Re: [gmx-users] a99SB-disp forcefield

Yes. E-mail him directly. J On Wed, Jul 3, 2019 at 8:48 AM Timofey Tyugashev wrote: > Paul as Paul Robustelli, the paper author? > > 02.07.2019 17:00, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет: > > Message: 3 > > Date: Tue, 2 Jul 2019 09:52:04 +0200 > > From: Jo?o Henriques > >

Re: [gmx-users] a99SB-disp forcefield

Ask Paul, they have a Gromacs version of it and he'll most likely be happy to share it with you. J On Mon, Jul 1, 2019 at 8:19 PM Joe Greener wrote: > Dear Gromacs users, > > I am looking to use the a99SB-disp forcefield from Robustelli et al. > PNAS 2018

Re: [gmx-users] Coarse-grained Protein-ligand simulations

R-membrane simulation in a month of total > CPU > >> time. It has 512 processing nodes. > >> > >> Best regards, > >> Mac Kevin E. Braza > >> > >> On Tue, Apr 2, 2019, 12:40 AM Benson Muite > >> wrote: > >> > >>> Hi Mac

Re: [gmx-users] Coarse-grained Protein-ligand simulations

GPCR + membrane systems are notoriously big systems to work with for most research groups, regardless of your location on the map. Even in "privileged Europe" many research groups would struggle to produce microsecond long atomistic simulations of this system within a short period of time.

Re: [gmx-users] gmx do_dssp

Hello Eduardo, The xpm file contains all the info about axes, keys, etc. Look at this excerpt from a random xpm file from one of my simulations: /* This file can be converted to EPS by the GROMACS program xpm2ps */ /* title: "Secondary structure" */ /* legend: "" */ /* x-label: "Time (us)" */

Re: [gmx-users] Is there any way to count the number of water molecules around a ligand during simulation of its binding pathway?

Hi Hassan, Yes, this is something that I usually do with MDAnalysis, but from experience I've noticed that people are often reluctant to try it. Therefore you could try playing with gmx_select. Something like this should output the number of water oxygen atoms within 5 Å of residue 1 as a

Re: [gmx-users] How to fix the box size during the simulation?

"Is it possible to fix dimensions of the simulation box during the production run?" ---> Of course, simulate in the canonical ensemble (NVT). The isothermal-isobaric ensemble (NPT) employs a barostat, which means that the box volume will have to vary in order to keep the pressure constant. J --

Re: [gmx-users] Population Density Plot

, Sep 17, 2018 at 3:43 PM Vytautas Rakeviius wrote: > Also you can use R for that task. Very easy like:density(x, ...) > > On Monday, September 17, 2018, 4:26:38 PM GMT+3, João Henriques < > joao.m.a.henriq...@gmail.com> wrote: > > How does that reply the OP'

Re: [gmx-users] Population Density Plot

How does that reply the OP's question? To calculate the joint probability distribution you need to perform a kernel density estimation. I'd recommend either SciPy or Seaborn if you're not averse to coding in Python:

Re: [gmx-users] Regarding index .ndx files

What is your system composed of? It is generally a good idea to couple solvent and solute separately (as long as solute is "big enough", see http://www.gromacs.org/Documentation/Terminology/Thermostats), so Vytautas reply isn't the best advice. It will solve your problem, but that's generally not

Re: [gmx-users] How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

on defining these points in a .ndx file, I suggest you get familiar with the selection syntax: http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html J On Wed, Sep 12, 2018 at 8:04 PM rose rahmani wrote: > On Wed, Sep 12, 2018 at 9:15 PM João Henriques < > joao.m.a.henriq...@

Re: [gmx-users] How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

> > > > Best > > Rose > > On Wed, 12 Sep 2018, 20:04 João Henriques, > > > wrote: > > > >> Ok, being that the reference is a surface gmx gangle might work. Notice > >> that I wrote might, because I believe it will still be cumbersome for >

Re: [gmx-users] How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

"being that the reference is a surface" ---> I meant a "planar surface" J On Wed, Sep 12, 2018 at 5:34 PM João Henriques wrote: > Ok, being that the reference is a surface gmx gangle might work. Notice > that I wrote might, because I believe it will still be cu

Re: [gmx-users] How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

art" and/or fast. I'd still probably look into doing my own code using some third party module/package to parse and analyze trajectories. J On Wed, Sep 12, 2018 at 5:01 PM rose rahmani wrote: > On Wed, 12 Sep 2018, 19:13 João Henriques, > wrote: > > > "It gives me the h

Re: [gmx-users] How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

n Wed, Sep 12, 2018 at 3:41 PM rose rahmani wrote: > Thank you Joao, > > On Wed, 12 Sep 2018, 14:04 João Henriques, > wrote: > > > Dear Rose, > > > > Spamming is not the answer. There have been quite a few threads about > this > > subject in the recent

Re: [gmx-users] How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?

