Re: [gmx-users] correct rlist and Verlet scheme
Hi, You have to take into account that your box-solute distance is applied on both sides of your solute. This means that your minimum periodic distance will be 2*box-solute distance. Regards Dries On 19 Feb 2016 1:21 p.m., "Timofey Tyugashev" <tyugas...@niboch.nsc.ru> wrote: > And here my hope for quick and easy solution hath end. > All of the points you make ring true. Especially ones about software > engineering and funding in science (or maybe I'm more familiar with them). > > Actually, ne relatively recent paper, "Phosphorylation of PPARγ Affects > the Collective Motions of the PPARγ-RXRα-DNA Complex" ( > http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0123984#sec008), > uses AMBER99SB-ILDN with GROMACS 4.6 and Justin Lemkul is listed as the > first author. And the simulated structure is a protein-DNA complex. So it > should be very close to my case. > The one thing that looks strange to me: both rvdw (LJ interacions) and > box-solute distance set at 1.0 nm. Shouldn't the latter be larger to avoid > probable periodic image interactions problems? > Otherwise, looks like my settings are generally the same, except > forgetting that LINCS allows 2fs step. > > > 17.02.2016 19:45, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет: > >> Message: 4 >> Date: Wed, 17 Feb 2016 13:45:46 + >> From: Mark Abraham<mark.j.abra...@gmail.com> >> To:gmx-us...@gromacs.org,gromacs.org_gmx-users@maillist.sys.kth.se >> Subject: Re: [gmx-users] correct rlist and Verlet scheme >> Message-ID: >> < >> camnumarkusmbzbrvneie35aahdwkpo-mgbejewxzgpueew6...@mail.gmail.com> >> Content-Type: text/plain; charset=UTF-8 >> >> Hi, >> >> Yes, what you say is true, but very much "in short" and AFAIK true of all >> MD packages.:-) >> >> If e.g. AMBER (or anyone else) has a test suite for any force field, then >> we'll seriously consider implementing it, to e.g. verify before each >> release.:-) IMO, defining such a suite is a research topic itself - >> particularly as the original parameterizations did so in the context of >> limitations in the methods of the day. If a force field was parameterized >> with a fixed buffer because nobody then knew how large a buffer was >> necessary for a given quality of relevant observable, it does not follow >> that the only possible acceptable practice now is to use that fixed >> buffer. >> >> Similar considerations apply to things like e.g. the use of long-ranged >> corrections for dispersion interactions. e.g. AMBER99 was parameterized >> without such corrections, so probably has built into its parameters some >> compensating errors, and any kind of validation-by-replication should in >> principle not use such corrections. But these days, I think that nobody >> would actually recommend parameterizing a force field without something >> like that, and experience suggests that using one is an improvement, even >> if though the change is not officially sanctioned anywhere that I know of. >> IMO showing that some range of force fields shows satisfactory agreement >> with experiment under certain .mdp setting combinations is useful evidence >> of an implementation that is valid, and that is what one can see in the >> literature. >> >> The state of the art in software engineering is that nobody much has time >> to test all the things that they'd like to test. (One large exception is >> software for control of devices that potentially affect human health.) >> Scientific software development has additional challenges because the >> people doing it are often lacking in formal training in best practice, and >> have to appear to publish science, in order to keep attracting funding, >> and >> this directly conflicts with spending time on good software engineering >> practice that granting and tenure committees will ignore later in their >> careers... >> >> Mark >> >> On Wed, Feb 17, 2016 at 1:01 PM Timofey Tyugashev<tyugas...@niboch.nsc.ru >> > >> wrote: >> >> >In short, FFs were tested to some degree when they were added in GROMACS >>> >to reproduce AMBER results, but there is no certainty if they actually >>> >do this now and 'correct' mdp settings to run them are unknown. For any >>> >of the versions that are listed in GROMACS. >>> >Is that correct, or I'm missing something in translation? >>> > >>> >16.02.2016 18:03,gromacs.org_gmx-users-requ...@maillist.sys.kth.se >>> ?: >>> >>>> > >Message: 2 >>>> > &
