[gmx-users] wrong number of control atoms (2 iso 3) on line: 2 3 N -C -CA
Mehreen Jan
mehreen_jan1990 at yahoo.com
Tue Feb 9 11:42:03 CET 2016
gromacs4.5.5
phosphorylated protein - protein-protein interaction
phosphate at "SEP" and TPO
forcefield 43A1p download from gromacs web page
command:
pdb2gmx -f protein.pdb -p protein.top -o protein.gro
fatal error:
error in hdb file ./gromos43A1p.ff/aminoacid.hdb
wrong number of control atoms (2 iso 3) on line:
2 3 N -C -CA
i read manual but i can't remove error. i did not get the point how to remove error
HDB file s given:
ABU 1
1 1 H N -C CA
ACEH 1
3 4 HA CA C O
AIB 1
1 1 H N -C CA
ALA 1
1 1 H N -C CA
ARG 4
1 1 H N -C CA
1 1 HE NE CD CZ
2 3 HH1 NH1 CZ NE
2 3 HH2 NH2 CZ NE
ARGN 4
1 1 H N -C CA
1 1 HE NE CD CZ
1 2 HH1 NH1 CZ NE
2 3 HH2 NH2 CZ NE
ASN 2
1 1 H N -C CA
2 3 HD2 ND2 CG CB
ASP 1
1 1 H N -C CA
ASP1 2
1 1 H N -C CA
1 2 HD1 OD1 CG CB
ASPH 2
1 1 H N -C CA
1 2 HD2 OD2 CG CB
BEN 7
1 1 H2 C2 C1 C3
1 1 H3 C3 C2 C4
1 1 H4 C4 C3 C5
1 1 H5 C5 C4 C6
1 1 H6 C6 C5 C1
2 3 H1 N1 C7 C1
2 3 H2 N2 C7 C1
CYS2 1
1 1 H N -C CA
CYSH 2
1 1 H N -C CA
1 2 HG SG CB CA
FAD 7
2 3 HN6 AN6 AC6 AC5
1 2 HO2* AO2* AC2* AC1*
1 2 HO3* AO3* AC3* AC2*
1 2 H4* O4* C4* C5*
1 2 H3* O3* C3* C4*
1 2 H2* O2* C2* C3*
1 2 H3 N3 C4 C4A
GLN 2
1 1 H N -C CA
2 3 HE2 NE2 CD CG
GLU 1
1 1 H N -C CA
GLUH 2
1 1 H N -C CA
1 2 HE2 OE2 CD CG
GLY 1
1 1 H N -C CA
HEME 4
1 1 HHA CHA C1A C4D
1 1 HHB CHB C1B C4A
1 1 HHC CHC C1C C4B
1 1 HHD CHD C1D C4C
HIS1 2
1 1 H N -C CA
1 1 HD1 ND1 CG CE1
HISA 2
1 1 H N -C CA
1 1 HD1 ND1 CG CE1
HISB 2
1 1 H N -C CA
1 1 HE2 NE2 CE1 CD2
HISH 3
1 1 H N -C CA
1 1 HD1 ND1 CG CE1
1 1 HE2 NE2 CE1 CD2
HO4 1
3 10 HW OW
HOH 1
2 7 HW OW
HYP 1
1 2 HD1 OD1 CG CB
ILE 1
1 1 H N -C CA
LEU 1
1 1 H N -C CA
LYS 2
1 1 H N -C CA
2 4 HZ NZ CE CD
LYSH 2
1 1 H N -C CA
3 4 HZ NZ CE CD
MET 1
1 1 H N -C CA
NAC 1
1 1 H N -C CA
NACH 2
1 1 H N -C CA
3 4 HA CA N NH
NH2 1
2 3 H N -C -CA
PHE 6
1 1 H N -C CA
1 1 HD1 CD1 CG CE1
1 1 HD2 CD2 CG CE2
1 1 HE1 CE1 CD1 CZ
1 1 HE2 CE2 CD2 CZ
1 1 HZ CZ CE1 CE2
PHEU 1
1 1 H N -C CA
PHL 7
1 1 H N -C CA
1 1 HD1 CD1 CG CE1
1 1 HD2 CD2 CG CE2
1 1 HE1 CE1 CD1 CZ
1 1 HE2 CE2 CD2 CZ
1 1 HZ CZ CE1 CE2
1 2 HY OY CX CA
SER 2
1 1 H N -C CA
1 2 HG OG CB CA
TFE 1
1 2 H O CH2 C
THR 2
1 1 H N -C CA
1 2 HG1 OG1 CB CA
TRP 7
1 1 H N -C CA
1 1 HD1 CD1 CG NE1
1 1 HE1 NE1 CD1 CE2
1 1 HE3 CE3 CD2 CZ3
1 1 HZ3 CZ3 CE3 CH2
1 1 HH2 CH2 CZ3 CZ2
1 1 HZ2 CZ2 CE2 CH2
TRPU 2
1 1 H N -C CA
1 1 HE1 NE1 CD1 CE2
TYR 6
1 1 H N -C CA
1 1 HD1 CD1 CG CE1
1 1 HD2 CD2 CG CE2
