[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 of

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

om ids 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

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 > o

[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. Taking

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

g_gmx-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 enf

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

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 potentials I have generated a really smooth rotation > of my ligand the catalytic binding domain of my protein

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

users-boun...@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

[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 use

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

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 w

[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 of

[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 everyth

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, but

[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 explicit

[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 S

Re: [gmx-users] Enforced rotation errors

gt;rotation group, so that the slabs move with the rotation group. >See equations 6.46 and 6.47 in the GROMACS 5.0 PDF manual. > >Carsten > > >> On 20 Jul 2015, at 16:20, Nash, Anthony wrote: >> >> Dear All, >> >> I hope you can help. I am using 'flex&#

Re: [gmx-users] Enforced rotation errors

On 24/07/2015 00:16, "Nash, Anthony" wrote: >Dear Carsten, > >Thanks for that suggestion. Seems like that solved that particular >problem. Unfortunately though, my trajectory is not what I expected. > >I have been able to rotate the cylindrical ligand about it¹s p

[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 zin

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" wrote: > > >On 8/6/15 3:56 AM, Nash, Antho

[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

[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 gr

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

pull group (pull-group1-name). Thanks Anthony Dr Anthony Nash Department of Chemistry University College London On 12/08/2015 19:35, "Mark Abraham" wrote: >Hi, >On Wed, Aug 12, 2015 at 6:20 PM Nash, Anthony wrote: > >> Dear all, >> >> This is the first

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

l_group1_name = ZINC 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" wrote: > > >On 8/12/15 3:20 PM, Nash, Anthony

[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 to

[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 on

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

e can see both the >things mdrun reports early and late. > >Mark > >On Thu, Aug 20, 2015 at 8:22 AM Nash, Anthony 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% wit

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

: consider using FFTW even with the Intel compilers it's often >faster for our small FFTs than MKL; 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 performan

[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 too

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] 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 gromac

Re: [gmx-users] syntax for gmx distance

ul" wrote: > > >On 9/14/15 4:28 AM, Nash, Anthony wrote: >> 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. >

Re: [gmx-users] syntax for gmx distance

on -select syntax error invalid selection 'group' Thanks Anthony Dr Anthony Nash Department of Chemistry University College London On 14/09/2015 11:18, "Justin Lemkul" wrote: > > >On 9/14/15 4:28 AM, Nash, Anthony wrote: >> Dear all, >> >

Re: [gmx-users] syntax for gmx distance

defined in an index file. Thanks Anthony On 14/09/2015 11:57, "Justin Lemkul" wrote: > > >On 9/14/15 6:29 AM, Nash, Anthony wrote: >> Just downloaded the .tpr and .trr to my machine and tried exactly the >>same >> command: >> >> gmx distance -

Re: [gmx-users] syntax for gmx distance

(which your quotes in principle would do), but the error message >indicates that each word is getting parsed as a separate selection, so >your >shell is passing them as separate arguments. > >Best regards, >Teemu > >On Mon, Sep 14, 2015, 11:28 Nash, Anthony wrote: > >

Re: [gmx-users] syntax for gmx distance

were over lapping in all 3 dimensions given that I am using an absolute distance reaction coordinate. Thanks Anthony Dr Anthony Nash Department of Chemistry University College London On 14/09/2015 12:12, "Justin Lemkul" wrote: > > >On 9/14/15 7:08 AM, Nash, Anthony

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" wrote: >Thanks Teemu, > >I’ll look into this further.