Re: [gmx-users] correct rlist and Verlet scheme
And here my hope for quick and easy solution hath end. All of the points you make ring true. Especially ones about software engineering and funding in science (or maybe I'm more familiar with them). Actually, ne relatively recent paper, "Phosphorylation of PPARγ Affects the Collective Motions of the PPARγ-RXRα-DNA Complex" (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0123984#sec008), uses AMBER99SB-ILDN with GROMACS 4.6 and Justin Lemkul is listed as the first author. And the simulated structure is a protein-DNA complex. So it should be very close to my case. The one thing that looks strange to me: both rvdw (LJ interacions) and box-solute distance set at 1.0 nm. Shouldn't the latter be larger to avoid probable periodic image interactions problems? Otherwise, looks like my settings are generally the same, except forgetting that LINCS allows 2fs step. 17.02.2016 19:45, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет: Message: 4 Date: Wed, 17 Feb 2016 13:45:46 + From: Mark Abraham<mark.j.abra...@gmail.com> To:gmx-us...@gromacs.org,gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] correct rlist and Verlet scheme Message-ID: <camnumarkusmbzbrvneie35aahdwkpo-mgbejewxzgpueew6...@mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Hi, Yes, what you say is true, but very much "in short" and AFAIK true of all MD packages.:-) If e.g. AMBER (or anyone else) has a test suite for any force field, then we'll seriously consider implementing it, to e.g. verify before each release.:-) IMO, defining such a suite is a research topic itself - particularly as the original parameterizations did so in the context of limitations in the methods of the day. If a force field was parameterized with a fixed buffer because nobody then knew how large a buffer was necessary for a given quality of relevant observable, it does not follow that the only possible acceptable practice now is to use that fixed buffer. Similar considerations apply to things like e.g. the use of long-ranged corrections for dispersion interactions. e.g. AMBER99 was parameterized without such corrections, so probably has built into its parameters some compensating errors, and any kind of validation-by-replication should in principle not use such corrections. But these days, I think that nobody would actually recommend parameterizing a force field without something like that, and experience suggests that using one is an improvement, even if though the change is not officially sanctioned anywhere that I know of. IMO showing that some range of force fields shows satisfactory agreement with experiment under certain .mdp setting combinations is useful evidence of an implementation that is valid, and that is what one can see in the literature. The state of the art in software engineering is that nobody much has time to test all the things that they'd like to test. (One large exception is software for control of devices that potentially affect human health.) Scientific software development has additional challenges because the people doing it are often lacking in formal training in best practice, and have to appear to publish science, in order to keep attracting funding, and this directly conflicts with spending time on good software engineering practice that granting and tenure committees will ignore later in their careers... Mark On Wed, Feb 17, 2016 at 1:01 PM Timofey Tyugashev<tyugas...@niboch.nsc.ru> wrote: >In short, FFs were tested to some degree when they were added in GROMACS >to reproduce AMBER results, but there is no certainty if they actually >do this now and 'correct' mdp settings to run them are unknown. For any >of the versions that are listed in GROMACS. >Is that correct, or I'm missing something in translation? > >16.02.2016 18:03,gromacs.org_gmx-users-requ...@maillist.sys.kth.se ?: > >Message: 2 > >Date: Tue, 16 Feb 2016 11:23:06 + > >From: Mark Abraham<mark.j.abra...@gmail.com> > >To:gmx-us...@gromacs.org,gromacs.org_gmx-users@maillist.sys.kth.se > >Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 142, Issue > > 76 > >Message-ID: > > < >camnumasutdhr8sot1qt4xdczogsdjsfgo8umiuhrpffxxfa...@mail.gmail.com> > >Content-Type: text/plain; charset=UTF-8 > > > >Hi, > > > >The ports of all the AMBER force fields were all tested to reproduce >AMBER > >when when they were added to GROMACS. Many of our regressiontests use >those > >force fields, so there is reason to expect that they all continue to >work. > >The Verlet scheme is tested to implement what the documentation says it > >does. There have been bugs introduced (and fixed) in how GROMACS > >preprocessing tools implement the requirements of AMBER force fields, > >including ILDN. > &g
