Re: [gmx-users] SARS-CoV-2 main protease with ligand from acpype, but converting to vsites?

, and that strategy risk causing silent errors in the simulations. Kind regards, Erik __ Erik Marklund, PhD, Associate Professor of Biochemistry Associate Senior Lecturer in Computational Biochemistry Department of Chemistry – BMC, Uppsala University +46 (0

Re: [gmx-users] Force field for urea and urea-TMAO mixture

Dear Ishrat, I recommend this article and references therein for TMAO + urea parameters: http://dx.doi.org/10.1021/jacs.7b11695. Kind regards, Erik __ Erik Marklund, PhD, Associate Professor of Biochemistry Associate Senior Lecturer in Computational

[gmx-users] Fourier dihedrals

for the Fourier-type dihedrals (C1,C2,C3,C4,C5). How does gromacs actually handle this? With 4 or 5 parameters? Kind regards, Erik __ Erik Marklund, PhD, Associate Professor of Biochemistry Associate Senior Lecturer in Computational Biochemistry Department

Re: [gmx-users] Tpr version check

Hi, Thanks Mark. See https://redmine.gromacs.org/issues/2924. Kind regards, Erik __ Erik Marklund, PhD, Associate Professor of Biochemistry Associate Senior Lecturer in Computational Biochemistry Department of Chemistry – BMC, Uppsala University +46 (0

[gmx-users] Tpr version check

rik __ Erik Marklund, PhD, Associate Professor of Biochemistry Associate Senior Lecturer in Computational Biochemistry Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4562 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> När du har ko

Re: [gmx-users] NVT equilibration in vacuum

Additionally, be aware of the tumbling ice cube effect and set comm-mode to angular to avoid it. Kind regards, Erik __ Erik Marklund, PhD, Associate Professor of Biochemistry Associate Senior Lecturer in Computational Biochemistry Department

Re: [gmx-users] Different models of TMAO

to know long-term anyway if you plan on doing MD in the future. Kind regards, Erik __ Erik Marklund, PhD, Associate Professor of Biochemistry Associate Senior Lecturer in Computational Biochemistry Department of Chemistry – BMC, Uppsala University +46 (0

Re: [gmx-users] Vanishing cofactors

Hm. Issue largely resolved itself. The chain labels disappear with 2019.1, which is why I might have misinterpreted the output pdb. Still an issue, but minor. Redmine issue updated. Kind regards, Erik > On 20 Mar 2019, at 14:45, Erik Marklund wrote: > > Sorry. Wrong link. Here is th

Re: [gmx-users] Vanishing cofactors

Sorry. Wrong link. Here is the correct one http://redmine.gromacs.org/issues/2900 __ Erik Marklund, PhD, Associate Professor of Biochemistry Associate Senior Lecturer in Computational Biochemistry Department of Chemistry – BMC, Uppsala University +46 (0

[gmx-users] Vanishing cofactors

in redline, so I created an issue http://redmine.gromacs.org/projects/gromacs/issues/new?issue%5Btracker_id%5D=1<http://redmine.gromacs.org/projects/gromacs/issues/new?issue[tracker_id]=1> Kind regards, Erik __ Erik Marklund, PhD, Associate Pro

Re: [gmx-users] protein dna pulling

with your setup. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4542 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 27 Aug 2018, at 20:11, a

Re: [gmx-users] Speed up simulations with GROMACS with virtual interaction sites

Hi, We are working on a tool for automatic vsite parameter generation, which works with most force fields including CHARMM. Stay tuned. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala

Re: [gmx-users] Regarding calculation of Hydrogen-Bond

t; University of Texas at Austin > jeremy_fi...@utexas.edu > (443) 243-1187 > > On Tue, Mar 13, 2018 at 7:25 AM, Erik Marklund <erik.markl...@kemi.uu.se> > wrote: > >> The point is that Calpha don’t form hydrogen bonds. >> >> Erik >> __

Re: [gmx-users] Regarding calculation of Hydrogen-Bond

The point is that Calpha don’t form hydrogen bonds. Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On