[gmx-users] restart issues with Gromacs

Hi all, Running Grimaces 5.0.4 with PLUMED 2.2 on a cluster, number of ranks (MPI processes) is 24. The simulation successfully ran for the maximum cluster wall time (48 hours). I attempt to restart the simulations using the following command (with a sun microsystem grid engine submission script)

Re: [gmx-users] restart issues with Gromacs

an'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 wrote: > >> Hi all, >> >> Running Grimaces 5.0.4 with PLUMED 2.2 on a cluster, number of ranks >>(MPI >>

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

Hi all, I am using PLUMED 2.2 and gromacs 5.0.4. For a while I had been testing the viability of three collective variables for plumed, two dihedral angles and one centre of mass distance. After observing my dimer rotate about each other I decided it needed an intrahelical distance between two of

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

CVs to the PLUMED people. mdrun knows nothing at all about the PLUMED CVs. >The most likely explanation is that they have some data structure that >works OK on small scale problems, but which doesn't do well as the number >of atoms, CVs, CV complexity, and/or ranks increases. >

[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, 3.2.1

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 ff

Re: [gmx-users] Amber to Gromacs

kth.se] 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-

[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 pl

[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] 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 transiti

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

ng, please 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 o

[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] energy minimisation - LINCS WARNING

02/10/2016 23:16, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul" wrote: > >Please don't reply to digests or unrelated threads when starting a new >topic; it >creates a mess in the archive. > >On 10/2/16 6:11 PM, Nash, Anthon

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

se on behalf of Mark Abraham" wrote: >Hi, > >Sounds like you could check the output from that tool, and if it gave no >warning (or offers you no way to choose another rotamer) then you could >make some constructive feedback to its authors :-) > >Mark > >On Mon,

[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 parameter

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

From: 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, An

[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 modelling

Re: [gmx-users] CG Lincs errors

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 deal with the velocity of the >> recoil... >> >> Mark >> >> On Thu, 15 Dec 2016 23:06 Nash,

Re: [gmx-users] CG Lincs errors

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) > > >On 16-12-16 00:21, Nash, Anthony wrote: >> Alex and Mark, thanks for th

[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

[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 Chemistry

[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) impl

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

latest .trr, and thrown them both into VMD). Any thoughts? Many thanks Anthony On 06/01/2016 19:18, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul" wrote: > > >On 1/6/16 2:00 PM, Nash, Anthony wrote: >> Hi all, >> >> I

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

5 Justin Lemkul wrote: > >> >> >> On 1/8/16 3:38 AM, Nash, Anthony wrote: >> > Many thanks Justin, that¹s solved it. >> > >> > The simulation is now running, reporting that 8 POPC molecules and 12 >>SOL >> > molecules have been remov

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

ehalf of Nash, Anthony" 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 and I¹m getting the response: > >Reading file membed_NPT_B.tpr, VER

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

, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Nash, Anthony" 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 documentation, I can’t see a >reference to a parallelized version of mdrun -membed

[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] crosslinking polypeptide chains

ther than confusing the web >archives with replies to digests :-) > >On Tue, Feb 16, 2016 at 5:00 PM Nash, Anthony wrote: > >> 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 o

[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 pro

Re: [gmx-users] Unknown bond_atomtype

lf of Mark Abraham" wrote: >Hi, > >You've specified a type for your atom in [atoms] and elsewhere a bond that >uses it. Grompp has to find parameters for a bond between those two types, >etc. Choose existing types ;-) > >Mark > >On Wed, 17 Feb 2016 17:27 Nash, A

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" wrote: >Hi Mark, > >Thanks for the reply. I’m a little confused when you say “Choose existing >types”. Are you saying that

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" wrote: >Hi Mark, > >Further to my earlier email. I’ve an

Re: [gmx-users] Unknown bond_atomtype

he 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 wrote: > >> >> Dear Mark, >> >> >> I didn’t expect the problem was in ffnonbonded.i

Re: [gmx-users] Unknown bond_atomtype

Thanks Justin, I think that¹s everything I need to know. Kind regards Anthony Dr Anthony Nash Department of Chemistry University College London On 17/02/2016 22:18, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul" wrote: > > >On 2/

[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. F

[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. Th

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

mdp file) ― Dr Anthony Nash Department of Chemistry University College London On 24/02/2016 14:04, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham" wrote: >Hi, > >On Tue, Feb 23, 2016 at 11:03 AM Nash, Anthony wro