Re: [gmx-users] correct rlist and Verlet scheme
Yes, the implementation is clearly different from AMBER and I don't really want to try hard to get Identical results. I picked AMBER ff99sb-ildn because it looked to be both quite popular for protein and nucleic acids simulations (going by the number of cites for its paper) and reasonably recent. Our home-grown software uses a derivative of ff99 for implicit solvent calculations, so I wanted to spare myself the trouble of parametrising non-standard residues and ligands by using a ff from the same family and using already existing ones. So i'm interested in simply running it in gromacs with adequate setup. And I'm just not sure what .mdp parameters to set. For P.S.: Different version of it. Authors use different cutoffs. 17.02.2016 23:16, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет: Message: 1 Date: Wed, 17 Feb 2016 18:07:28 +0100 From: Szil?rd P?ll<pall.szil...@gmail.com> To: Discussion list for GROMACS users<gmx-us...@gromacs.org> Cc: Discussion list for GROMACS users <gromacs.org_gmx-users@maillist.sys.kth.se> Subject: Re: [gmx-users] correct rlist and Verlet scheme Message-ID:
Re: [gmx-users] correct rlist and Verlet scheme
romacs.org_gmx-users@maillist.sys.kth.se >>> > Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 142, Issue >>> > 76 >>> > Message-ID: >>> > < >>> camnumasutdhr8sot1qt4xdczogsdjsfgo8umiuhrpffxxfa...@mail.gmail.com> >>> > Content-Type: text/plain; charset=UTF-8 >>> > >>> > Hi, >>> > >>> > The ports of all the AMBER force fields were all tested to reproduce >>> AMBER >>> > when when they were added to GROMACS. Many of our regressiontests use >>> those >>> > force fields, so there is reason to expect that they all continue to >>> work. >>> > The Verlet scheme is tested to implement what the documentation says it >>> > does. There have been bugs introduced (and fixed) in how GROMACS >>> > preprocessing tools implement the requirements of AMBER force fields, >>> > including ILDN. >>> > >>> > To be able to say "this force field is tested to work correctly with this >>> > cutoff scheme in this version of GROMACS" requires the community to agree >>> > on what that means, e.g. a large collection of single-point >>> energies+forces >>> > agree to within a certain precision, and simulations done in a particular >>> > model physics produce these ensembles with these observables, etc. That >>> > hasn't happened yet. As far as I know, the ability of the different AMBER >>> > code versions to correctly continue to implement all the AMBER force >>> fields >>> > has a similar kind of question mark over it. Just having the same name is >>> > not enough;-) >>> > >>> > Mark >>> > >>> > On Tue, Feb 16, 2016 at 11:17 AM Timofey Tyugashev< >>> tyugas...@niboch.nsc.ru> >>> > wrote: >>> > >>> >> >So, are there any other Amber force fields more suitable and more >>> tested >>> >> >for GROMACS? >>> >> > >>> >> >15.02.2016 21:00,gromacs.org_gmx-users-requ...@maillist.sys.kth.se >>> ?: >>> >>> > >Message: 1 >>> >>> > >Date: Mon, 15 Feb 2016 13:15:02 + >>> >>> > >From: Mark Abraham<mark.j.abra...@gmail.com> >>> >>> > >To:gmx-us...@gromacs.org,gromacs.org_gmx-users@maillist.sys.kth.se >>> >>> > >Subject: Re: [gmx-users] correct rlist and Verlet scheme >>> >>> > >Message-ID: >>> >>> > > < >>> >> >camnumatmbmgvbfj49ez+4k_bftdmkyfyiw5iz-eecwicujb...@mail.gmail.com> >>> >>> > >Content-Type: text/plain; charset=UTF-8 >>> >>> > > >>> >>> > >Hi, >>> >>> > > >>> >>> > >On Mon, Feb 15, 2016 at 12:17 PM Timofey Tyugashev< >>> >> >tyugas...