Re: [gmx-users] Regarding calculation of Hydrogen-Bond

Dear Dilip, The Calpha is not considered a hbond donor. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.ma

Re: [gmx-users] Calculation of potential of mean force between sodium and chloride ion pair in water using replica exchange umbrella sampling in gromacs

Hi, Just out of curiosity, what is the point of REMD for such a simple system? Is the enhanced sampling really worth the overhead? Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala

Re: [gmx-users] Potential energy coming out to be zero but not negative

Dear Shayantani, The output you quote show a negative potential energy. Is that not for the run you refer to? (With regards to “Hello Sir”, may I suggest a more gender inclusive greeting.) Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska

Re: [gmx-users] Why the '5-Helix' randomly displayed in the scount.xvg after running do_dssp?

Dear Cheng, Gromacs is open source. Implement this at your own will. If there is a sufficient interest in such a feature it might even have a place in the official release at some point. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska

Re: [gmx-users] gmx hbond

Hi Negar, Correct, the -dist option doesn’t do what you want it to. I cannot come up with a recipe for how to do this, but I suspect multiple rounds of gmx select and gmx hbond might do the trick. Kind regards, Erik __ Erik Marklund, PhD, Marie

Re: [gmx-users] how to set hetrodimer for MD Simulation

__ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 22 Nov 2017, at 22:15, Rana Rehan Khalid <rrkha...@umich.edu<

Re: [gmx-users] autocorrelation function and residence time

Dear Tsaneem, Negative values don’t signify lack of correlation, but anticorrelation. Also, by omitting negative values you introduce a slight bias in your fit towards longer half-life. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie

Re: [gmx-users] autocorrelation function and residence time

that gmx hbond mentions, where the four quantities in the output are defined. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se

Re: [gmx-users] Regarding calculation of Lennard-Jones potential

Dear Dilip, The LJ parameters are present in the topology file and the force-field files included within. So no need to calculate anything, just to locate them in said files. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA

Re: [gmx-users] regarding hydrogen bond correlation function for Cdd for TIP4P/2005 water model

jconv -nojump. Try that and see if you get more reasonable output. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:er

Re: [gmx-users] Difference in hydrogen bond lifetimes with and without pbc

Dear Apramita, What version are you using? There might have been some PBC-related bugs that were fixed if memory serves me right. Kind regards Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala

Re: [gmx-users] Difference in Hydrogen Bond Lifetimes on truncating trajectory and also on using pbc

correctly, your trajectories with and without pic have different length, so I’m not surprised that the kinetic constants that you get out are different. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry

Re: [gmx-users] gmx analyze Luzar analysis

Dear Valerio, Have a glance at the paper by Luzar and Chandler. Btw: your data doesn’t fit with the kinetic model very well, hence the -666 for the integral. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department

Re: [gmx-users] g_cluster

Dear Nikolai, Group 1. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 24 Aug 2017, at

Re: [gmx-users] g_hbonds calculation on GPU

Dear Rraj, Nope. No-one has made GPU support for gmx hbond (or any other analysis tool as far as I know). Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539

Re: [gmx-users] Regarding indexing to calculate hydrogen bond autocorrelation function

On 26 Jul 2017, at 19:04, Dilip H N > wrote: but i dont have any OH or NH groups in glycine,water mixture... Your water is packed with OH, and glycine has both NH and OH. Kind regards, Erik -- Gromacs Users mailing list * Please

Re: [gmx-users] ForceField for Zn

…here: https://kamerlinlab.com/ On 24 Jul 2017, at 14:14, Erik Marklund <erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>> wrote: Hi, Metal ions are tricky, and Zn is particularly beasty. Check out Kammerlin’s work in this area. Kind r

Re: [gmx-users] ForceField for Zn

Hi, Metal ions are tricky, and Zn is particularly beasty. Check out Kammerlin’s work in this area. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539

Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

angle requirement." Mark On Thu, Jun 1, 2017 at 3:47 PM Erik Marklund <erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>> wrote: Yes. The sets have no overlap. But for some reason putting that in a short description seems difficult :-) On 1 Jun 2017, at 15:31, Mark Ab

Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

* > pairs within 0.35 that do not satisfy the angle criterion? > > Mark > > On Sat, May 27, 2017 at 4:36 PM Erik Marklund <erik.markl...@kemi.uu.se> > wrote: > >> >> >> On 26 May 2017, at 22:12, David van der Spoel <sp...@xray.bmc.uu.se >> &l

Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

ls about this? > > Mark > > On Sat, May 27, 2017 at 4:36 PM Erik Marklund <erik.markl...@kemi.uu.se> > wrote: > >> >> >> On 26 May 2017, at 22:12, David van der Spoel <sp...@xray.bmc.uu.se >> <mailto:sp...@xray.bmc.uu.se>> wrote: >> &g

Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

On 26 May 2017, at 22:12, David van der Spoel <sp...@xray.bmc.uu.se<mailto:sp...@xray.bmc.uu.se>> wrote: On 26/05/17 22:05, Erik Marklund wrote: “Pairs within 0.35 nm”. They also don’t fulfil the angle criterion, which is why they are sometimes fewer than the hbonds. Therefore I

Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

“Pairs within 0.35 nm”. They also don’t fulfil the angle criterion, which is why they are sometimes fewer than the hbonds. Kind regards, Erik > On 26 May 2017, at 19:38, Adarsh V. K. wrote: > > Dear all, > > The 'gmx hbond' command returns a *.xvg file... viz. "

Re: [gmx-users] gmx hbond

Dear Moshen, I doubt the difference in versions will cause any problems in this case. The second column is ill-described. It contains the number of pairs within 0.3 nm that don’t fulfil the angle criterion. Kind regards, Erik __ Erik Marklund, PhD

Re: [gmx-users] Md simulation by Gromacs

Dear Maria, Let’s keep this to the user list. I am first of all not a private tutor. Secondly, the answers you get (below) might be relevant for others. > On 6 Apr 2017, at 16:04, maria khan <mariabiochemi...@gmail.com> wrote: > > Good evening Dear sir Erik Marklund.. > &g

Re: [gmx-users] Fast energy evaluation

Dear Andras, Concatenate all structures into one trajectory and issue gmx mdrun -rerun. That will evaluate the energies for all conformations. You will of course need a tpr file too. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie

Re: [gmx-users] (no subject)

only once in the manual, in the sentence quoted above. What made you think gromacs is united-atom only? Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471

Re: [gmx-users] Hydrogen bond occupancy

Dear Neha, What fraction of the time the ligand hydrogen bonds to whatever it interacts with. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl

Re: [gmx-users] Charmm ff compatibility with Gromacs

Dear Maria, Please see below. Kind regards, Erik > On 5 Apr 2017, at 09:08, maria khan wrote: > > Hello Gromacs users.. > > Charmm 37 ff is for charmm and Namd which is all atom ff using codes,,and > gromacs is united atom so how can its results will be reliable

Re: [gmx-users] vsites with CHARMM force fields

nstrain bond distances, will a 4 fs time-step be stable? No. Kind regards, Erik Marklund -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (

Re: [gmx-users] solvate with hexagonal box

Done! https://redmine.gromacs.org/issues/2148 On 28 Mar 2017, at 10:24, Erik Marklund <erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>> wrote: Hi Mark, Thanks. I will do so once my collaborators confirm that it’s ok that I upload the structure files. Kind r

Re: [gmx-users] Bond energy difference between CHARMM and GROMACS

Dear Yvon, Are you sure you ‘re not constraining, say, H-bonds in one and not the other? Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl

Re: [gmx-users] solvate with hexagonal box

Hi Mark, Thanks. I will do so once my collaborators confirm that it’s ok that I upload the structure files. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471

[gmx-users] solvate with hexagonal box

boxes as arguments for -cs? The whole point in doing it this way was to avoid water molecules being inserted in the membrane. Perhaps overkill, but I am quite surprised at how bad things went with gmx solvate. Kind regards, Erik __ Erik Marklund

Re: [gmx-users] COMMAND IN HBOND

Dear Neha, Gromacs doesn’t offer that much in terms of viewing. This sounds more like a PyMol/VMD/Other question. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18

Re: [gmx-users] Failed to execute command: Try specifying your dssp version with the -ver option.

