that what I should expect? >>>

Re: [gmx-users] Accelerating data analysis.

Dear Dawid, The best thing I can think of is to analyse different parts of the trajectory in parallel, using separate g_rms processes, then concatenating the output. Use -b and -e options to limit the analysis to specific intervals. Kind regards, Erik > On 15 Sep 2015, at 13:37, Dawid das

Re: [gmx-users] h-bonds by g_hbond and VMD and ptraj

Hi Ondrej, They use different angles to determine if it is a bond or not. See respective manuals. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow Fulford JRF, Somerville College Department of Chemistry Physical & Theoretical Chemistry Laboratory University of Oxford S

Re: [gmx-users] pressure and temperature coupling is off in vacuum simulations

> On 23 Sep 2015, at 12:35, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 9/23/15 6:37 AM, Erik Marklund wrote: >> >> On 23 Sep 2015, at 08:28, Mark Abraham >> <mark.j.abra...@gmail.com<mailto:mark.j.abra...@gmail.com>> wrote: >&g

Re: [gmx-users] pressure and temperature coupling is off in vacuum simulations

On 23 Sep 2015, at 08:28, Mark Abraham > wrote: Hi, On Wed, Sep 23, 2015 at 8:32 AM tasneem kausar > wrote: Dear Gromacs users I have performed MD simulation for protein in

Re: [gmx-users] distance dependent energy

Dear Van, Plot against the COM distance, which you can get as a function of time too. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow Fulford JRF, Somerville College Department of Chemistry Physical & Theoretical Chemistry Laboratory University of Oxford South Parks

Re: [gmx-users] fix simulation box corners NVE

Hi, I suspect the question is ill-formed. In what way are the corners not fixed when you run NVE/T? All you need to do is turn off pressure coupling. Kind regards, Erik > On 4 Jan 2016, at 21:42, Sereda, Yuriy Vladimirovich > wrote: > > How to fix corners of the NVE or

Re: [gmx-users] fix simulation box corners NVE

The system is still periodic, so particles can indeed cross the boundaries. This is a good thing in the majority of cases, because the alternative, where particles are trapped, gives rise to really severe boundary effects. Kind regards, Erik > On 4 Jan 2016, at 22:15, Sereda, Yuriy

Re: [gmx-users] GMX analysis (g_gyrate) cannot open just the md.trr file

Dear Sajjad, As you can see, you don’t have a file called md.trr. Provide another file with the -f option. Kind regards, Erik > On 29 Nov 2015, at 11:45, Sajjad Kavyani wrote: > > Dear all, > Recently, I simulated a system with gromacs 5.0.4. But now, when I am >

Re: [gmx-users] Why did the aggregate of salt happen when I used Gromacs to perform the simulation in 1.5 M KCl solution?

Dear Shaoqu, This is likely to be a problem with the force field rather than with Gromacs. Unfortunately, it is more difficult to parameterise ions than one might expect, and some forcefields indeed have been reported to yield salt aggregates at unexpected concentrations. Kind regards, Erik

Re: [gmx-users] Calculating Eccentricity

Dear Sanket, Removing periodicity is difficult if SDS molecules transiently leave the micelle and return after having moved one or more unit cells. You might want to try using gmx clustsize to generate snapshots along the trajectory and use trjconv on them to put all molecules in the same unit

Re: [gmx-users] Open-closed transition in a dimeric enzyme, WTM simulations

Dear Tarak, My guess is that your reaction coordinate is ill-chosen and that it fails to capture some significant transitions in orthogonal directions. This can be difficult to know beforehand unfortunately. Kind regards, Erik > On 10 Jun 2016, at 19:09, tarak karmakar

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