Dear Rose, Spamming is not the answer. There have been quite a few threads about this subject in the recent past. Searching the mailing list before posting is usually good practice. If then something remains unclear, please feel free to ask. I remember having quite long discussions with a Dilip

Re: [gmx-users] Regarding rigidity of water models

Hi, [1] CHARMM36 is to be used with the CHARMM-modified TIP3P water model (TIP3P with LJ parameters on the water molecule hydrogen atoms). [2] By default it's rigid, but check "define =" under your mdout.mdp file. If there's no -DFLEXIBLE, then it's rigid. [3] No idea of what that is, sorry.

Re: [gmx-users] gmx mindist error

tainly imagine an MD > > package that hard codes the assumption of a cubic box with normal 3D > > periodicity. But there's nothing intrinsic to the file format that > implies > > any periodicity to a box. That's either a convention, or given by other > > information from

Re: [gmx-users] gmx mindist error

> Hi, > > The box sizes say nothing about whether the boundary is fully or partially > periodic, or screw, or not. > > Mark > > On Tue, Mar 27, 2018, 16:13 João Henriques <joao.m.a.henriq...@gmail.com> > wrote: > > > Thanks Justin, I was really trying to av

Re: [gmx-users] gmx mindist error

at 4:04 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/27/18 9:59 AM, João Henriques wrote: > >> Dear users and developers, >> >> I am trying to use gmx mindist to calculate the minimum distance between >> periodic images but I get the

Re: [gmx-users] gmx mindist error

18 at 3:59 PM, João Henriques < joao.m.a.henriq...@gmail.com> wrote: > Dear users and developers, > > I am trying to use gmx mindist to calculate the minimum distance between > periodic images but I get the following error: > > Fatal error: > pbc = no is not supported b

[gmx-users] gmx mindist error

Dear users and developers, I am trying to use gmx mindist to calculate the minimum distance between periodic images but I get the following error: Fatal error: pbc = no is not supported by g_mindist This is the command I am running: gmx_mpi mindist -f output.xtc -s structure.pdb -od -pi -pbc

Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1

t does the same things as dssp, it won't > > > work. > > > > > > > > Mark > > > > > > > > On Tue, Mar 13, 2018 at 9:56 AM Simon Kit Sang Chu < > > > simoncks1...@gmail.com > > > > > > > > > wrote: > &g

Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1

gt; Simon > > 2018-03-13 15:58 GMT+08:00 João Henriques <joao.m.a.henriq...@gmail.com>: > > > "Fatal error: Failed to execute command: Try specifying your dssp version > > with the -ver option." > > > > Did you follow the error message suggesti

Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1

and executable name must match. J On Tue, Mar 13, 2018 at 8:58 AM, João Henriques < joao.m.a.henriq...@gmail.com> wrote: > "Fatal error: Failed to execute command: Try specifying your dssp version > with the -ver option." > > Did you follow the error message suggesti

Re: [gmx-users] GROMACS 5.1.4 and dssp 2.2.1

"Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option." Did you follow the error message suggestion? With DSSP 2.2.1 you need to set "-ver 2" on your gmx do_dssp command. J On Tue, Mar 13, 2018 at 8:45 AM, Simon Kit Sang Chu

Re: [gmx-users] g_sans calculation

I understand your pain, and the same could be said about gmx saxs as well. As Micholas said, CRYSON might be a good choice as far as implicit solvent methods go. Please notice that CRYSON is closed source, but it is well documented in the literature (it is basically a reimplementation of CRYSOL*).