Dear Atila, Have you confirmed that your dssp is working? Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC, Uppsala University +46 (0)18 471 4539 erik.markl...@kemi.uu.se<mailto:erik.ma

Re: [gmx-users] run parameters

regards, __ Erik Marklund, PhD Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC Uppsala Universtity erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 10 Feb 2017, at 13:06, NIKHIL JOSHI <nikhil.joshi...@gmail.com<mailto:nikhil.joshi.

Re: [gmx-users] Hydrogen bond problem

Dera Tasneem, First thing to check is if you have read the -hbn or -hbm output upside down. This is a common mistake. Seriously. Kind regards, Erik __ Erik Marklund, PhD Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC Uppsala Universtity erik.markl

Re: [gmx-users] ignoring -h atoms

Dear Maria, I’m not saying that it never makes a difference for the topology generation, but it depends on the quality of your input structure. Justin and I both gave examples of why you might want to use it. When you do, -ignh ignores the hydrogens in the input pdb and uses the rtp to model

Re: [gmx-users] Ignoring H-atoms.

> On 7 Feb 2017, at 08:35, Amir Zeb wrote: > > Hello Maria, > > f igoring h-atom command is applied ,,then forcefield will ignore all the > added h-atoms > > What I know about -ignh flag, it does not mean to remove the h-atoms, > alternatively means that during the

Re: [gmx-users] INDEX

Dear Subashini, You forgot to provide trjconv with the index file you created. Try gmx trjconv -n your_index_file.ndx … Kind regards, Erik __ Erik Marklund, PhD Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC Uppsala Universtity erik.markl

Re: [gmx-users] Installing DSSP

Dear Soumadwip, This is not a problem with do_dssp, but with your deep installation. My guess is that you have not completed the installation of dssp. Kind regards, Erik __ Erik Marklund, PhD Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC Uppsala

Re: [gmx-users] posre.itp for dimer protein

Hi, Check your top-file. It will include all relevant posre.itp files if the POSRE preprocessor macro is defined, assuming you created your topology with pdb2gmx. Add -DPOSRE to the definitions in your mdp-file and everything will be taken care of. Kind regards, Erik > On 1 Feb 2017, at

Re: [gmx-users] (no subject)

Dear Mahbodeh, No. You need to restart your simulations. If the beginning of the trajectories can be recovered, then you can make a continuation from the intact part, but that continuation will not be exact. Kind regards, Erik > On 31 Jan 2017, at 06:51, Mahboobeh Eslami

Re: [gmx-users] Dynamics

Dear Rahul, I really don’t think you understand the concept of pbc in molecular simulations. Please read up on the concept in appropriate literature. Kind regards, Erik __ Erik Marklund, PhD Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC Uppsala

Re: [gmx-users] Farideh Khamseh shared "profileNH2.xlsx" with you

That ACF looks very strange. How did you calculate it? Kind regards, Erik __ Erik Marklund, PhD Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC Uppsala Universtity erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 25 Jan 2017, at

Re: [gmx-users] simulation of ternary complex

Dera Maria, Yes that is possible. Be sure to make a good choice of forcefield, so that you have decent parameters for all molecule types in your simulation. Kind regards, Erik __ Erik Marklund, PhD Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC

Re: [gmx-users] How to concatenate tpr files?

