[gmx-users] Exploding temp/pressure.

Hi all, I¹m trying to equilibrate a Martini CG simulation from an initial atomistic structure. Eq and Fc values were derived using an atomistic system. I¹ve started the dt at 0.0005 for 60 steps, moving through 0.001, 0.0015 and 0.002 for the same number of steps, using the .mdp details below

Re: [gmx-users] CG Lincs errors

dy rather low. I do agree that longer equilibration at low timestep >(5 or 10) might help. > >Alternatively, Do you think a semiisotropic pressure coupling might be >applicable in this case, since it's an infinite collagen polymer? > > >Peter (PhD in the Martini group) > &

Re: [gmx-users] CG Lincs errors

t;> take a subset of your protein and see what happens. Or simulate in vacuo >> for a while. Your topology could be unsuited to your starting structure, >> e.g. some part is under a lot of tension that gets released at some >>point >> and no finite time step can in practice

[gmx-users] CG Lincs errors

Hi all, I¹m hoping for some help. I¹m very sorry, this is a bit of a long one. I¹ve been struggling for almost a month trying to run a CG representation of our all-atom model of a collagen protein (3 polypeptide chains in a protein). Our original AMBER all-atom model had been successful

Re: [gmx-users] Fine tune the RDF of water around a dummy metal

: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 12 October 2016 22:56 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Fine tune the RDF of water around a dummy metal On 10/12/16 5:32 PM, Nash, Anthony

[gmx-users] Fine tune the RDF of water around a dummy metal

Hi all, I¹m trying to fine tune the rdf of tip3p water molecules around a central metal dummy molecule ("Force Field Independent Metal Parameters Using a Nonbonded Dummy Model²), essentially a central metal (with vdw parameter and -1 charge) covalently bonded to six Œdummy¹ atoms (no vdw

Re: [gmx-users] energy minimisation - LINCS WARNING

ould >make some constructive feedback to its authors :-) > >Mark > >On Mon, 3 Oct 2016 11:22 Nash, Anthony <a.n...@ucl.ac.uk> wrote: > >> >> Hi Justin, >> >> >> I’ve tried out all of your suggestions, they worked to an extent but the >> in vac

Re: [gmx-users] energy minimisation - LINCS WARNING

opic; it >creates a mess in the archive. > >On 10/2/16 6:11 PM, Nash, Anthony wrote: >> Hi all, >> >> I had a homology/de-novo model .pdb converted into .gro, solvated, >> neutralised and now I¹m going through a series of energy minimisation >> steps. Unfortunately, du

[gmx-users] energy minimisation - LINCS WARNING

Hi all, I had a homology/de-novo model .pdb converted into .gro, solvated, neutralised and now I¹m going through a series of energy minimisation steps. Unfortunately, during energy minimisation I get LINCS WARNINGS (angle relative constraint deviation). The the naked eye, the atoms involved don¹t

Re: [gmx-users] A charge group moved too... during backward transition of dual topologies

check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Dr Anthony Nash Department of Chemistry University College London On 03/08/2016 08:11, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Nash, An

[gmx-users] A charge group moved too... during backward transition of dual topologies

Hi all, I¹m performing free energy calculations based on Crooks Fluctuation Theorem. To do this I¹ve used PMX to implement a dual topology. To keep things simple, it is a transmembrane polyleucine helical protein where one leucine is transforming into a serine - then there is the backward

[gmx-users] Masses and atomic radii for SASA

Hi all, I am a little concerned by the warning given (by default) when I use gmx_d sasa Š WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input

[gmx-users] Surface Distribution Function in gromacs

Hi all, A very quick sanity check question regarding one of the gromacs analysis tools. Does the -surf option in gmx_d rdf (or rdf_d in 5.0.#) yield a Surface Distribution Function plot I.e., related to the average density of water molecules around the protein surface? I¹ve tried, and I get a