1 1 HE1 CE1 CD1 CZ
1 1 HE2 CE2 CD2 CZ
1 2 HH OH CZ CE1
TYRU 2
1 1 H N -C CA
1 2 HH OH CZ CE1
VAL 1
1 1 H N -C CA
SEP 1
1 1 H N -C CA
TPO 1
1 1 H N -C CA
PTR 5
1 1 H N -C CA
1 1 HD1 CD1 CG CE1
1 1 HD2 CD2 CG CE2
1 1 HE1 CE1 CD1 CZ
1 1 HE2 CE2 CD2 CZ
SEPH 2
1 1 H N -C CA
1 2 H3P O3P P OG
TPOH 2
1 1 H N -C CA
1 2 H3P O3P P OG1
PTRH 6
1 1 H N -C CA
1 1 HD1 CD1 CG CE1
1 1 HD2 CD2 CG CE2
1 1 HE1 CE1 CD1 CZ
1 1 HE2 CE2 CD2 CZ
1 2 H3P O3P P OH
thank you
mehreen
--------------------------------------------
On Tue, 9/2/16, gromacs.org_gmx-users-request at maillist.sys.kth.se <gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
Subject: gromacs.org_gmx-users Digest, Vol 142, Issue 44
To: gromacs.org_gmx-users at maillist.sys.kth.se
Received: Tuesday, 9 February, 2016, 2:47 PM
Send gromacs.org_gmx-users mailing
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Today's Topics:
1. Fw: wrong number of control
atomes in hdb (Mehreen Jan)
----------------------------------------------------------------------
Message: 1
Date: Tue, 9 Feb 2016 09:47:18 +0000 (UTC)
From: Mehreen Jan <mehreen_jan1990 at yahoo.com>
To: <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] Fw: wrong number of control
atomes in hdb
Message-ID:
<1051880887.1321499.1455011238466.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset=UTF-8
--- On Tue, 9/2/16, Mehreen Jan <mehreen_jan1990 at yahoo.com>
wrote:
> From: Mehreen Jan <mehreen_jan1990 at yahoo.com>
> Subject: wrong number of control atomes in
hdb
> To: "Mehreen Jan" <mehreen_jan1990 at yahoo.com>
> Received: Tuesday, 9 February, 2016, 2:44 PM
>
> --------------------------------------------
> On Tue, 9/2/16, Mehreen Jan <mehreen_jan1990 at yahoo.com>
> wrote:
>
> Subject: Re: gromacs.org_gmx-users Digest, Vol
142, Issue
> 42
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Received: Tuesday, 9 February, 2016, 2:43 PM
>
> ? Subject: Fw: wrong number of control
> atomes in
> > hdb
> > >
>
>
> > > > > respected sir!
> > > > > thank you for advise
> > > > >
> > > > > thank you sir for advise i
just copy
> folder
> > 43A1p
> > > and
> > > > past
> > > > > in top file and in GMXLIB and
it work
> error
> > is
> > > solved
> > > > know
> > > > > after running the command:
> > > > >? pdb2gmx -f protein.top -o
> protein.gro
> > > > > select the forcefield 43A1p
the
> following
> > error
> > > is
> > > > occurs
> > > > > i google it but i can't get
it exactly
> and i
> > read
> > > > manual but
> > > > > difficult to understand
because of?