Dear Leila, The RMSD is, by default, calculated with respect to the coordinates in the tpr file, which is why you get different results with different tprs. Which one to choose depends on exactly what you want to measure. Kind regards, Erik __ Erik Marklund, PhD

Re: [gmx-users] Problem with the autocorrelation of Rg

s://www.dropbox.com/s/8yqkrr0hym6c899/Rg9-polymer%2BLigand.xlsx?dl=0 > > Let me know if you need any other files or information. > > Regards, > F. > > On Mon, Jan 23, 2017 at 2:07 PM, Erik Marklund <erik.markl...@kemi.uu.se> > wrote: > >> Hi, >> >&g

Re: [gmx-users] Problem with the autocorrelation of Rg

at case. The only > difference of that system with this one was in the terminal groups of > polymer. The first polymer has protonated surface groups (NH3+) but the > second one is neutral (acetylene). > > Best, > F. > > On Mon, Jan 23, 2017 at 1:42 PM, Erik Marklund <erik

Re: [gmx-users] Problem with the autocorrelation of Rg

Dear Farideh, Can you please inform us about how you calculated the ac? Hard to help otherwise. Also, is it exactly zero or just very small numbers? Kind regards, Erik > On 23 Jan 2017, at 10:50, faride badalkhani wrote: > > Dear GROMACS users, > > I am performing

Re: [gmx-users] Simulation in vacuum

are constrained, if any. I can’t remember what LINCS parameters we used, but be prepared to increase the order and/or iter. Consult the manual for details. Kind regards, Erik __ Erik Marklund, PhD Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC Uppsala

Re: [gmx-users] Creating a temperature gradient in water

Dear Ibrahim, Do you use pbc? If so, how does that work with your gradient? Kind regards, Erik > On 10 Jan 2017, at 15:00, ibrahim khalil > wrote: > > Dear gromacs users, > > I have a simulation box containing nothing but water (TIP3P). I want to > create a

Re: [gmx-users] generation of ions additional to solvent molecules

Dear Raag, Where would those extra ions go? If you need a higher number density of ions than the solvent (assuming the box is full of water, plus the protein) you will most likely raise the pressure of the system to bizarre levels. What ion concentration are you aiming for? Is that a

Re: [gmx-users] correction of pmf profile due to entropic decrease

Dear Alex, No. First of all, this is taken care of by gmx wham if I remember correctly. And it does so by looking at the dimensionality of your umbrella sampling setup. Secondly, there are cases where you don’t want that correction at all. The manual mentions one such example. In such cases

Re: [gmx-users] trjconv

Dear Apramita, Unfortunately, the short answer is that you need to think it through. What is being calculated, and how is the trajectory information affected by trjconv? If you for instance apply trjconv -fit rot+trans prior to RDF calculations, you might influence the results. Kind regards,

Re: [gmx-users] Regarding trjconv

Dear Aparamita, trjconv can enable or preclude subsequent analysis of trajectories, depending on what you want to do. For example, by fitting chosen groups to a reference structure. By centering your protein, you effectively remove all lateral diffusion, so it’s not surprising that a very low

Re: [gmx-users] Molecular dynamic simulations of Protein-DNA complex

Dear Khadija, Whether this is a real problem or not is not clear from what you have told us. It could be that what you see in the simulation is real, or it could be that the physical model is inadequate. Or you might even be reporting a visualisation artefact. Can you please elaborate what

Re: [gmx-users] gromacs 2016 vs 5.1.4

Dear Nikhil, Use gmx2016. The 5.1.X versions only get bug fixes and a few backports now as far as I know. Kind regards, Erik > On 11 Oct 2016, at 07:19, Nikhil Maroli wrote: > > Dear all > > We have Workstation with GTX 1070 Cards, Which Gromacs I should install >

Re: [gmx-users] Center-of-Mass motion removal setting for Membrane system with multiple peptides.

Hi, I don’t simulate membranes much, so perhaps someone else’s input might be more valuable. But unless the relative motion of the membrane with respect to the rest is artificial and not just diffusion, I would still recommend COM-motion removal of the whole system. Kind regards, Erik > On

Re: [gmx-users] Center-of-Mass motion removal setting for Membrane system with multiple peptides.