Re: [gmx-users] minor edits to a .gro file

to neutral fragments, dissociation of fragments, charging of fragments. > >Mark > >On Fri, Jun 10, 2016 at 12:12 PM Nash, Anthony <a.n...@ucl.ac.uk> wrote: > >> Hi Mark, >> >> I had considered (and I still am) defining a distance constraint between >> the l

[gmx-users] Missing oxyz in vmx distance output

Hi all, I¹m really hoping this is my own oversight. Using Gromacs 5.0.4 (can¹t upgrade, this is a distribution on a cluster) I can generate each of the output options (-oav -oall -oh -oallstat) apart from -oxyz when I run the command: gmx_d distance -f NPT_0_40ns_compress.gro -s

Re: [gmx-users] minor edits to a .gro file

t. > >Mark > >On Fri, Jun 10, 2016 at 11:32 AM Nash, Anthony <a.n...@ucl.ac.uk> wrote: > >> James and Justin, >> >> Thanks for your suggestions. This was ultimately to hack around with the >> PMX toolkit for making dummy atoms in preparation for fr

Re: [gmx-users] minor edits to a .gro file

James and Justin, Thanks for your suggestions. This was ultimately to hack around with the PMX toolkit for making dummy atoms in preparation for free energy calculations. Unfortunately, I’m back to the drawing board (likely to be umbrella sampling) as an alchemical morphing of a glycated cross

[gmx-users] minor edits to a .gro file

Hi all, I¹m looking to open a .gro file, add in six hydrogen dummy atoms (I can rename the atom name/type, I just need the correct x, y and z coords) to the end of an amino acid sidechain and save whilst preserving as much of the .gro format as it can. I would normally load the crystal/derived

Re: [gmx-users] Clarity on TI free energy terms

Loeffler" <gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of hannes.loeff...@stfc.ac.uk> wrote: >On Wed, 1 Jun 2016 16:15:31 + >"Nash, Anthony" <a.n...@ucl.ac.uk> wrote: > >> In the mean while, do you know of any tutorials (besides the methane &

Re: [gmx-users] Clarity on TI free energy terms

University College London On 01/06/2016 16:55, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Nash, Anthony" <gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of a.n...@ucl.ac.uk> wrote: >Thanks for all of this material. I’ll take some time and

Re: [gmx-users] Clarity on TI free energy terms

mx-users-boun...@maillist.sys.kth.se on behalf of hannes.loeff...@stfc.ac.uk> wrote: >On Wed, 1 Jun 2016 15:00:51 +0000 >"Nash, Anthony" <a.n...@ucl.ac.uk> wrote: > >> > This also assumes that >> >you have vanishing atoms only. If you have appearing atoms only you

Re: [gmx-users] Clarity on TI free energy terms

Dear Hannes, please see my comment below.. On 01/06/2016 14:45, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Hannes Loeffler" <gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of hannes.loeff...@stfc.ac.uk> wrote: >On Wed, 1 Jun 2016 12:06:20 +0

Re: [gmx-users] Clarity on TI free energy terms

e vector to all-zeroes (or ones). > > >On Wed, 1 Jun 2016 09:47:59 + >"Nash, Anthony" <a.n...@ucl.ac.uk> wrote: > >> Hi Hannes, >> >> >> Many thanks for the reply. With regards to your final comment I >> understand conserving mass in

Re: [gmx-users] Clarity on TI free energy terms

macs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of hannes.loeff...@stfc.ac.uk> wrote: >On Wed, 1 Jun 2016 07:54:56 + >"Nash, Anthony" <a.n...@ucl.ac.uk> wrote: > >> In the tutorial, charges are off in the topology and the electrostatic >> coupling to

[gmx-users] Clarity on TI free energy terms

Dear all, I¹m trying to understand the finesse behind the TI free energy in gromacs, before taking it anywhere near a real production run, by running through the FE methane in solvent tutorial and the thermodynamic cycles of small peptides in the PMX paper. I roughly-understand a fair chunk,

Re: [gmx-users] Free Energy Topology between A and B.