Re: [gmx-users] Calculate RDF within a certain distance from atom

Justin already properly addressed the original post, so I'll just add a few comments about the last message: > I have the RDF between Calpha-Ow, and it is showing a slight hump/peak around 0.47nm. So you've managed to calculate it then as Justin suggested? FYI the RDF minimum occurs at a larger

Re: [gmx-users] simulation time vs side chain flexibility

Feb 20, 2018 at 12:09 PM, João Henriques < > joao.m.a.henriq...@gmail.com> wrote: > > > This is not strictly a gromacs related question, but long answer short: > it > > depends, but most likely not. You must be able to convince people that > the > > property you'

Re: [gmx-users] simulation time vs side chain flexibility

This is not strictly a gromacs related question, but long answer short: it depends, but most likely not. You must be able to convince people that the property you're interested in is properly converged within the simulation time you're considering. Multiple, reversible events need to be clearly

Re: [gmx-users] How to obtain TIP4P/ε water model topology file

I'm not very familiar with the TIP4P/ε water model, but if my memory serves me correctly, isn't it meant for pure water simulations? I'm not sure it's a good idea to mix it up with a protein force field without proper testing. Also, CHARMM36 was parametrized to be used with the CHARMM-modified

Re: [gmx-users] installation problem

This is completely vague. Please report what the actual error is and then people might be able to help. J On Mon, Feb 19, 2018 at 9:43 AM, banijamali_fs wrote: > Hi there, > > unfortunately I uninstall the gromacs program from my PC and I couldn't > install it again

Re: [gmx-users] Calculation of shape change of a protein during simulation

You can calculate the asphericity, for example. You just need the components of the gyration tensor which are given by gmx polystat, if my memory serves me right. There are several papers about this. A quick search on Google scholar will surely produce results. I would link the papers or the

Re: [gmx-users] Possibility of adding external forces to simulating molecules

That sounds like what metadynamics. Is that what you want to do? Can you elaborate a bit more about the your objective? J On Tue, Jan 30, 2018 at 4:40 PM, Lovuit CHEN wrote: > Hi, > > > When doing MD simulation of certain molecule, is it possible to add some > external

Re: [gmx-users] (no subject)

> You need some ions to neutralise the system for long range electrostatics to work. This mostly applies to PME. However, because PME is basically *de facto* nowadays, it will most likely apply in most situations. However, I recently learned that PME can also be run with a non-neutral system, as

Re: [gmx-users] An conda package for installing gromacs 4.5.5 on 64-bit

I see what you mean. I've also worked with methods that required modification/wrapping of specific (older) versions of gromacs. The amount of people that do this is however much lower than those running vanilla gromacs, so you should probably conserve your time and effort, unless there's a big

Re: [gmx-users] An conda package for installing gromacs 4.5.5 on 64-bit linux system

Exactly, that version is 7 years old or so. It's a good initiative nonetheless, just wished it offered a more recent version. J On Fri, Jan 19, 2018 at 6:08 AM, James Krieger wrote: > Why 4.5.5? > > On Thu, Jan 18, 2018 at 11:26 PM, 蕭毅 wrote: >

Re: [gmx-users] -inter command

e or > error-free as information could be intercepted, corrupted, lost, destroyed, > delayed, or may contain viruses. The recipient must verify the integrity of > this e-mail message. """ J On Mon, Jan 15, 2018 at 11:51 AM, João Henriques < joao.m.a.henriq...

Re: [gmx-users] -inter command

-inter sets the interactive mode for a bunch of other flags. Most are used for selecting the protonation states of the termini and other residues. It can also be used for interactive SS bridge selection. > "for setting the protonation state of charged amino acids in order to perform simulation at

Re: [gmx-users] Umbrella sampling-gmx distance

The output is very explicitly telling you what the problem is. You didn't provide a topology. Pass one the the -s flag. How do you want the COM to be computed when you're not providing any masses? J On Jan 13, 2018 9:19 AM, "rose rahmani" wrote: > I'm relly sorry for

Re: [gmx-users] phi/psi

Hello, Don't know if there's a native gromacs tool to do so, but I'd use PLUMED for this sort of thing: https://plumed.github.io/doc-v2.3/user-doc/html/_t_o_r_s_i_o_n.html The last example on that page shows something similar to what you want to do. It's that simple. P.S.: I am not affiliated

Re: [gmx-users] Simulation of aggregated proteins

If the PDB has each protein with separate chain entries (A, B, etc) then this shouldn't be a problem. pdb2gmx will produce separate topologies for each chain and an overall topology that reads from each of the individual topologies and contains the other directives about FF, water model, posre,

Re: [gmx-users] PROTEIN FOLDING

com> wrote: > Thank you Joao and Aman. > > I have noted the points you have suggested. > > Do you think analyzing DSSP would help? > > Thanks, > Neha > > On Wed, Dec 20, 2017 at 4:03 PM, João Henriques < > joao.m.a.henriq...@gmail.com> wrote: > > >