@niboch.nsc.ru> >>> >>> > >wrote: >>> >>> > > >>> >>>>> > >> >I've studied the relevant sections of the manual, but I don't >>> consider >>> >>>>> > >> >myself to be familiar enough with this field to successfully >>> guess the >>> >>>>> > >> >right settings. >>> >>>>> > >> > >>> >>>>> > >> >ff99sb-ildn is included in the gromacs distribution, so >>> shouldn?t be >>> >>>>> > >> >there some recommended settings for it? >>> >>> > >Ideally, yes. But nobody has made a particular effort for that >>> >> >combination. >>> >>> > > >>> >>> > >Or else how was it tested to run >>> >>>>> > >> >properly? >>> >>>>> > >> > >>> >>> > >In principle, one would have to e.g. show that >>> >>> > >https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970904/ can be >>> >> >replicated. >>> >>> > >That's not a straightforward proposition... >>> >> >-- >>> >> >Gromacs Users mailing list >>> >> > >>> >> >* Please search the archive at >>> >> >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> >> >posting! >>> >> > >>> >> >* Can't post? Readhttp://www.gromacs.org/Support/Mailing_Lists >>> >> > >>> >> >* For (un)subscribe requests visit >>> >> >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> >> >send a mail togmx-users-requ...@gromacs.org. >>> >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >> mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] correct rlist and Verlet scheme
In short, FFs were tested to some degree when they were added in GROMACS to reproduce AMBER results, but there is no certainty if they actually do this now and 'correct' mdp settings to run them are unknown. For any of the versions that are listed in GROMACS. Is that correct, or I'm missing something in translation? 16.02.2016 18:03, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет: Message: 2 Date: Tue, 16 Feb 2016 11:23:06 + From: Mark Abraham<mark.j.abra...@gmail.com> To:gmx-us...@gromacs.org,gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 142, Issue 76 Message-ID: <camnumasutdhr8sot1qt4xdczogsdjsfgo8umiuhrpffxxfa...@mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Hi, The ports of all the AMBER force fields were all tested to reproduce AMBER when when they were added to GROMACS. Many of our regressiontests use those force fields, so there is reason to expect that they all continue to work. The Verlet scheme is tested to implement what the documentation says it does. There have been bugs introduced (and fixed) in how GROMACS preprocessing tools implement the requirements of AMBER force fields, including ILDN. To be able to say "this force field is tested to work correctly with this cutoff scheme in this version of GROMACS" requires the community to agree on what that means, e.g. a large collection of single-point energies+forces agree to within a certain precision, and simulations done in a particular model physics produce these ensembles with these observables, etc. That hasn't happened yet. As far as I know, the ability of the different AMBER code versions to correctly continue to implement all the AMBER force fields has a similar kind of question mark over it. Just having the same name is not enough;-) Mark On Tue, Feb 16, 2016 at 11:17 AM Timofey Tyugashev<tyugas...@niboch.nsc.ru> wrote: >So, are there any other Amber force fields more suitable and more tested >for GROMACS? > >15.02.2016 21:00,gromacs.org_gmx-users-requ...@maillist.sys.kth.se ?: > >Message: 1 > >Date: Mon, 15 Feb 2016 13:15:02 + > >From: Mark Abraham<mark.j.abra...@gmail.com> > >To:gmx-us...@gromacs.org,gromacs.org_gmx-users@maillist.sys.kth.se > >Subject: Re: [gmx-users] correct rlist and Verlet scheme > >Message-ID: > > < >camnumatmbmgvbfj49ez+4k_bftdmkyfyiw5iz-eecwicujb...@mail.gmail.com> > >Content-Type: text/plain; charset=UTF-8 > > > >Hi, > > > >On Mon, Feb 15, 2016 at 12:17 PM Timofey Tyugashev< >tyugas...@niboch.nsc.ru> > >wrote: > > > >> >I've studied the relevant sections of the manual, but I don't consider > >> >myself to be familiar enough with this field to successfully guess the > >> >right settings. > >> > > >> >ff99sb-ildn is included in the gromacs distribution, so shouldn?t be > >> >there some recommended settings for it? > >Ideally, yes. But nobody has made a particular effort for that >combination. > > > >Or else how was it tested to run > >> >properly? > >> > > >In principle, one would have to e.g. show that > >https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970904/ can be >replicated. > >That's not a straightforward proposition... >-- >Gromacs Users mailing list > >* Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >posting! > >* Can't post? Readhttp://www.gromacs.org/Support/Mailing_Lists > >* For (un)subscribe requests visit >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >send a mail togmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] correct rlist and Verlet scheme