So there is! Many thanks for bringing this to my attention. Thanks Anthony On 29/05/2016 20:40, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul" <gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of jalem...@vt.edu> wrote: > > >

[gmx-users] Free Energy Topology between A and B.

Dear all, I¹m a total newbie when it comes to Thermodynamic Integration, and until now I¹ve been happy with umbrella sampling. However, I¹ve found myself in a situation where I believe TI would be the most appropriate technique. I would like to determine the energetic contribution that a mutant

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

th.se on behalf of Justin Lemkul" <gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of jalem...@vt.edu> wrote: > > >On 5/3/16 9:16 AM, Nash, Anthony wrote: >> >> Hi all, >> >> Can gmx hbond accept user specified atoms for the donors (default OH a

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

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. I have a post-trans modified protein from a rather bulk cross-linked peptide chain. I defined unique atom times but I

[gmx-users] Constant Density

Hi all, At the risk of bending the rules of thermodynamics, I¹m wondering whether Gromacs can maintain density of a water box (0.750 g/L density of water in a collagen fibril environment) whilst applying an NPT ensemble? gmx_d solvate, fills up to 2/3 of my truncated oct cell, with my protein at

Re: [gmx-users] Thermodynamic integration

so you might consider pmx >http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4365728/ for such topology >generation. There is further work in the pipeline, so do get in touch with >Bert if there's something of interest. > >Mark > >On Mon, Apr 18, 2016 at 11:56 AM Nash, Anthony <a.n...@ucl.ac.uk> wrot

[gmx-users] Thermodynamic integration

Hi all, I¹m looking for a guide on performing TI between a protein in its crystal periodicity with a particular residue (state A), to the same system but with a different residue (state B). I¹m currently using http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free

[gmx-users] pull code for Gromacs 5

Hi all, I¹m very unfamiliar with the pull code as of Gromacs 5. Unfortunately my system is not experiencing any noticeable Œpull¹. From the options below, which is the group experiencing the pull and which is the reference group? Would applying a set of position restraints on the reference group

Re: [gmx-users] Can I fix two of the cubic cell dimensions during an NPT simulation?

Justin, that’s awesome. Thanks On 14/03/2016 22:34, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul" <gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of jalem...@vt.edu> wrote: > > >On 3/14/16 6:31 PM, Nash,

[gmx-users] Can I fix two of the cubic cell dimensions during an NPT simulation?

Hi all, Is there a way of keeping the x, y box dimensions fixed during an NPT simulation, with changes to volume only changing in the Z dimension? Semiisotropic is not quite working out, see below. Context: I want a coiled-coil dimer aligned in the Z direction. Each coiled-coil will see it¹s

[gmx-users] Suggestions on running simulations of very long polypeptide chains

Hi all, I¹m looking to run MD simulations of regions of a collagen molecule. A whole collegen molecule is made up of three polypeptide chains, each around 1000 residues long (gross generalisation as there are around 24 different collagen protein families). I am only interested in modelling a

Re: [gmx-users] Minimising forces for vibrational normal mode analysis

ifferent eigenvalues and eigenvectors. > >Regards, >Peter Stern > >Sent from my iPhone > >> On 29 Feb 2016, at 3:23 PM, Nash, Anthony <a.n...@ucl.ac.uk> wrote: >> >> Hi all, >> >> Hoping this will be the final stumbling block. I’v

Re: [gmx-users] Minimising forces for vibrational normal mode analysis

y Dr Anthony Nash Department of Chemistry University College London On 29/02/2016 16:25, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Nash, Anthony" <gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of a.n...@ucl.ac.uk> wrote: >Dear Mark an

Re: [gmx-users] Minimising forces for vibrational normal mode analysis

using position restraints. There >should be no need for this, nor any problem, but what happens without >them? > >Mark > >On Mon, 29 Feb 2016 15:39 Nash, Anthony <a.n...@ucl.ac.uk> wrote: > >> Hi Justin, >> >> After some digging I had found that link and made some