Re: [gmx-users] PROTEIN FOLDING

"You can use various supporting tools from R language to debug your trajectory but most third party software support NAMD and charmm format. You can use VMD to convert the trajectory to dcd and use R language based packages to read your trajectory" What? How is this useful or helpful? At most it

Re: [gmx-users] Dynamic selection of a shell in a trajectory

Very unlikely and/or impractical. The water selections/analyses you can do with gromacs' native tools are unfortunately rather limited. From personal experience I'd suggest trying MDAnalysis or something similar, because it gives you the freedom to code your our analysis routine with minimal

Re: [gmx-users] WHAM

This has nothing to do with your initial question, but I there are a few misconceptions in your last email that you should be aware of. First, you don't need "special computers" to run or compile gromacs. It helps to have multiple compute nodes at your disposal, but it isn't a requirement *per

Re: [gmx-users] SPC model hydrogen bonding

"Is my simulation wrong or SPC give similar values. Please give a suggestion." My suggestion is that you look at the extensive literature on bulk water simulations using the SPC water model (and other more recent and accurate water models for bulk water studies). There have been studies on the

Re: [gmx-users] DSSP installation

I already told you, use a DSSP executable that is compatible (versions 1 or 2) and pass the right version number to the -ver flag of do_dssp. J On Sat, Dec 9, 2017 at 1:06 PM, <sp...@iacs.res.in> wrote: > - Message from João Henriques <joao.m.a.henriq...@gmail.com> > --

Re: [gmx-users] DSSP installation

The output is telling you what is wrong. Gromacs doesn't support version 3. Install either version 1 or 2. In fact, I didn't even know there was a version 3 of DSSP, where did you get it? It certainly isn't on the official website (http://swift.cmbi.ru.nl/gv/dssp/). J On Fri, Dec 8, 2017 at

Re: [gmx-users] DSSP

There's no DSSP version 3 that I know of. That can't be right. J On Tue, Dec 5, 2017 at 5:52 PM, Vidya R <vidyadevi2...@gmail.com> wrote: > Hi, > > I have installed dssp version > > > *3.0.0-win32* > > *What should be the command now?* > > On Tue, Dec

Re: [gmx-users] DSSP

, line: 663 > > Fatal error: > Failed to execute command: Try specifying your dssp version with the -ver > option . > > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromac

Re: [gmx-users] DSSP

Hi! This is not so much for you as it is for the other users and developers. I think I found a problem with the DSSP code when compiling using the latest boost version (1.65.1). "tr1/tuple.hpp" cannot be found within the "include" directory of this new boost, and the compilation fails. The error

Re: [gmx-users] Regarding calculating the water orientation profile

Orientation has nothing to do with proximity. You can have orientation as a function of proximity, but orientation *per se* does not necessarily involve a distance, it just tells you about a preferential orientation of the water molecules towards a reference. We've already been through this in

Re: [gmx-users] THE max number of atoms in gromacs?

Hi, The PDB format is fixed, so it's not really a gromacs problem *per se*. Take a look at this : "A model cannot have more than 99,999 atoms. Where the entry does not contain an ensemble of models, then the entry

Re: [gmx-users] Regarding calculating the water orientation profile

Wait, now I remember, you even approached me in a private message and we exchanged quite a few emails. Did you try any of my suggestions? No success? J On Thu, Nov 23, 2017 at 7:36 PM, João Henriques < joao.m.a.henriq...@gmail.com> wrote: > Hi, > > I clearly remember replyi

Re: [gmx-users] Regarding calculating the water orientation profile

Hi, I clearly remember replying to something similar sometime ago, and I'm almost sure the post was yours. It may be a good idea to rummage through the mailing list, because I'm pretty sure this type of analysis has been discussed here more than once. Cheers, J On Thu, Nov 23, 2017 at 4:41 PM,

Re: [gmx-users] Typo for atom in charmm36-jul2017 ff for residue NAI

Good to know, thanks. J On Wed, Nov 8, 2017 at 12:54 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/8/17 5:52 AM, João Henriques wrote: > >> Hi Johannes, >> >> I'd suggest contacting someone at the MacKerell Lab instead. I believe >> they