; for the > integration of the equations of motion with timesteps of 2.0, 2.0, > and 6.0 fs for the bonded, short-range nonbonded, and long-range > nonbonded interactions, respectively. To check for potential biases > introduced by long-range interactions between peptides in periodic > images, we repeated these simulations for four of the amino acids > (Xaa: Ile, Leu, Asp, and Asn) using a larger box with side length 37 > Å. We found that the results of these control simulations were > within error of those using the smaller box sizes. > > > 12.02.2016 22:06, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет: > > Message: 1 > > Date: Fri, 12 Feb 2016 14:09:28 + > > From: Mark Abraham<mark.j.abra...@gmail.com> > > To:"gromacs.org_gmx-users@maillist.sys.kth.se" > > <gromacs.org_gmx-users@maillist.sys.kth.se>," > gmx-us...@gromacs.org" > > <gmx-us...@gromacs.org> > > Subject: Re: [gmx-users] correct rlist and Verlet scheme > > Message-ID: > > < > camnumar1-sqgc4_tmwjtzv1uwy6+nkbwxayz2h+paba3y-k...@mail.gmail.com> > > Content-Type: text/plain; charset=UTF-8 > > > > Hi, > > > > As Adam says, you want to understand the reason why the forcefield > > specifies the settings it does. For example, until at least AMBER 2003, > > their force field papers did not specify PME parameters more precisely > than > > "x nm cutoff was used." If PME was used at all.;-) So you can be guided > > also by the parameters reported by successful users of these forcefields, > > particularly those of the various force field and software authors. > > > > rlist is a free parameter so long as you choose it large enough to avoid > > missing a significant number of interactions over the lifetime of the > list > > - but it affects performance strongly. rcoulomb can be varied for > > equivalent accuracy if matching changes occur to PME parameters. VDW > > parameters should generally follow the force field derivation precisely > > (but add long-range corrections for dispersion) - GROMACS will not change > > these. You should check out the background information in the reference > > manual, sections 3.4.2 and 3.17.5 > > > > Mark > > > > On Fri, Feb 12, 2016 at 1:56 PM Hardy, Adam<ah...@hw.ac.uk> wrote: > > > >> >There are people more qualified than me to explain the fine details of > >> >this, but in brief: > >> > > >> >Verlet on it's own doesn't adjust rvdw or rcoloumb (rcoulomb may be > >> >adjusted if you rae using PME for the coulomb interactions), but by > default > >> >it will adjust the neighbour list cut-off (rlist) to remain with a > >> >specified energy tolerance given by verlet-buffer-tolerance. You can > >> >overide this behaviour and manually set rlist by setting > >> >verlet-buffer-tolerance=-1. Whether you want to or not will depend on > why > >> >the forcefield has specified that cut-off, it may well be to achieve > the > >> >same purpose, which is to propely catch interactions between atoms > which > >> >move in or out of the cut-off radii between rlist update steps. > >> > > >> >Adam > >> > > >> > > >> >From:gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > >> >gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of > Timofey > >> >Tyugashev<tyugas...@niboch.nsc.ru> > >> >Sent: 12 February 2016 12:47 > >> >To:gromacs.org_gmx-users@maillist.sys.kth.se > >> >Subject: [gmx-users] correct rlist and Verlet scheme > >> > > >> >I have trouble in correctly setting cut-offs with Verlet scheme to > match > >> >force-field specific settings. > >> >It automatically adjusts cut-off and it looks like they change their > >> >values from ones recommended for the force field. > >> >Is there a way to correct it and set up them properly? > >> > > >> >The paper on FF lists 1.0 nm for short-range electrostatic and LJ > >> >interactions. > >> >The cut-off of pairlists is 1.05 nm. > >> > > >> >The forcefield is 99SB-ILDN and is present in GROMACS itself. > >> >-- > >> >Gromacs Users mailing list > >> > > >> >* Please search the archive at > >> >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> >posting! > >> >
Re: [gmx-users] correct rlist and Verlet scheme
I've studied the relevant sections of the manual, but I don't consider
myself to be familiar enough with this field to successfully guess the
right settings.
ff99sb-ildn is included in the gromacs distribution, so shouldn’t be
there some recommended settings for it? Or else how was it tested to run
properly?