Re: [gmx-users] Minimising forces for vibrational normal mode analysis

don On 29/02/2016 12:49, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul" <gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of jalem...@vt.edu> wrote: > > >On 2/29/16 3:41 AM, Nash, Anthony wrote: >> Hi Tsjerk, >> >&

Re: [gmx-users] Minimising forces for vibrational normal mode analysis

these forces down first now that I’ve included lincs. Dr Anthony Nash Department of Chemistry University College London On 29/02/2016 08:41, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Nash, Anthony" <gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of a.n

Re: [gmx-users] Minimising forces for vibrational normal mode analysis

was >changed >implicitly. > >Cheers, > >Tsjerk > >On Mon, Feb 29, 2016 at 6:57 AM, Nash, Anthony <a.n...@ucl.ac.uk> wrote: > >> Hi Tsjerk, >> >> Compiled in double precision. I’ve alternated between steepest and >> conjugate gradient. I am sli

Re: [gmx-users] Minimising forces for vibrational normal mode analysis

u can try another minimization >method. Sometimes alternating minimization methods may help to reach a >proper minimum. > >Cheers, > >Tsjerk > >On Sun, Feb 28, 2016 at 11:27 AM, Nash, Anthony <a.n...@ucl.ac.uk> wrote: > >> Hi all, >> >> I would li

[gmx-users] Minimising forces for vibrational normal mode analysis

Hi all, I would like to pull out the vibrational normal modes using gromacs over a customised fragment to compare back with the original QM frequency analysis. I¹ve performed an integrator=cg over my structure, and monitored the potential energy which converges. The forces also converge beneath

Re: [gmx-users] generating an initial structure with a gromacs compatible tool

for helping me trouble shoot. Anthony On 25/02/2016 13:12, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham" <gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of mark.j.abra...@gmail.com> wrote: >Hi, > >On Wed, Feb 24, 2016 at 4

Re: [gmx-users] generating an initial structure with a gromacs compatible tool

ondon On 24/02/2016 14:33, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham" <gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of mark.j.abra...@gmail.com> wrote: >Hi, > >On Wed, Feb 24, 2016 at 3:26 PM Nash, Anthony <a.n.

Re: [gmx-users] generating an initial structure with a gromacs compatible tool

bra...@gmail.com> wrote: >Hi, > >On Tue, Feb 23, 2016 at 11:03 AM Nash, Anthony <a.n...@ucl.ac.uk> wrote: > >> Hi all, >> Is there a friendly Gromacs compatible tool for generating a .gro/.pdb >> file using a specific forcefield topology specification within G

[gmx-users] structure expanding beyond eq values

Hi all, Any thoughts on what could be causing my structure to expand and distort well beyond (about 2 to 3 angstrom with some distorted angles) the equilibrium bond lengths during energy minimisation? I¹ve fully parameterised two new fragments, which include new atom types and force constants.

[gmx-users] generating an initial structure with a gromacs compatible tool

Hi all, Is there a friendly Gromacs compatible tool for generating a .gro/.pdb file using a specific forcefield topology specification within Gromacs itself? For context: I¹m in the process of fully parameterising five custom protein residues for the amber forcefield from ab initio calculations.