Re: [gmx-users] Writing pdb snapshot with charge from gro trajectory

Hi, The PDB format is strict by definition ( http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html). Every single character (and column) within a line has a specific purpose and charges are not included there. I doubt trjconv or other gromacs tools will allow you to tamper

Re: [gmx-users] Typo for atom in charmm36-jul2017 ff for residue NAI

Hi Johannes, I'd suggest contacting someone at the MacKerell Lab instead. I believe they are responsible for the FF and for its maintenance. Otherwise this issue might get lost here and never make it to the people that absolutely need to know about it. Look at the original paper and send an

Re: [gmx-users] non-neutral system

Understood. Thank you Justin. J On Mon, Nov 6, 2017 at 1:11 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/6/17 7:06 AM, João Henriques wrote: > >> Hi Johannes, >> >> I just meant that from a purely theoretical point of view, it ne

Re: [gmx-users] non-neutral system

.tu-muenchen.de> wrote: > Hey Joao, > > are you sure? I think PME will introduce a neutralizing background charge? > > All the best > > Johannes > > > > On 06.11.2017 11:57, João Henriques wrote: > >> ​Hi, >> >> You shouldn't use PME wit

Re: [gmx-users] non-neutral system

​Hi, You shouldn't use PME without neutralizing the system's charge. ​It's a limitation of the Ewald summation. Take a look at the literature for further details. I don't know much about viscosity, so I'll leave that for someone else. Cheers, J On Mon, Nov 6, 2017 at 11:50 AM, Faezeh Pousaneh

Re: [gmx-users] how to do neutralization?

rge less than 1, idont know what should > i do,i optimized the structure in Gaussian and put H atom for make it more > stable but its not included in itp file. > > On Thu, Nov 2, 2017 at 1:23 PM, João Henriques < > joao.m.a.henriq...@gmail.com > > wrote: > > > Hi,

Re: [gmx-users] how to do neutralization?

Hi, What system is that and what force field are you using? Building blocks usually have integer net charges, this is rather unusual. Cheers, J On Thu, Nov 2, 2017 at 10:02 AM, Seera Suryanarayana wrote: > Dear gromacs users > > I got the system non-zero total charge:

Re: [gmx-users] Regarding water orientation profile

​Hi, I've had similar issues in the past with the calculation of angular distribution functions of water in respect to a given point or amino acid residue and it wasn't easy/possible to solve with standard gromacs tools. I'd suggest using MDAnalysis or some other equivalent tool. It definitely

Re: [gmx-users] How good to use triclinic box for gormacs simulations?

Hi, How does the link to "editconf" help in answering the original question? Anyway, no, there is no specific recipe to select a box type. You generally have to make an educated guess by using your scientific intuition and knowledge about the shape (and conformational plasticity) of your system.

Re: [gmx-users] CHARMM36 older version (GROMACS)

Hi Simon, Aren't they the same force field though? As far as I've noticed they're identical if you use them for proteins (without any fancy residues). The latest one just includes more atom types, etc. From my understanding the latest one is more "complete", but both are essentially the same

Re: [gmx-users] RMSD in Angstrom

​Hi, This is more of a xmgrace related issue. Gromacs' length units have always been nm and there's no way to "ask" for different units. Now you either modify the file yourself (manually or with a simple awk one-liner) or ask the plotting program to convert the units. I don't know about xmgrace,

Re: [gmx-users] CHARMM ff cutoffs

Micholas Dean Smith, PhD. > Post-doctoral Research Associate > University of Tennessee/Oak Ridge National Laboratory > Center for Molecular Biophysics > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > groma

Re: [gmx-users] CHARMM ff cutoffs

ty of Tennessee/Oak Ridge National Laboratory > Center for Molecular Biophysics > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of João > Henriques <joao.m.a.henriq..

[gmx-users] CHARMM ff cutoffs

Dear all, Is there any piece of literature that explicitly states what is the *de facto* cutoff for CHARMM FFs, i.e., for the LJ and electrostatic interactions? The old gromacs site states it's 1.2 nm: http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM However, I've read

Re: [gmx-users] Fwd: Related to PCA

Hello! From your email it's difficult to understand whether you're familiar with the analysis and just seek specialized help on a particular interpretation, or whether you're completely new to PCA and want an overall explanation of it. In case of the latter, I suggest literature research. To

Re: [gmx-users] Charges and Antechamber

Or this... :) I've never used it, but I'm sure it works like a charm. I personally prefer to be more involved in all stages of the process, but I'm a bit old school and I like to avoid "black boxes" for my own learning benefit. That being said, I'm sure it does the job and it's faster & simpler.