> no
> > experience
> > > .
> > > > > respected sir kiendle find
the
> attachment .
> > > > >
> > > > >? ?
> > > > > error in hdb file
> > ./gromacs43A1p/aminoacid.hdb:
> > > > >
> > > > > wrong number of control atoms
(2 iso3)
> on
> > line:
> > > > > 2 3 N -C -CA
> --------------------------------------------
> On Tue, 9/2/16, gromacs.org_gmx-users-request at maillist.sys.kth.se
> <gromacs.org_gmx-users-request at maillist.sys.kth.se>
> wrote:
>
> ? Subject: gromacs.org_gmx-users Digest, Vol 142,
Issue
> 42
> ? To: gromacs.org_gmx-users at maillist.sys.kth.se
> ? Received: Tuesday, 9 February, 2016, 1:20 PM
> ?
> ? Send gromacs.org_gmx-users mailing
> ? list submissions to
> ? ??? gromacs.org_gmx-users at maillist.sys.kth.se
> ?
> ? To subscribe or unsubscribe via the World Wide Web,
> visit
> ? ??? https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> ? or, via email, send a message with subject or body
> 'help'
> ? to
> ? ??? gromacs.org_gmx-users-request at maillist.sys.kth.se
> ?
> ? You can reach the person managing the list at
> ? ??? gromacs.org_gmx-users-owner at maillist.sys.kth.se
> ?
> ? When replying, please edit your Subject line so it
is
> more
> ? specific
> ? than "Re: Contents of gromacs.org_gmx-users
> digest..."
> ?
> ?
> ? Today's Topics:
> ?
> ? ???1. Different results for same protein's
> ? simulation in??? 4.6.5 and
> ? ? ? ? 5.0.4 (SAPNA BORAH)
> ? ???2. Re: Different results for same
> ? protein's simulation in 4.6.5
> ? ? ? ? and 5.0.4 (Mark Abraham)
> ? ???3. Re: creating representative structures
> ? (Mark Abraham)
> ? ???4. Re: pp/pme ratio differences between
> ? gromacs 5.0.x and??? 5.1.x
> ? ? ? ? (Mark Abraham)
> ? ???5. Re: Fwd: FW: PME settings in free
> ? energy calculations
> ? ? ? ? (Mark Abraham)
> ?
> ?
> ?
>
----------------------------------------------------------------------
> ?
> ? Message: 1
> ? Date: Tue, 9 Feb 2016 12:52:41 +0530
> ? From: SAPNA BORAH <sapnauser365 at gmail.com>
> ? To: gmx-users at gromacs.org
> ? Subject: [gmx-users] Different results for same
> protein's
> ? simulation
> ? ??? in??? 4.6.5 and 5.0.4
> ? Message-ID:
> ? ??? <CAEL2Jf7tNT94MnMbW3h6YnsKL63tC0+xeZQhMFnre7WVpngVCQ at mail.gmail.com>
> ? Content-Type: text/plain; charset=UTF-8
> ?
> ? Dear all,
> ?
> ? I have tried running the same protein in the two
> versions
> of
> ? gromacs 4.6.5
> ? and 5.0.4. Now, both the runs are producing entirely
> ? different results.
> ?
> ? The results till equilibration are same.
> ?
> ? After the run however, there is a total change in
> the
> ? production results. I
> ? have used the same mdp files.
> ?
> ? I have rerun the systems and they still produce
> similar
> ? results in the same
> ? version.
> ?
> ? The protein structure is a modelled one.
> ?
> ?
> ? Thanks in advance.
> ? Sapna.
> ?
> ? Sapna Mayuri Borah
> ? c/o Dr. A. N. Jha
> ? Research student
> ? Tezpur University,
> ? India
> ?
> ?
> ? ------------------------------
> ?
> ? Message: 2
> ? Date: Tue, 09 Feb 2016 07:37:54 +0000
> ? From: Mark Abraham <mark.j.abraham at gmail.com>
> ? To: gmx-users at gromacs.org
> ? Subject: Re: [gmx-users] Different results for same
> ? protein's
> ? ??? simulation in 4.6.5 and 5.0.4
> ? Message-ID:
> ? ???