Re: [gmx-users] Unknown bond_atomtype

mx-users-boun...@maillist.sys.kth.se on behalf of jalem...@vt.edu> wrote: > > >On 2/17/16 5:11 PM, Nash, Anthony wrote: >> Hi, >> >> Thanks for the information, Mark. I fully parameterised the bonded terms >> using QM data and some software I wrote. Now that I¹ve sorted out >

Re: [gmx-users] Unknown bond_atomtype

e specialized atom types, then yes, those bonded and non-bonded >parameters need to go into the databases for grompp to look up (or then >can >also go in the [bonds] section of the .rtp, I think). > >Mark > >On Wed, Feb 17, 2016 at 10:39 PM Nash, Anthony <a.n...@ucl

Re: [gmx-users] Unknown bond_atomtype

Dear Mark, I didn’t expect the problem was in ffnonbonded.itp. Problem solved. Thanks for the earlier hint. Anthony On 17/02/2016 18:01, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Nash, Anthony" <gromacs.org_gmx-users-boun...@maillist.sys.kth.se on

Re: [gmx-users] Unknown bond_atomtype

Department of Chemistry University College London On 17/02/2016 17:18, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Nash, Anthony" <gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of a.n...@ucl.ac.uk> wrote: >Hi Mark, > >Thanks for the rep

Re: [gmx-users] Unknown bond_atomtype

>etc. Choose existing types ;-) > >Mark > >On Wed, 17 Feb 2016 17:27 Nash, Anthony <a.n...@ucl.ac.uk> wrote: > >> Hi all, >> >> As per a previous email (cross linking two peptide chains), I¹ve >>created a >> brand new crosslink (think disulphide

[gmx-users] Unknown bond_atomtype

Hi all, As per a previous email (cross linking two peptide chains), I¹ve created a brand new crosslink (think disulphide bond) residue from scratch. I have defined it in all the files necessary (.rtp, residuetypes, specbond, atomtypes, ffbonded, ffnonbonded) and it has got past pdb2gmx with no

Re: [gmx-users] crosslinking polypeptide chains

f mark.j.abra...@gmail.com> wrote: >Hi, > >Please start new topics in new emails, rather than confusing the web >archives with replies to digests :-) > >On Tue, Feb 16, 2016 at 5:00 PM Nash, Anthony <a.n...@ucl.ac.uk> wrote: > >> Hi all, >> >> When executi

[gmx-users] crosslinking polypeptide chains

Hi all, When executing pdb2gmx I am getting a fatal error due to dangling bonds. I know that it will be down to how I¹ve organised the .pdb file, I¹m just lacking in the experience with TERs, -chainsep and -merge to solve this. I would appreciate hints/tips/outright-solutions. My protein is very

Re: [gmx-users] membed in mdrun VERSION 5.0.4

, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Nash, Anthony" <gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of a.n...@ucl.ac.uk> wrote: >Hi, >Just to add to my earlier message, I went through all release notes after >5.0.4, and besides a change in membed d

Re: [gmx-users] membed in mdrun VERSION 5.0.4

ehalf of Nash, Anthony" <gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of a.n...@ucl.ac.uk> wrote: >Justin and Mark, many thanks for your help. > >With regards to the parallelization, when did parallel membed become >supported? I¹ve just tried on 5.0.4

Re: [gmx-users] membed in mdrun VERSION 5.0.4

gt; >On 1/6/16 2:00 PM, Nash, Anthony wrote: >> Hi all, >> >> I thought I would try using the -membed option of mdrun to insert a >> helical dimer into a lipid bilayer. I¹ve followed the .mdp instructions >>on >> g_membed to generate my required .tpr file.

Re: [gmx-users] membed in mdrun VERSION 5.0.4

aking subsets from well chosen >index groups. > >Mark > >On Fri, 8 Jan 2016 13:35 Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 1/8/16 3:38 AM, Nash, Anthony wrote: >> > Many thanks Justin, that¹s solved it. >> > >> > Th

[gmx-users] membed in mdrun VERSION 5.0.4

Hi all, I thought I would try using the -membed option of mdrun to insert a helical dimer into a lipid bilayer. I¹ve followed the .mdp instructions on g_membed to generate my required .tpr file. Upon calling grommp I get: ERROR 1 [file membed_NPT.mdp]: Energy group exclusions are not (yet)