Re: [gmx-users] Charges and Antechamber

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Re: [gmx-users] Charges and Antechamber

w.phap.no/ | FAP ] From: "João Henriques" <joao.m.a.henriq...@gmail.com> To: "gmx-users" <gmx-us...@gromacs.org> Sent: Tuesday, October 3, 2017 3:50:55 PM Subject: Re: [gmx-users] Charges and Antechamber Hi! If your goal is to generate the atomic partial charges fo

Re: [gmx-users] Charges and Antechamber

Hi! If your goal is to generate the atomic partial charges for a new residue/molecule (not existing in the FF you are interested in using), then doing the QM calculations is a must in most cases. For example, AMBER FFs have a well documented and specific recipe you can easily follow, which

Re: [gmx-users] Torsion analysis

gmx chi? http://manual.gromacs.org/documentation/2016.3/onlinehelp/gmx-chi.html I never used it though. I personally like to use PLUMED for this: https://plumed.github.io/doc-v2.3/user-doc/html/_t_o_r_s_i_o_n.html João On Thu, Aug 24, 2017 at 1:43 PM, RAHUL SURESH

[gmx-users] Compiling DSSP-2.2.1 from source

Dear users and developers, I have compiled DSSP from source a bunch of times in the past, but I stopped being able to do it recently. I've set the make.config file appropriately, since my boost (version 1.59.0_3) was installed through MacPorts: BOOST_LIB_SUFFIX = -mt BOOST_LIB_DIR=

Re: [gmx-users] 4-letter residues

Absolutely spot on Justin! I just discovered it by myself 30 seconds ago. Thanks! João On Thu, Jul 13, 2017 at 4:17 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/13/17 10:16 AM, João Henriques wrote: > >> Dear all, >> >> I have a pro

[gmx-users] 4-letter residues

Dear all, I have a protein with a phosphorylated threonine and the corresponding residue name in my FF of interest is THP1. 4-letter residues and PDB files are a recipe for disaster, but somehow pdb2gmx detects the residue's name and number perfectly. What happens next is somewhat odd (at least

Re: [gmx-users] Issue with the PDB generated after topology

To renumber a gro file: gmx editconf -resnr OR Script it, I'm sure there's a one liner for that in awk (even in Python that shouldn't take more than 10 lines of code). /J On Mon, Jul 3, 2017 at 11:37 AM, Khadija Amine wrote: > Hi, > > I have already converted the .gro

Re: [gmx-users] use INTERFACE Force Field

, 2017 at 4:13 PM, João Henriques < joao.m.a.henriq...@gmail.com> wrote: > If only it was that straightforward. I am not familiar with this INTERFACE > ff, but this is not just about format and layout. There's much more at > stake. However, the team behind it appears to be planning

Re: [gmx-users] use INTERFACE Force Field

If only it was that straightforward. I am not familiar with this INTERFACE ff, but this is not just about format and layout. There's much more at stake. However, the team behind it appears to be planning to port it soon: "Developments in progress include a graphical user interface to construct

Re: [gmx-users] DNA splitting in simulations

Hi! Your mdp file doesn't tell the engine to apply the restraints during the simulation... You need to specify: define = -DPOSRES Also, didn't Justin already warn you about using separate temperature couplings for every component of your system? Please check the "What Not To Do" section under:

Re: [gmx-users] MD simulation at different pH

Hi! You technically can't perform constant-pH simulations with a regular, straight out of the box GROMACS distribution. You can change the residue protonation states to mimic the "pH" you're interested in simulating, but keep in mind that these will be fixed during the entire simulation, i.e.