XY direction should be fine; but any diffusion along > Z would not be acceptable. Not sure, how this can be correctly handled. > > There have been studies like this with other peptides, but none of them > have commented on the above aspect. > > On Tue, Sep 27, 2016 at 2:36 PM, Eri

Re: [gmx-users] Center-of-Mass motion removal setting for Membrane system with multiple peptides.

to know how different nstcomm values would >> effect the result especially in the context of complex systems such as >> this. >> >> Just wanted to be sure, before I start the production runs. >> >> >> >> On Tue, Sep 27, 2016 at 1:01 PM, Erik Marklund &

Re: [gmx-users] Center-of-Mass motion removal setting for Membrane system with multiple peptides.

> On 27 Sep 2016, at 06:26, Abhi Acharya wrote: > > Dear Gromacs users, > > I am trying to perform a simulations of different concentration of peptides > in a box with lipid bilayer. In this context, I had a query regarding the > correct Center-of-Mass removal

Re: [gmx-users] Interest of c alpha atoms for least square fitting?

Yes > On 22 Sep 2016, at 06:45, Seera Suryanarayana wrote: > > Dear gromacs users, > > Can I give my interest of c alpha atoms for least square fitting in gmx rms > for RMSD calculation? > > Thanks in advance > Surya > Graduate student > India. > -- > Gromacs Users

Re: [gmx-users] Large (600k particle) semi-isotropic lipid bilayer system transformed into vacuum-separated coordinates by grompp and mdrun

Dear George, Is this not just a visualisation issue because of periodic boundary conditions? Are you sure that the vacuum was not present in the input coordinate file? Kind regards, Erik > On 7 Sep 2016, at 23:58, George Pantelopulos wrote: > > Dear all, > > I have

Re: [gmx-users] forced conformational change by MD

Dear Pappu, You could use position restraints for the two conformations and switch between them by gradually shifting the lambda parameter from zero to one. Kind regards, Erik > On 1 Sep 2016, at 12:47, Pappu Kumar wrote: > > I want to run MD to simulate conformational

Re: [gmx-users] How to run MD simulation remotely

Dear Charles, Is mdrun_mpi available on the node side? Nothing in the script suggests it is, but sometimes part of the environment is inherited from the session where sub was run. Do you get any output files at all? I would expect the stdout and stderr to provide some error message. Kind

Re: [gmx-users] Hbond occupancy

gmx hbond > On 8 Jul 2016, at 12:24, Amali Guruge wrote: > > Dear All, > > Can anyone know how to calculate H bond occupancy with Gromacs? > > Thank you > -- > Gromacs Users mailing list > > * Please search the archive at >

Re: [gmx-users] charge of aminoacids in an special pH

Hi, In addition, if you only wish to alter the protonation states of, say, aspartates, you can use the -asp flag so that you don’t have to go through all possible titratable residues. See vmx pdb2gmx for more residue-specific options. Erik > On 28 Jun 2016, at 09:34, Marlon Sidore

Re: [gmx-users] Number of H bonds formed between ligand and amino acid residues

Hi Amali, gmx hbond identifies typical acceptor and donor groups by default. In fact, analysing non-standard donors/acceptors is a bit underdeveloped. What the program basically does, if memory serves me right, is to identify N and O with H bound to them, or optionally without H in case of

Re: [gmx-users] selection of start or end terminus

Dear Alex, A single amino acid is not a peptide sine it has no peptide bonds. Kind regards, Erik > On 22 Jun 2016, at 20:19, Alexander Alexander > wrote: > > Thanks for your response. > > And then why does "1" go wrong for a single amino acid in zwitterions >

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

Re: [gmx-users] gmx hbond - specify precise atom names involved

Hi, Not as of yet I’m afraid. Erik > On 3 May 2016, at 08:16, Nash, Anthony wrote: > > > Hi all, > > Can gmx hbond accept user specified atoms for the donors (default OH and > NH) and acceptor (default O and N)? I don¹t seem to find any mention of > this in the -help text.