[gmx-users] inserting TM protein dimer into lipid bilayer using Gromacs

Dear all, It¹s been almost two and a 1/2 years since I tried my hands at TM protein modelling using Gromacs. What is the latest and most reliable means of inserting a TM alpha helical dimer into a lipid bilayer using Grimaces (if possible)? Thanks Anthony Dr Anthony Nash Department of

Re: [gmx-users] gmx mdrun std::bad_alloc whilst using PLUMED

't do well as the number >of atoms, CVs, CV complexity, and/or ranks increases. > >Mark > >On Tue, Nov 17, 2015 at 11:05 PM Nash, Anthony <a.n...@ucl.ac.uk> wrote: > >> Hi all, >> >> I am using PLUMED 2.2 and gromacs 5.0.4. For a while I had been testing >

Re: [gmx-users] restart issues with Gromacs

t (for "performance" or >erroneous reasons), then all bets are off. mdrun can't even know if it's >being lied to, because, well, it's being lied to... > >Mark > >On Sun, 15 Nov 2015 22:30 Nash, Anthony <a.n...@ucl.ac.uk> wrote: > >> Hi all, >

Re: [gmx-users] syntax for gmx distance

Thanks Teemu, That was spot on. I simply took the -select argument and dropped it into a text file then used the -sf option instead. Works perfectly. Thanks again Anthony On 14/09/2015 12:34, "Nash, Anthony" <a.n...@ucl.ac.uk> wrote: >Thanks Teemu, > >I’ll look int

[gmx-users] syntax for gmx distance

Dear all, I understand that this is quite a basic question, but I think I need a fresh set of eyes to figure out what¹s going on with gmx distance -select syntax. In my index file, I have 23 groups, two of which are ³ZINC² and ³CARBONYL² Based on numerous mail archive suggestions and the

Re: [gmx-users] Membrane protein insertion

Hi, I used this method recently and I was experiencing the same errors. As Mark suggested, makes sure your protein survives an energy minimisation. My error was a result of poor preparation of the .pdb file before running pdb2gmx. My .itp file contained a long bond between the C and N termini of

[gmx-users] Force field parameterisation

Hi all, I am trying to parameterise a new compound in Gromacs (theoretical compound - my experimental collaborators are still trying to purify and mass spec it) using the Amber 99sb force field. After asking about, I now know that in Amber I would take my QM structure run antechamber (or R.E.D

[gmx-users] High load imbalance: 31.8%

Hi all, I appear to have a very high load imbalance on some of my runs. Values starting from approx. 7% up to 31.8% with reported vol min/aver of around 0.6 (I haven¹t found one under half yet). When I look through the .log file at the start of the run I see: Initializing Domain Decomposition

Re: [gmx-users] High load imbalance: 31.8%

the things mdrun reports early and late. Mark On Thu, Aug 20, 2015 at 8:22 AM Nash, Anthony a.n...@ucl.ac.uk wrote: Hi all, I appear to have a very high load imbalance on some of my runs. Values starting from approx. 7% up to 31.8% with reported vol min/aver of around 0.6 (I haven¹t found

Re: [gmx-users] High load imbalance: 31.8%

; and GNU iso Intel compiler is often faster too.] Fixing the above issues should not only reduce imbalance but most likely also allow you to gain quite some simulation performance! Let us know if it worked. Cheers, -- Szilárd On Thu, Aug 20, 2015 at 5:08 PM, Nash, Anthony a.n...@ucl.ac.uk wrote

[gmx-users] distance issues with umbrella sampling

As far as I¹ve understood, the absolute distance reported using g_dist (note: alternative name in 5+) and the reported harmonic potential between two groups using pull code in grompp, doesn¹t always match. As such, I some times end up with neighbouring umbrella histograms practically sitting on

Re: [gmx-users] Change to umbrella sampling pull code

pull_group2_name = CARBONYL pull_coord1_init = 0 pull_coord1_rate = 0 pull_coord1_k = 1000 pull_nstxout= 1000 ; every 2 ps pull_nstfout= 1000 ; every 2 ps On 12/08/2015 21:26, Justin Lemkul jalem...@vt.edu wrote: On 8/12/15 3:20 PM, Nash, Anthony wrote: Hi Mark, Thanks