For now I've settled on the following parameters (the following is
copied from mdout.mdp):
; NEIGHBORSEARCHING PARAMETERS
; cut-off scheme (Verlet: particle based cut-offs, group: using charge
groups)
cutoff-scheme= Verlet
; nblist update frequency
nstlist = 40
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz, no, xy
pbc = xyz
periodic-molecules = no
; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,
; a value of -1 means: use rlist
verlet-buffer-tolerance = 0.005
; nblist cut-off
rlist= 1.0
; long-range cut-off for switched potentials
rlistlong= 1.05
nstcalclr= -1
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
coulomb-modifier = Potential-shift-Verlet
rcoulomb-switch = 0
rcoulomb = 1.0
; Relative dielectric constant for the medium and the reaction field
epsilon-r= 1
epsilon-rf = 0
; Method for doing Van der Waals
vdw-type = Cut-off
vdw-modifier = Potential-shift-Verlet
; cut-off lengths
rvdw-switch = 0
rvdw = 1.0
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1
; Separate tables between energy group pairs
energygrp-table =
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.16
; FFT grid size, when a value is 0 fourierspacing will be used
fourier-nx = 0
fourier-ny = 0
fourier-nz = 0
; EWALD/PME/PPPM parameters
pme_order= 4
ewald-rtol = 1e-05
ewald-rtol-lj= 0.001
lj-pme-comb-rule = Geometric
ewald-geometry = 3d
epsilon-surface = 0
And this is what the paper on it says:
Each system was equilibrated at 300 K and 1 atm with 2.4 ns of MD
simulation in the NPT ensemble. Then, MD simulations were carried
out in the NVT ensemble for 720 ns using the Nosé-Hoover thermostat
with a relaxation time of 1 ps. All simulations were performed using
the Desmond MD program^16
<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970904/#b16> version
2.1.1.0 and either the Amber ff99SB^7
<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970904/#b7> or the
modified Amber ff99SB force field described herein, which we have
termed ff99SB-ILDN. All bonds involving hydrogen atoms were
constrained with the SHAKE algorithm.^17
<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970904/#b17> A cutoff
of 10 Å was used for the Lennard-Jones interaction and the
short-range electrostatic interactions. The smooth particle mesh
Ewald method^18
<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970904/#b18> with a
32 × 32 × 32 grid and a fourth-order interpolation scheme was used
to compute the long-range electrostatic interactions. The pairlists
were updated every 10 fs with a cutoff of 10.5 Å. We used a
multistep RESPA scheme^19
<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970904/#b19> for the
integration of the equations of motion with timesteps of 2.0, 2.0,
and 6.0 fs for the bonded, short-range nonbonded, and long-range
nonbonded interactions, respectively. To check for potential biases
introduced by long-range interactions between peptides in periodic
images, we repeated these simulations for four of the amino acids
(Xaa: Ile, Leu, Asp, and Asn) using a larger box with side length 37
Å. We found that the results of these control simulations were
within error of those using the smaller box sizes.
