[gmx-users] gromos43a1p-4.5.1.tgz can alos used for TPO and SEP
Mehreen Jan
mehreen_jan1990 at yahoo.com
Wed Feb 3 08:45:05 CET 2016
repected sir !
i also used the following forefield but it did not work. same error residue TPO is not found in residues topology database
gromos43a1p-4.5.1.tgz
Force field files for Gromos96 43a1p, re-formatted to be compatible with newer versions of Gromacs (4.0 and beyond). This particular archive organizes the files such that they are compatible with version 4.5.x. Please note that the parameters are unmodified relative to what was contributed by Graham Smith. I take no credit for these parameters; I just made the files compatible with the current version of Gromacs. This version includes files that were missing in the previous tarball.
--------------------------------------------
On Tue, 2/2/16, 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 10
To: gromacs.org_gmx-users at maillist.sys.kth.se
Received: Tuesday, 2 February, 2016, 8:16 PM
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Today's Topics:
1. Verlet scheme and relative free binding
energy (Dries Van Rompaey)
2. Re: Nstlist and constrain simulations
(Michail Palaiokostas Avramidis)
3. Re: Verlet scheme and relative free
binding energy (Mark Abraham)
4. Re: Verlet scheme and relative free
binding energy (Mark Abraham)
----------------------------------------------------------------------
Message: 1
Date: Tue, 2 Feb 2016 15:19:11 +0100
From: Dries Van Rompaey <dries.vanrompaey at gmail.com>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Verlet scheme and relative free binding
energy
Message-ID:
<CAJefogf0RigA1gsyb1SNr2win=r9PeWFC_iMj=t5J=10UPs-xA at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi gmx-users,
I have a question regarding the correct treatment of
cut-offs for
amber99sb-ildn in relative free binding energy calculations,
using the
verlet scheme. Many articles seem to use a 1.2 nm cutoff for
coulomb
interactions and a vdw interaction switched off between 0.9
and 1 nm (for
instance: DOI: 10.1039/c5sc02678d). However, this setup is
only possible
with the now deprecated group scheme.
I haven't been able to find any papers using amber99sb-ildn
for relative
free energy calculations with a setup suitable for verlet
scheme. Does
anyone have experience with such a setup for relative free
binding energy
calculations?
Thanks in advance,
Dries
------------------------------
Message: 2
Date: Tue, 2 Feb 2016 14:34:16 +0000
From: Michail Palaiokostas Avramidis <m.palaiokostas at qmul.ac.uk>
To: <gmx-users at gromacs.org>
Subject: Re: [gmx-users] Nstlist and constrain simulations
Message-ID: <56B0BE68.2070109 at qmul.ac.uk>
Content-Type: text/plain; charset="utf-8"
On 02/02/16 14:04, Szil?rd P?ll wrote:
> On Tue, Feb 2, 2016 at 11:17 AM, Michail Palaiokostas
Avramidis
> <m.palaiokostas at qmul.ac.uk>
wrote:
>> Hi Mark and thank you for your answer.
>> Please see below :)
>>
>> On 01/02/16 18:28, Mark Abraham wrote:
>>> Hi,
>>>
>>> On Mon, Feb 1, 2016 at 6:42 PM Michail
Palaiokostas Avramidis <
>>> m.palaiokostas at qmul.ac.uk>
wrote:
>>>
>>>> Dear GMX users,
>>>>
>>>>
>>>> I would like to ask about your opinion on
the size of the neighbour list
>>>> (nstlist).
>>>>
>>>>
>>>> I am running constraint simulations
>>> What do you mean by a "constraint simulation?"
>> Sorry, I should have been clearer. I am using the
z-constraint method in
>> which I constrain the permeant along the z-axis in
various positions and
>> I record the constraint force. Similar to umbrella
sampling but with
>> constrained distances between the permeant and
membrane.
>>>> of a permeant along a lipid bilayer. In the
initial setup the system runs
>>>> on NPT and nstlist 10 (which GROMACS
changes to 40 automatically). With
>>>> this setup my simulation is very fast but
always crashes at various points
>>>> with the same way always. Initially it
gives some LINCS warnings and then
>>>> it gives an error that a particle
"communicated to PME rank 2 are more than
>>>> 2/3 times the cut-off out of the domain
decomposition cell".
>>>>
>>> Usually this indicates your setup is unstable
e.g. see
>>> http://www.gromacs.org/Documentation/Terminology/Blowing_Up.
I'll proceed
>>> by assuming you're very confident that your
membrane system has had a
>>> suitable few dozen+ nanoseconds of
equilibration ;-)
>> Yes absolutely confident. The system does not crash
with unconstrained
>> simulations. The membrane-solvent system is well
equilibrated for 1?s
>> and then, after I introduce the permeant, I perform
an energy
>> minimization and a short 500ps NPT-Berendsen
equilibration to relax the
>> pressure that the permeant might have introduced.
>>> When I see the last pdb steps before crash,
sometimes there seem to be
>>>> overlaps between the permeants and the
lipids and then system explosions
>>>> and PBChaos. Other times it is not so
dramatic.
>>>>
>>>>
>>>> So the question is, should I be
conservative with the nstlist? When I run
>>>> NPT simulations and change the nstlist to
1, the system does not fail.
>>>> Alternatively, if I change to NVT and
nstlist to 10, again the system runs
>>>> successfully. But NVT and 40 crashes.