> ? <CAMNuMARf1tJD+thVQvoSuN9SPkYhW06Oo2w6=bbFh6UdvFsyYw at mail.gmail.com>
> ? Content-Type: text/plain; charset=UTF-8
> ?
> ? Hi,
> ?
> ? This is quite normal.
> ?
>
http://www.gromacs.org/Documentation/Terminology/Reproducibility.
> ? You
> ? should see a similar range of variation in the
> trajectories
> ? produced in the
> ? two versions that are incompletely sampling the same
> ? ensemble, but one can
> ? say very little about two single observed
> trajectories
> ? sampled from them.
> ?
> ? Mark
> ?
> ? On Tue, Feb 9, 2016 at 8:23 AM SAPNA BORAH <sapnauser365 at gmail.com>
> ? wrote:
> ?
> ? > Dear all,
> ? >
> ? > I have tried running the same protein in the
> two
> ? versions of gromacs 4.6.5
> ? > and 5.0.4. Now, both the runs are producing
> entirely
> ? different results.
> ? >
> ? > The results till equilibration are same.
> ? >
> ? > After the run however, there is a total change
> in the
> ? production results. I
> ? > have used the same mdp files.
> ? >
> ? > I have rerun the systems and they still produce
> similar
> ? results in the same
> ? > version.
> ? >
> ? > The protein structure is a modelled one.
> ? >
> ? >
> ? > Thanks in advance.
> ? > Sapna.
> ? >
> ? > Sapna Mayuri Borah
> ? > c/o Dr. A. N. Jha
> ? > Research student
> ? > Tezpur University,
> ? > India
> ? > --
> ? > 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-request at gromacs.org.
> ? >
> ?
> ?
> ? ------------------------------
> ?
> ? Message: 3
> ? Date: Tue, 09 Feb 2016 07:46:31 +0000
> ? From: Mark Abraham <mark.j.abraham at gmail.com>
> ? To: gmx-users at gromacs.org
> ? Subject: Re: [gmx-users] creating representative
> structures
> ? Message-ID:
> ? ??? <CAMNuMAQgBnhazSinyeDzpLdwEZDuNSbDmZ77bLJhO5qkt7w06g at mail.gmail.com>
> ? Content-Type: text/plain; charset=UTF-8
> ?
> ? Hi,
> ?
> ? On Mon, Feb 8, 2016 at 6:24 PM Shyno Mathew <sm3334 at columbia.edu>
> ? wrote:
> ?
> ? > Dear all,
> ? >
> ? >
> ? > I have few questions regarding creating
> representative
> ? structures. For
> ? > simplicity, let?s say I have a trajectory of 5
> frames:
> ? >
> ? > 1.? ? ???g_rmsf: After reading
> ? previous posts, here is what I understood.
> ? > The average structures calculated using g_rmsf
> (by
> ? specifying ?ox) is
> ? > literally the average of x, y, z co-ordinates
of
> each
> ? atom over all the 5
> ? > frames in my case. Energy minimizing this
> averaged
> ? structure might give a
> ? > meaningful structure?
> ? >
> ?
> ? It'll give a structure that conforms to chemical
> ? expectations, but the
> ? "meaning" of any plausible candidate for an
> "average"
> ? structure is doubtful
> ? at best. If there is a group of microstates that
> share
> ? structural
> ? similarity, it does not follow that RMSD will
> identify it,
> ? nor that
> ? averaging of coordinates will produce a meaningful
> average.
> ? What is the RMS
> ? average position of a set of balls being juggled?
> ?
> ?
> ? > 2.? ? ???g_cluster: Here I am
> ? using the gromos method. I read the reference
> ? > paper (Daura et al.). Using gromos method and
by
> just
> ? specifying ?cl (not
> ? > ?av) I get the middle structures for each
> cluster.
> ? Let?s say I get 2
> ? > clusters using rmsd 0.16. Now the
> representative
> ? structures of these two
> ? > clusters (obtained in the out.pdb) should
> exactly
> ? correspond to two frames
> ? > in my original trajectory (the one with 5
> frames)?
> ? >
> ?