Re: [gmx-users] Difference between Err. Est. And RMSD

​Hi, It is stated in the program's description (gmx energy -h): "An error estimate of the average is given based on a block averages over 5 blocks using the full-precision averages. The error estimate can be performed over multiple block lengths with the options -nbmin and -nbmax. Note that in

Re: [gmx-users] hydrogen bond analysis

Dear Imrul, I believe the information you seek is right there in your xvg file header: @xaxis label "Time (ns)" @yaxis label "Number" ... @ s0 legend "Hydrogen bonds" @ s1 legend "Pairs within 0.35 nm" First column is always time (x-axis). All other columns are y-axes for different

Re: [gmx-users] Remove all but N closest water molecules from protein

ut needing > to serialize and de-serialize files (and the new GROMACS analysis framework > has such support, but we don't have much funding for implementing / porting > tools to it). > > Mark > > On Thu, Jun 8, 2017 at 10:48 AM João Henriques < > joao.m.a.henriq...@gmail.co

Re: [gmx-users] Remove all but N closest water molecules from protein

, 2017 at 10:34 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > Or gmx select to make an index group for the nearest waters, and gmx > trjconv to make the subset with the index group. > > Mark > > On Thu, Jun 8, 2017 at 9:05 AM João Henriques < > j

Re: [gmx-users] Remove all but N closest water molecules from protein

Hi, trjorder can reorder the water molecules in each frame according to their distance to the protein. Then you either manually prune the gro file(s) or use an index file to get rid of the extra stuff. I don't know of any native tool that does all of this in one step but I may be outdated

Re: [gmx-users] Simulate protein at subzero condition in aqueous buffer

during the simulation) make it almost impossible to unfold it completely at any temperature using molecular dynamics. /J On Wed, Jun 7, 2017 at 7:15 PM, João Henriques <joao.m.a.henriq...@gmail.com > wrote: > ​Higher complexity water models such as TIP5P and so on are able to better &g

Re: [gmx-users] Simulate protein at subzero condition in aqueous buffer

​Higher complexity water models such as TIP5P and so on are able to better reproduce bulk water properties (please check the paper I linked in my earlier email). However, these models require more computational effort (due to the increased number of interactions) and may not work well in

Re: [gmx-users] Simulate protein at subzero condition in aqueous buffer

Hello, "spc216.gro" is not a water model, it's just a pre-equilibrated simulation box (300 K and 1 bar) with the coordinates of 216 3-site water molecules. SPC and TIP3P are two examples of 3-site water models. Water model properties are well studied and tabled (e.g.

Re: [gmx-users] mdp options in GROMACS 4.5.5

Yeah, I just checked and GMX < 4.6 does not come with Verlet (the list I mean, not the integration). /J On Tue, Jun 6, 2017 at 5:45 PM, João Henriques <joao.m.a.henriq...@gmail.com > wrote: > Hi! > > I'm not sure Verlet was already implemented in GMX 4.5.5, but

Re: [gmx-users] mdp options in GROMACS 4.5.5

Hi! I'm not sure Verlet was already implemented in GMX 4.5.5, but check the manual for that version (or the closest one). Cheers, /J On Tue, Jun 6, 2017 at 3:27 PM, wrote: > Hi All, > I have used below mdp options in GROMACS version 5.0.4. ; minim.mdp - used > as

Re: [gmx-users] mdp file for 370 K MD based on Justin's tutorial

You haven't adjusted the temperature on the production mdp file, it's still 300 K. J On Mon, May 22, 2017 at 12:37 PM, ZHANG Cheng <272699...@qq.com> wrote: > Dear Gromacs, > I am performing 370 K MD based on Justin's tutorial. > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ >

Re: [gmx-users] HPC resources in Europe (preferably Northern/Central Europe)

Thank you very much Stéphane, I will certainly investigate this possibility. Best regards, João On Mon, May 15, 2017 at 5:12 PM, ABEL Stephane wrote: > Hello, > > You could write a proposal to have access to the supercomputers of the > PRACE consortium |1]. The access to

[gmx-users] HPC resources in Europe (preferably Northern/Central Europe)

Dear users and developers, Our research group is having trouble finding enough computational resources to run our GROMACS simulations and it was decided that I would be in charge of finding new alternatives. I know this topic is not 100% GROMACS related in a strict sense, but I've seen threads

Re: [gmx-users] MD at different pH

he Poisson-Boltzmann/Monte Carlo steps. On Thu, May 4, 2017 at 3:02 PM, João Henriques <joao.m.a.henriq...@gmail.com > wrote: > Technically, Helmut Grubmüller's group is not the only performing > constant-pH MD using Gromacs. António Baptista and Miguel Machuqueiro's > gro

Re: [gmx-users] MD at different pH

Technically, Helmut Grubmüller's group is not the only performing constant-pH MD using Gromacs. António Baptista and Miguel Machuqueiro's groups in Portugal have done it with explicit solvent since 2002: http://aip.scitation.org/doi/abs/10.1063/1.1497164 It is not fully integrated in Gromacs,

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