>>>>
>>> This might all be a wild goose chase. If you
are pulling permeants into the
>>> membrane, then that creates pressure on the
membrane and perhaps
>>> destabilizes the pressure coupling. If that's
with Parrinello-Rahman then
>>> it can easily oscillate out of control, ending
up violating the assumptions
>>> under which the code is written.
>> Yes, this is why I run an small equilibration in
the beginning. And to
>> be honest, technically, I do not pull the
permeants. For each position,
>> I add it to the system in VMD, and then run the
>> minimization-equilibration-production sequence.
>>> Since GROMACS was doing the nstlist update
automatically, I thought it was
>>>> a "safe" option. Based on the
above,however, I believe that since the
>>>> simulation runs with constraints, the
system is more sensitive and thus the
>>>> nstlist should be smaller. Can anyone
validate that my hypothesis is
>>>> correct?
>>>>
>>> On the limited evidence available, I think your
observations are more
>>> likely to be symptoms of the problem than the
problem itself. How does e.g.
>>> one permeant molecule behave?
>> Once again sorry for not being clear. The plural in
permeants comes from
>> the fact that I test several molecules (e.g. water,
ammonia etc) but it
>> is only one per simulation/system.
>>
>> So, you think that the updating of neighbour list,
shouldn't affect the
>> problem?
> No, it should not; for details see manual section
3.4.2.
>
> What GROMACS version are you using?
I am using GROMACS 5.1.1
The thing is that I see a difference on the stability when I
change
nstlist. In fact it is not crashing when I reduce the
nstlist. And to be
honest intuitively it should affect it. Anyway I looked at
the manual
but I couldn't see anything directly related to the question
posed here.
If as you say, it doesn't affect it, then I am really
unaware of the
reason behind the constant LINCS warnings and systems
explosion in a
well equilibrated system..
In any case, thank you for your answer.
Kind Regards,
Michail
>> Kind Regards,
>> Michail
>>
>>> Mark
>>>
>>> Thanks in advance.
>>>> Kind Regards,
>>>>
>>>> Michail
>>>>
>>>>
>>>>
-------------------------------------------------------------------
>>>> Michail (Michalis) Palaiokostas
>>>> PhD Student
>>>> School of Engineering and Materials
Science
>>>> Queen Mary University of London
>>>>
-------------------------------------------------------------------
>>>> --
>>>> Gromacs Users mailing list
>>>>
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>>>> posting!
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------------------------------
Message: 3
Date: Tue, 02 Feb 2016 15:16:02 +0000
From: Mark Abraham <mark.j.abraham at gmail.com>
To: gmx-users at gromacs.org,
gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] Verlet scheme and relative free
binding
energy
Message-ID:
<CAMNuMAR1WcYWi1po-iBUM9ex+mVf_7gDO559892q+aLq5p8a4A at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi,
One can vary PME parameters for electrostatics at
approximately constant
accuracy by scaling the Fourier grid spacing and short-range
cutoff by the
same factor. (This is what mdrun does during PME tuning.) So
you can use
rcoulomb = 1.0 and spacing scaled accordingly.
In GROMACS 2016, the Verlet scheme will likely support
specifying such
setups directly.
Mark
On Tue, Feb 2, 2016 at 3:19 PM Dries Van Rompaey <dries.vanrompaey at gmail.com>
wrote:
> Hi gmx-users,
>
> I have a question regarding the correct treatment of
cut-offs for
> amber99sb-ildn in relative free binding energy
calculations, using the
> verlet scheme. Many articles seem to use a 1.2 nm
cutoff for coulomb
> interactions and a vdw interaction switched off between
0.9 and 1 nm (for
> instance: DOI: 10.1039/c5sc02678d). However, this setup
is only possible
> with the now deprecated group scheme.
>
> I haven't been able to find any papers using
amber99sb-ildn for relative
> free energy calculations with a setup suitable for
verlet scheme. Does
> anyone have experience with such a setup for relative
free binding energy
> calculations?
>
> Thanks in advance,
>
> Dries
> --
> 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, 02 Feb 2016 15:16:02 +0000
From: Mark Abraham <mark.j.abraham at gmail.com>
To: gmx-users at gromacs.org,
gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] Verlet scheme and relative free
binding
energy
Message-ID:
<CAMNuMAR1WcYWi1po-iBUM9ex+mVf_7gDO559892q+aLq5p8a4A at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi,
One can vary PME parameters for electrostatics at
approximately constant
accuracy by scaling the Fourier grid spacing and short-range
cutoff by the
same factor. (This is what mdrun does during PME tuning.) So
you can use
rcoulomb = 1.0 and spacing scaled accordingly.
In GROMACS 2016, the Verlet scheme will likely support
specifying such
setups directly.
Mark
On Tue, Feb 2, 2016 at 3:19 PM Dries Van Rompaey <dries.vanrompaey at gmail.com>
wrote:
> Hi gmx-users,
>
> I have a question regarding the correct treatment of
cut-offs for
> amber99sb-ildn in relative free binding energy
calculations, using the
> verlet scheme. Many articles seem to use a 1.2 nm
cutoff for coulomb
> interactions and a vdw interaction switched off between
0.9 and 1 nm (for
> instance: DOI: 10.1039/c5sc02678d). However, this setup
is only possible
> with the now deprecated group scheme.
>
> I haven't been able to find any papers using
amber99sb-ildn for relative
> free energy calculations with a setup suitable for
verlet scheme. Does
> anyone have experience with such a setup for relative
free binding energy
> calculations?
>
> Thanks in advance,
>
> Dries
> --
> 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.
>
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