> ? I don't know, but you should try it and see. Make a
> ? trajectory of a water
> ? molecule as PDB with a few frames and play with
> editing
> the
> ? coordinates by
> ? hand and passing them to g_cluster until you are
> happy you
> ? understand how
> ? it works.
> ?
> ?
> ? > 3.? ? ???My final question is
> ? regarding how exactly g_cluster works, here
> ? > is what I understand from Daura et al.
> ? >
> ? > If I use g_cluster with gromos method, the code
> will
> ? look for neighbors of
> ? > each frame within specified cutoff.
> ? >
> ? > Assume the first time the code finds the
> following:
> ? >
> ? > frame 0 has two neighbors: frames 2,3? within
> ? cutoff
> ? >
> ? > frame 1 has three neighbors: frames 2, 3, 4
> within
> ? cutoff
> ? >
> ? > frame 2 has four neighbors: frames 0, 1, 3, 4
> within
> ? cutoff
> ? >
> ? > frame 3 has three neighbors: frames 0,1, 2
> within
> ? cutoff
> ? >
> ? > frame 4 has two neighbors: frames 1,2 within
> cutoff
> ? >
> ? >
> ? >
> ? > Since frame 2 has the highest number of
> neighbors,
> it's
> ? considered the
> ? > center cluster and this frame along with
> neighbors
> are
> ? removed. The same
> ? > calculation is performed on the remaining
frames
> if I
> ? had more frames.
> ? >
> ?
> ? No idea, but again try it and see.
> ?
> ? Mark
> ?
> ?
> ? > Thanks in advance for your help,
> ? >
> ? > Sincerely,
> ? >
> ? > Shyno
> ? >
> ? > --
> ? > Shyno Mathew
> ? > PhD Candidate
> ? > Department of Chemical Engineering
> ? > Graduate Assistant
> ? > Office of Graduate Student Affairs
> ? > The Fu Foundation School Of Engineering and
> Applied
> ? Science
> ? > Columbia University
> ? > --
> ? > 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-request at gromacs.org.
> ?
> ?
> ? ------------------------------
> ?
> ? Message: 4
> ? Date: Tue, 09 Feb 2016 07:59:18 +0000
> ? From: Mark Abraham <mark.j.abraham at gmail.com>
> ? To: gmx-users at gromacs.org
> ? Subject: Re: [gmx-users] pp/pme ratio differences
> between
> ? gromacs
> ? ??? 5.0.x and??? 5.1.x
> ? Message-ID:
> ? ??? <CAMNuMAReBaEYCG6fok-3MG5w0p4NUWats93xQvY6ge3ngPpNhw at mail.gmail.com>
> ? Content-Type: text/plain; charset=UTF-8
> ?
> ? Hi,
> ?
> ? On Sun, Feb 7, 2016 at 8:00 PM Johannes Wagner <johannes.wagner at h-its.org>
> ? wrote:
> ?
> ? > hey guys,
> ? > came across an issue with pp/pme ratio
> difference
> from
> ? 5.0 to 5.1. For a
> ? > system running on 2 nodes with a pp/pme ratio
> of
> 80:16
> ? on 5.0, the same
> ? > thing starts with 72:24 on gromacs 5.1. The 5.1
> run
> has
> ? a much higher load
> ? > imbalance and is hence slower. Are there known
> changes
> ? from 5.0 to 5.1 in
> ? > the pp/pme ratio that cause this?
> ? >
> ?
> ? Yes and no. Even on only two nodes, your
observations
> can
> be
> ? affected by
> ? network congestion, so I would investigate whether
> you can
> ? reproduce the
> ? observations. The changes that I identified that had
> the
> ? capacity to change
> ? performance are noted at
> ?
>
http://manual.gromacs.org/documentation/5.1/ReleaseNotes/performance.html.
> ? For example, if you're using LINCS then the SIMD
> ? improvements there affect
> ? only the PP ranks so it might seem to the auto-tuner
> that
> ? it's more
> ? efficient to use fewer PP ranks. Then later some
kind
> of
> ? load imbalance has
> ? a stronger effect. The interactions of DD DLB and
> PME
> tuning
> ? are complex,
> ? and we can't rule out that there's a problem that we
> should
> ? fix. But we
> ? can't say much without being able to compare some
> ? (reproducible) log files.