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" wrote: >Hi, > >On Wed, Feb 24, 2016 at 3:26 PM Nash, Anthony wrote: > >> Hi Mark, >> >> When you generate a peptide sequences in Avogadro the atom

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

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" wrote: >Hi, > >On Wed, Feb 24, 2016 at 4:00 PM Nash, Anthony wrote: > >> Hi Mark, >> >> I’m afraid I am not sure

[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] Minimising forces for vibrational normal mode analysis

may help to reach a >proper minimum. > >Cheers, > >Tsjerk > >On Sun, Feb 28, 2016 at 11:27 AM, Nash, Anthony wrote: > >> Hi all, >> >> I would like to pull out the vibrational normal modes using gromacs >>over a >> customised fragment to compare back

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

nimized structure as input for the nm run, then it seems >something's fishy. You could make a run input file with integrator=cg and >integrator=nm and compare the two tpr files to see if something was >changed >implicitly. > >Cheers, > >Tsjerk > >On Mon, Feb 29,

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

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" wrote: >Hi Tsjerk, > >The two .mdp files are virtually

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" wrote: > > >On 2/29/16 3:41 AM, Nash, Anthony wrote: >> Hi Tsjerk, >> >> The two .mdp files are virtually identical (the only exception being >>what &

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

t >them? > >Mark > >On Mon, 29 Feb 2016 15:39 Nash, Anthony wrote: > >> Hi Justin, >> >> After some digging I had found that link and made some adjustments (as >> presented in the later email). >> >> After a series of energy minimisations (incl

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" wrote: >Dear Mark and Justin, > >By removing the restraints (your suggestions) it appears to have worked! &g

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

gt;of >> the values is negative. Also, there were no eigenvalues set to zero >> (hence, I can only assume I have no negative eigenvalues). >> >> Would appreciate a little insight. >> Many thanks >> Anthony >> >> Dr Anthony Nash >> Department of

[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 secti

[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 e

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" wrote: > > >On 3/14/16 6:31 PM, Nash, Anthony wrote: >> Hi all, >> >> Is there a way of keeping the x, y box dimensions fi

[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

[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 _energy/01_

Re: [gmx-users] Thermodynamic integration

point is http://www.alchemistry.org/ which has quite a >lot of detail on relative alchemical free energy simulations (not only >TI). > >On Mon, 18 Apr 2016 09:27:02 + >"Nash, Anthony" wrote: > >> Hi all, >> >> I¹m looking for a guide on performing TI betwee

Re: [gmx-users] Thermodynamic integration

n. 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 wrote: > >> From the site, “..or the free energy of a mutation of a side chain.” >> >>

[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

[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 h

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

se on behalf of Justin Lemkul" 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 and >> NH) and acceptor (default O and N)? I don¹t seem to find any mention of &g

[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 a

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" wrote: > > >On 5/29/16 3:37 PM, Nash, Anthony wrote: >> Dear all, >> >>

[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, howev

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

ed, 1 Jun 2016 07:54:56 + >"Nash, Anthony" wrote: > >> In the tutorial, charges are off in the topology and the electrostatic >> coupling to lambda remains 0 throughout the 20 windows. I assume >> setting col_lambdas=0 0 0 Š was for that very reason I.e., the >

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

ct to get a true understanding of it yet :-) Thanks again Anthony On 01/06/2016 12:43, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Hannes Loeffler" wrote: > >Set the vector to all-zeroes (or ones). > > >On Wed, 1 Jun 2016 09:47:59 + >"

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" wrote: >On Wed, 1 Jun 2016 12:06:20 + >"Nash, Anthony" wrote: > >> vdw_lambdas = 0.00 0.05 0.

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

2016 15:00:51 + >"Nash, Anthony" wrote: > >> > This also assumes that >> >you have vanishing atoms only. If you have appearing atoms only you >> >would obviously have to revers the order, and when you have both you >> >will have to run with tw

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