[gmx-users] Change to umbrella sampling pull code

Dear all, This is the first time I¹ve ran pull code (for umbrella sampling) since the change from Gromacs 4 to gromancs 5. I¹ve noticed some difference in the .mdp key-value parameters. Could I have a sanity check on the values below. Also, given that I want a harmonic potential between the two

Re: [gmx-users] Change to umbrella sampling pull code

for the pull group (pull-group1-name). Thanks Anthony Dr Anthony Nash Department of Chemistry University College London On 12/08/2015 19:35, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, On Wed, Aug 12, 2015 at 6:20 PM Nash, Anthony a.n...@ucl.ac.uk wrote: Dear all, This is the first time I¹ve

[gmx-users] Umbrella sampling sanity check

Hi all, I would appreciate a little sanity check for umbrella sampling pull code parameters. My reaction coordinate is defined as the distance between a globular soluble enzyme and a substrate in solution (water). I have already captured the individual windows using the trajectory generated from

Re: [gmx-users] Output frames within a defined distance range

[maxdistance], you end up with a .trr/.xtc/.gro file with only the frames that meets your distance criteria. Thanks Anthony Dr Anthony Nash Department of Chemistry University College London On 06/08/2015 13:03, Justin Lemkul jalem...@vt.edu wrote: On 8/6/15 3:56 AM, Nash, Anthony wrote

[gmx-users] Output frames within a defined distance range

Hi all, I¹m hoping to avoid putting together a simple script. Is there an option in Gromacs 5+ to only output frames from a trajectory if a certain criteria is meet? In this case, I only want the frames from a trajectory if the carbon-alpha of a particular GLY residue is within 0.8 - 1 nm of a

Re: [gmx-users] Enforced rotation errors

equations 6.46 and 6.47 in the GROMACS 5.0 PDF manual. Carsten On 20 Jul 2015, at 16:20, Nash, Anthony a.n...@ucl.ac.uk wrote: Dear All, I hope you can help. I am using 'flex' enforced rotation to rotate a cylindrical protein along the surface of a globular protein. Unfortunately my system

[gmx-users] Enforced rotation errors

Dear All, I hope you can help. I am using 'flex' enforced rotation to rotate a cylindrical protein along the surface of a globular protein. Unfortunately my system is experiencing what I can only assume is an IO problem: DD step 94 load imb.: force 2.9% pme mesh/force 0.677

[gmx-users] Gromacs with InflateGro

Hi all, I'm really struggling to get InflateGro to work in a dimer + lipid (no water or ions) system. The fault seems to happen when the regular expression to break the .gro entry reads in an entry from C to C1. I managed to generalise the regex further and now using substr to

[gmx-users] grompp_d fatal error in Amber FF

Hi all, Gromacs ver 5.0.4 - no forcefield modification (although I had, but changed back for testing purposes). Installed on a brand new machine: this is my laptop's first grompp. I was trying to inflate and deflate a bilayer using InflateGro but it through up a fatal error. I removed

Re: [gmx-users] grompp_d fatal error in Amber FF

...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Nash, Anthony [a.n...@ucl.ac.uk] Sent: 07 March 2015 08:05 To: gmx-us...@gromacs.org Subject: [gmx-users] grompp_d fatal error in Amber FF Hi all, Gromacs ver 5.0.4 - no forcefield modification (although I had

[gmx-users] g_sas values of zero and Warning

HI All, I'm trying to get a measure of the solvent accessible surface area of a protein's catalytic site. It is unknown precisely how the substrate actually fits in the site given that in the crystal structure the site it too enclosed for the bulky substrate. I am using a progressive measure