> ?
> ? Mark
> ?
> ? cheers, johannes
> ? >
> ? > --
> ? > 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-request at gromacs.org.
> ? >
> ?
> ?
> ? ------------------------------
> ?
> ? Message: 5
> ? Date: Tue, 09 Feb 2016 08:20:17 +0000
> ? From: Mark Abraham <mark.j.abraham at gmail.com>
> ? To: gmx-users at gromacs.org
> ? Subject: Re: [gmx-users] Fwd: FW: PME settings in
> free
> ? energy
> ? ??? calculations
> ? Message-ID:
> ? ??? <CAMNuMAQ9oJbDrAuW9danqaXXmhTNw=zsJXZ9S-tDw9WaRsrsgg at mail.gmail.com>
> ? Content-Type: text/plain; charset=UTF-8
> ?
> ? Hi,
> ?
> ? On Fri, Feb 5, 2016 at 1:32 PM Dries Van Rompaey
> <dries.vanrompaey at gmail.com>
> ? wrote:
> ?
> ? > Hi,
> ? >
> ? > The corresponding mdp output section is:
> ? >
> ? > ; 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
> ? > vdwtype? ? ? ? ? ? ?
> ? ? ? = cutoff
> ? > vdw-modifier? ? ? ? ?
> ? ???= Potential-switch
> ? > ; cut-off lengths
> ? > rvdw-switch? ? ? ? ? ?
> ? ? = 0.9
> ? > 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? ? ? ?
> ? ???= 0.08
> ? > ; 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? ? ? ? ? ?
> ? ? ? = 6
> ? > ewald_rtol? ? ? ? ? ?
> ? ???= 1e-06
> ? > ewald-rtol-lj? ? ? ? ? ?
> ? = 0.001
> ? > lj-pme-comb-rule? ? ?
> ? ???= Geometric
> ? > ewald-geometry? ? ? ?
> ? ???= 3d
> ? > epsilon_surface? ? ? ? ? = 0
> ?
> ?
> ? That all seems reasonable.
> ?
> ?
> ? > I evaluated the energy with:
> ? >
> ? > Verlet - settings above (with standard
> ? verlet-buffer-tolerance)
> ? > @ s0 legend "Coulomb-14"
> ? > @ s1 legend "Coulomb (SR)"
> ? > @ s2 legend "Coul. recip."
> ? >? ???0.000000?
> ? -2221.295898? -546205.250000? 9271.518555
> ? > Total -? ???539155.0273
> ? >
> ? > Verlet - settings above - with
> verlet-buffer-tolerance
> ? -1
> ? >? ???0.000000?
> ? -2221.295898? -546205.250000? 9271.516602
> ? > Total???-539155.029296
> ? >
> ?
> ? That kind of agreement is expected, but perhaps
> might
> agree
> ? exactly if you
> ? were following
> ? http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
> ?
> ? Group - settings above
> ? > @ s0 legend "Coulomb-14"
> ? > @ s1 legend "Coulomb (SR)"
> ? > @ s2 legend "Coul. recip."
> ? >? ???0.000000?
> ? -2221.296387? -487993.593750? -48931.437500
> ? > Total -539146.3276
> ? >
> ?
> ? The difference in those components is expected - in
> PME
> you
> ? have to avoid
> ? counting contributions in the long-range part from
> pairs
> ? that are excluded
> ? e.g. from the bonded topology. The two schemes
handle
> this
> ? in different
> ? places. Their sum should match (within the limits of
> ? floating-point
> ? arithmetic), and a relative error under 1e-5 for
> summing a
> ? few million
> ? numbers is acceptable for judging the equivalence of
> the
> ? implementations.
> ?
> ? Verlet - 3 nm cutoffs, 2.9 vdwswitch,
> coulomb-modifier
> none
> ? > @ s0 legend "Coulomb-14"
> ? > @ s1 legend "Coulomb (SR)"
> ? >? ???0.000000?