12.02.2016 22:06, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет:
Message: 1
Date: Fri, 12 Feb 2016 14:09:28 +
From: Mark Abraham<mark.j.abra...@gmail.com>
To:"gromacs.org_gmx-users@maillist.sys.kth.se"
<gromacs.org_gmx-users@maillist.sys.kth.se>,
"gmx-us...@gromacs.org"
<gmx-us...@gromacs.org>
Subject: Re: [gmx-users] correct rlist and Verlet scheme
Message-ID:
<camnumar1-sqgc4_tmwjtzv1uwy6+nkbwxayz2h+paba3y-k...@mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi,
As Adam says, you want to understand the reason why the forcefield
specifies the settings it does. For example, until at least AMBER 2003,
their force field papers did not specify PME parameters more precisely than
"x nm cutoff was
[gmx-users] correct rlist and Verlet scheme
I have trouble in correctly setting cut-offs with Verlet scheme to match force-field specific settings. It automatically adjusts cut-off and it looks like they change their values from ones recommended for the force field. Is there a way to correct it and set up them properly? The paper on FF lists 1.0 nm for short-range electrostatic and LJ interactions. The cut-off of pairlists is 1.05 nm. The forcefield is 99SB-ILDN and is present in GROMACS itself. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] correct rlist and Verlet scheme
There are people more qualified than me to explain the fine details of this, but in brief: Verlet on it's own doesn't adjust rvdw or rcoloumb (rcoulomb may be adjusted if you rae using PME for the coulomb interactions), but by default it will adjust the neighbour list cut-off (rlist) to remain with a specified energy tolerance given by verlet-buffer-tolerance. You can overide this behaviour and manually set rlist by setting verlet-buffer-tolerance=-1. Whether you want to or not will depend on why the forcefield has specified that cut-off, it may well be to achieve the same purpose, which is to propely catch interactions between atoms which move in or out of the cut-off radii between rlist update steps. Adam From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Timofey Tyugashev <tyugas...@niboch.nsc.ru> Sent: 12 February 2016 12:47 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] correct rlist and Verlet scheme I have trouble in correctly setting cut-offs with Verlet scheme to match force-field specific settings. It automatically adjusts cut-off and it looks like they change their values from ones recommended for the force field. Is there a way to correct it and set up them properly? The paper on FF lists 1.0 nm for short-range electrostatic and LJ interactions. The cut-off of pairlists is 1.05 nm. The forcefield is 99SB-ILDN and is present in GROMACS itself. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] correct rlist and Verlet scheme
Hi, As Adam says, you want to understand the reason why the forcefield specifies the settings it does. For example, until at least AMBER 2003, their force field papers did not specify PME parameters more precisely than "x nm cutoff was used." If PME was used at all. ;-) So you can be guided also by the parameters reported by successful users of these forcefields, particularly those of the various force field and software authors. rlist is a free parameter so long as you choose it large enough to avoid missing a significant number of interactions over the lifetime of the list - but it affects performance strongly. rcoulomb can be varied for equivalent accuracy if matching changes occur to PME parameters. VDW parameters should generally follow the force field derivation precisely (but add long-range corrections for dispersion) - GROMACS will not change these. You should check out the background information in the reference manual, sections 3.4.2 and 3.17.5 Mark On Fri, Feb 12, 2016 at 1:56 PM Hardy, Adam <ah...@hw.ac.uk> wrote: > There are people more qualified than me to explain the fine details of > this, but in brief: > > Verlet on it's own doesn't adjust rvdw or rcoloumb (rcoulomb may be > adjusted if you rae using PME for the coulomb interactions), but by default > it will adjust the neighbour list cut-off (rlist) to remain with a > specified energy tolerance given by verlet-buffer-tolerance. You can > overide this behaviour and manually set rlist by setting > verlet-buffer-tolerance=-1. Whether you want to or not will depend on why > the forcefield has specified that cut-off, it may well be to achieve the > same purpose, which is to propely catch interactions between atoms which > move in or out of the cut-off radii between rlist update steps. > > Adam > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Timofey > Tyugashev <tyugas...@niboch.nsc.ru> > Sent: 12 February 2016 12:47 > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] correct rlist and Verlet scheme > > I have trouble in correctly setting cut-offs with Verlet scheme to match > force-field specific settings. > It automatically adjusts cut-off and it looks like they change their > values from ones recommended for the force field. > Is there a way to correct it and set up them properly? > > The paper on FF lists 1.0 nm for short-range electrostatic and LJ > interactions. > The cut-off of pairlists is 1.05 nm. > > The forcefield is 99SB-ILDN and is present in GROMACS itself. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