Re: [gmx-users] Changing number of processors after a job restart

-users] Changing number of processors after a job restart On 1/9/15 2:00 AM, Nash, Anthony wrote: Hi all, This is probably quite a fundamental bit of knowledge I am missing (and struggling to find). In an effort to just get a system running rather than waiting on a queue I am considering taking

Re: [gmx-users] Changing number of processors after a job restart

[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 09 January 2015 12:49 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Changing number of processors after a job restart On 1/9/15 7:46 AM, Nash, Anthony wrote: Hi Justin, I thought I would just give

[gmx-users] Changing number of processors after a job restart

Hi all, This is probably quite a fundamental bit of knowledge I am missing (and struggling to find). In an effort to just get a system running rather than waiting on a queue I am considering taking my job which has already ran for 48 hours and reducing the requested number of nodes. I would

Re: [gmx-users] Umbrella sampling along a dihedral angle

...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 28 December 2014 19:57 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Umbrella sampling along a dihedral angle On 12/27/14 1:50 PM, Nash, Anthony wrote: Hi Justin, I think I've shot myself in the foot and I'm trawling the gromacs

Re: [gmx-users] Umbrella sampling along a dihedral angle

-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 27 December 2014 14:49 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Umbrella sampling along a dihedral angle On 12/26/14 6:11 PM, Nash, Anthony wrote: Dear Gromacs community, Using enforced rotation

Re: [gmx-users] Umbrella sampling along a dihedral angle

sampling along a dihedral angle On 12/26/14 6:11 PM, Nash, Anthony wrote: Dear Gromacs community, Using enforced rotation potentials I have generated a really smooth rotation of my ligand the catalytic binding domain of my protein. I then put together a simple perl script to calculate

[gmx-users] Umbrella sampling along a dihedral angle

Dear Gromacs community, Using enforced rotation potentials I have generated a really smooth rotation of my ligand the catalytic binding domain of my protein. I then put together a simple perl script to calculate the dihedral angle of four particular atoms at each time step using g_angle.

[gmx-users] Renumber atom ids and charge group in topology (.itp)

Dear gromacs users, Renumbering the atom ids in a .gro file is very straight forwards, however, after cutting out the first 1/2 of my protein I am having great difficulty aligning my .itp file upon running grompp. Till this stage, it has been far easier for me to remove one particular domain

Re: [gmx-users] Renumber atom ids and charge group in topology (.itp)

and charge group in topology (.itp) On 12/16/14 9:54 AM, Nash, Anthony wrote: Dear gromacs users, Renumbering the atom ids in a .gro file is very straight forwards, however, after cutting out the first 1/2 of my protein I am having great difficulty aligning my .itp file upon running grompp. Till

Re: [gmx-users] Renumber atom ids and charge group in topology (.itp)

atom ids and charge group in topology (.itp) On 12/16/14 10:16 AM, Nash, Anthony wrote: Hi Justin, If there isn't there isn't. I was just hoping to save myself the effort of correcting for the missing atoms on the crystal structure and the conversion of HIS to HIE/HID

[gmx-users] Amber to Gromacs

Hi All, I've been thrown upon a project which requires the use of the Amber FF. I have a crystal structure .pdb and I wish to make a topology file using the AMBER ff99SB forcefield. The gromacs website directs me to the ffamber ports program, which seems to require Gromacs versions 3.1.4,

Re: [gmx-users] Amber to Gromacs

...@gromacs.org Subject: Re: [gmx-users] Amber to Gromacs On 4/30/14, 8:25 AM, Nash, Anthony wrote: Hi All, I've been thrown upon a project which requires the use of the Amber FF. I have a crystal structure .pdb and I wish to make a topology file using the AMBER ff99SB forcefield. The gromacs

Re: [gmx-users] Amber to Gromacs

] on behalf of Nash, Anthony [anthony.n...@warwick.ac.uk] Sent: 30 April 2014 14:09 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Amber to Gromacs Wow! I am out of date. As always, thanks for the help Justin. From: gromacs.org_gmx-users-boun