> ? -2221.295898? -774817.875000
> ? > Total -777039.1709
> ? >
> ? >
> ? > Group - 3 nm cutoffs, 2.9 vdwswitch,
> coulomb-modifier
> ? none
> ? > @ s0 legend "Coulomb-14"
> ? > @ s1 legend "Coulomb (SR)"
> ? >? ???0.000000?
> ? -2221.296387? -553398.125000
> ? > Total -555619.4214
> ? >
> ?
> ? That ought to agree much better, but It's hard to
> speculate
> ? on where the
> ? problem lies without seeing log files. Please upload
> some
> to
> ? a file sharing
> ? service and post the links here (list doesn't take
> ? attachments)
> ?
> ? Mark
> ?
> ?
> ? > Thanks,
> ? >
> ? > Dries
> ? >
> ? > On 4 February 2016 at 14:48, Michael Shirts
> <mrshirts at gmail.com>
> ? wrote:
> ? >
> ? > > Also, can you be more precise about the
> ? inconsistency in the outputs
> ? > > you are seeing (with numerical output from
> GROMACS
> ? and analysis code).
> ? > >
> ? > > On Thu, Feb 4, 2016 at 6:17 AM, Michael
> Shirts
> ? <mrshirts at gmail.com>
> ? > wrote:
> ? > > > Hi, Dries-
> ? > > >
> ? > > > Can you print out what the
> corresponding
> ? section of mdout.mdp look
> ? > like?
> ? > > >
> ? > > > Have you? tried using the cutoffs
> above
> ? with group cutoffs, and seen
> ? > > > what the difference is?
> ? > > >
> ? > > > On Thu, Feb 4, 2016 at 4:59 AM, Dries
> Van
> ? Rompaey
> ? > > > <dries.vanrompaey at gmail.com>
> ? wrote:
> ? > > >> Hi,
> ? > > >>
> ? > > >> I'm using PME with the default
> ? Potential-Shift-Verlet modifier. If I'm
> ? > > >> interpreting the manual and
> comments on
> ? the mailinglist correctly, the
> ? > > >> settings for rcoulomb-switch
> shouldn't
> ? affect this and PME-switching
> ? > > >> shouldn't be necessary (although
> there
> ? seems to have been some
> ? > > discussion
> ? > > >> about this, https://gerrit.gromacs.org/#/c/2220/). Has a consensus
> ? > been
> ? > > >> reached elsewhere?
> ? > > >>
> ? > > >> Current nonbonded settings in my
> .mdp
> ? files are:
> ? > > >> ; Electrostatics
> ? > > >> coulombtype? ? ? ?
> ? ? ? ? = PME
> ? > > >> rcoulomb? ? ? ?
> ? ? ? ? ? ? ? = 1.0
> ? > > >>
> ? > > >> ; van der Waals
> ? > > >> vdwtype? ? ? ? ?
> ? ? ? ? ? ? = cutoff
> ? > > >> vdw-modifier? ? ? ?
> ? ? ? = Potential-switch
> ? > > >> rvdw-switch? ? ? ?
> ? ? ? ? = 0.9
> ? > > >> rvdw? ? ? ? ?
> ? ? ? ? ? ? ?
> ? ???= 1.0
> ? > > >>
> ? > > >> ; Apply long range dispersion
> corrections
> ? for Energy and Pressure
> ? > > >> DispCorr? ? ? ?
> ? ? ? ? ? ? = EnerPres
> ? > > >>
> ? > > >> ; Spacing for the PME/PPPM FFT
> grid
> ? > > >> fourierspacing? ? ? ?
> ? ???= 0.08
> ? > > >>
> ? > > >> ; EWALD/PME/PPPM parameters
> ? > > >> pme_order? ? ? ?
> ? ? ? ? ? = 6
> ? > > >> ewald_rtol? ? ? ?
> ? ? ? ? ???= 1e-06
> ? > > >> epsilon_surface? ? ?
> ? ? = 0
> ? > > >>
> ? > > >> Thanks in advance,
> ? > > >>
> ? > > >> Dries
> ? > > >>
> ? > > >> On 4 February 2016 at 00:56,
> Michael
> ? Shirts <mrshirts at gmail.com>
> ? > wrote:
> ? > > >>
> ? > > >>> Hi, Dries-
> ? > > >>>
> ? > > >>> Questions like this are
> probably
> best
> ? answered on the gmx-users list.