Re: [gmx-users] a suitable forcefield for ions

Hi, Which ions? The monovalent ions commonly used with Amber have a tendency to cluster in unrealistic ways at moderate concentrations if memory serves me right. Kind regards, Erik > On 25 May 2016, at 10:41, mah maz wrote: > > Hi all, > > i need forcefield parameters

Re: [gmx-users] query

To clarify: Your gromacs appears to be compiled for different hardware, most likely on a different machine. I strongly recommend to build on the same machine you will be running on. Kind regards, Erik > On 18 May 2016, at 11:28, Nikhil Maroli wrote: > > This is the

Re: [gmx-users] water model

Dear Mahdiyeh, For water molecules the constraints can be solved analytically with SETTLE, so no need to invoke SHAKE. SETTLE is used by default so just simulate as normal and you will have rigid water. Kind regards, Erik > On 9 May 2016, at 09:04, mahdiyeh poorsargol

Re: [gmx-users] gromacs fftw installation

Dear Neha, with -DGMX_BUILD_OWN_FFTW=ON you tell gromacs to download and build its own fftw. Turn this option off. Kind regards, Erik > On 6 May 2016, at 09:05, Neha Gandhi wrote: > > Dear List, > > I am trying to install gromacs on a machine which is not allowed to

Re: [gmx-users] distance restraint between 2 molecules

Hi, Or use the pull code. Kind regards, Erik > On 27 Apr 2016, at 08:09, Catarina A. Carvalheda dos Santos > wrote: > > Hi Hong, > > You have (at least) two options: > > 1) Edit the specbond.dat file so that the pdb2gmx creates a covalent bond > between the

Re: [gmx-users] Protein is Jumping from water Box

Dear Abid, I wouldn’t call it an issue nor an error. Your protein is still interacting with some periodic copy of the solvent molecules. See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions. Kind regards, Erik On 27 Apr 2016, at 05:23, Abid Channa

Re: [gmx-users] g_hbond: range checking error

Hi, Strange. Do you get the same error with 5.1.2? If so, can you please file a redmine issue (http://redmine.gromacs.org/) and upload the input files that generate this error? Assign the issue to me. Kind regards Erik Marklund On 26 Apr 2016, at 12:01, Shubhangi Gupta <ignahbuhs.

Re: [gmx-users] Flat-bottom potential SEGFAULT

Hi, >From what I have observed so far this appears to be a cluster configuration >issue rather than a gromacs error. Thanks for your input. Kind regards, Erik On 29 Mar 2016, at 15:14, Erik Marklund <erik.markl...@chem.ox.ac.uk<mailto:erik.markl...@chem.ox.ac.uk>> wrote

Re: [gmx-users] Problem in implementing do_dssp

with mpi as u can see this is my >>>> command >>>> : gmx_mpi do_dssp -f md.trr -s md.tpr -o ss.xpm -sc protein.xvg -ver 2 . >>>> After executing command I am able to select group for dssp calculation >>>> but >>>> it ends with fatal erro

Re: [gmx-users] Problem in implementing do_dssp

Dear Rishikesh, And you have tested that your dssp runs properly on your computer? Do you run do_dssp from a script? If so, can you please show the script and maybe someone spots something? Kind regards, Erik > On 6 Apr 2016, at 17:03, Rishikesh Parulekar >

Re: [gmx-users] on -dt of trjcat and trjconv

Dear Brett, MOD refers to the modulus operator. For example, trjconv -f infile.xvg -s infile.tpr -dt 1000 -o outfile.xvg will downsample a trajectory and save only the frames at multiples of 1000 ps (0 ps, 1000 ps, 2000 ps, …), assuming that infile.xvg starts at 0 ps. Kind regards, Erik > On

Re: [gmx-users] -pbc nojump failure

Dear Irem, You may want to run the trajectory through trjconv and translate it, or use e.g. -pbc whole, so that the protein is intact at frame 1. Then you can run trjconv -pbc nojump on the resulting trajectory. This usually requires a bit of trial and error. Kind regards, Erik > On 31 Mar

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