> ? > > >>> I can't say too much for the
> Verlet
> ? scheme -- I know that it was
> ? > > >>> relatively recently adapted
> for
> free
> ? energies, and there may be some
> ? > > >>> combinations of settings that
> could
> ? give unanticipated results.
> ? > > >>>
> ? > > >>> Pretty much all of our
> experience
> ? about nonbonded calculations and
> ? > > >>> free energies is collected in
> the
> ? following paper:
> ? > > >>> http://pubs.acs.org/doi/abs/10.1021/ct4005068. We used
> ? the group
> ? > > >>> cutoff scheme since that was
> the
> only
> ? one that was supported in
> ? > > >>> GROMACS at the time.
> ? > > >>>
> ? > > >>> Since you haven't sent any
> files,
> ? it's hard to tell what is actually
> ? > > >>> going on. The one thing that
> has a
> ? tendency to happen with the more
> ? > > >>> recent update schemes is if
> you set
> a
> ? potential modifier that is a
> ? > > >>> switch, but don't set the
> distance
> ? the switch starts at, then it is
> ? > > >>> automatically set to zero.?
> ? Check the mdout.mdp to see if this is
> ? > > >>> happening.
> ? > > >>>
> ? > > >>> > From: Van Rompaey Dries
> <Dries.VanRompaey at uantwerpen.be>
> ? > > >>> Date: Wednesday, February 3,
> 2016
> at
> ? 12:34 PM
> ? > > >>> To: Michael Shirts <michael.shirts at colorado.edu>
> ? > > >>> Subject: PME settings in free
> energy
> ? calculations
> ? > > >>>
> ? > > >>> Dear prof. Shirts,
> ? > > >>>
> ? > > >>> I'm currently trying to
figure
> out
> ? the PME settings for a relative
> ? > > >>> free binding energy
simulation
> I'm
> ? working on. I took the parameters
> ? > > >>> from Matteo Aldeghi's
> ? > > >>> paper(
> ? > > >>>
> ? > >
> ? > http://pubs.rsc.org/en/content/articlelanding/2015/sc/c5sc02678d#!divAbstract
> ? > > >>> )
> ? > > >>> as a starting point (adapted
> for
> the
> ? Verlet scheme by scaling the
> ? > > >>> fourierspacing to 0.08 and
> setting
> ? coulomb = rvdw = 1.0). I then
> ? > tried
> ? > > >>> to verify these settings by
> comparing
> ? a single point energy
> ? > > >>> calculation with these
> settings and
> ? one with very long coulomb
> ? > cutoffs
> ? > > >>> as recommended on
> alchemistry.org.
> ? > > >>>
> ? > > >>> Unfortunately, I can't seem
to
> get
> ? this quite right. I'm getting
> ? > > >>> differences in the hundreds
> of
> ? kj/mol, leading me to suspect I'm
> ? > doing
> ? > > >>> something wrong. I'm
> calculating
> the
> ? energy values by extracting
> ? > > >>> CoulombSR and Coul-recip from
> the
> ? energy.xvg files. I've tried
> ? > > >>> calculating the energy with
> coulomb
> ? cutoffs at 3 nm and 10 nm, but
> ? > > >>> agreement with the PME
> results
> ? remains rather poor. David Mobley
> ? > > >>> mentioned you performed
> extensive
> ? research on this topic, and I'm
> ? > > >>> hoping you could point me in
> the
> ? right direction.
> ? > > >>>
> ? > > >>> Thanks in advance,
> ? > > >>>
> ? > > >>> Dries
> ? > > >>>
> ? > > >>>
> ? > > >>>
> ? > > >>> ~~~~~~~~~~~~~~~~
> ? > > >>> Michael Shirts
> ? > > >>> Associate Professor
> ? > > >>> michael.shirts at colorado.edu
> ? > > >>> Phone: (303) 735-7860
> ? > > >>> Office: JSCBB D317
> ? > > >>> Department of Chemical and
> Biological
> ? Engineering
> ? > > >>> University of Colorado
> Boulder
> ? > > >>> --
> ? > > >>> Gromacs Users mailing list
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