[gmx-users] Re : gromacs.org_gmx-users Digest, Vol 152, Issue 55
Adel ASCHI
aschi13 at yahoo.fr
Sat Dec 17 09:26:31 CET 2016
Dear Sir,
I want to use the gromacs server, but, the probleme,how i can obtain the Certificate Authority. by the way i'm from tunisia
can you help me for this
Yours Sincerely
PhD. ASCHI Adel
Lab. de Physique de la Matière Molle
Département de Physique
Faculté des Sciences de Tunis; Campus Universitaire. 1060. Tunisia
Phone: 216 71 872 600 Phax : 216 71 885 073
e-mail: aschi13 at yahoo.fr
--------------------------------------------
En date de : Ven 16.12.16, gromacs.org_gmx-users-request at maillist.sys.kth.se <gromacs.org_gmx-users-request at maillist.sys.kth.se> a écrit :
Objet: gromacs.org_gmx-users Digest, Vol 152, Issue 55
À: gromacs.org_gmx-users at maillist.sys.kth.se
Date: Vendredi 16 décembre 2016, 22h26
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. Manual refinement of ATB topologies ?
(Sim gmx)
2. Re: CG Lincs errors (Nash, Anthony)
3. Re: Desolvation or hydration free
energy of an ION (Justin Lemkul)
----------------------------------------------------------------------
Message: 1
Date: Fri, 16 Dec 2016 13:46:43 +0100
From: Sim gmx <simgmx at gmail.com>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Manual refinement of ATB topologies ?
Message-ID:
<CAFNohVmw7QTj5g5sMBcugZuxcO7Z_hA4dbZA_8reNwgjngo29g at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi all,
I would like to know what you consider to be the ideal
refinement for a
topology created by ATB ?
How far should we go in the manual refinement ?
For instance, ATB gave me a topology for a molecule with an
unsaturated
acyl chain. Here are some potential issues with this
topology:
1) Three methyl groups at the end of the acyl chain (that
are "3 methyl
groups away" from a double bond) carry a small charge (with
a net group
charge of 0, however)
2) For the double bonds, parameters are "new parameters"
(not found in
ffbonded.itp file)
3) Some bonded parameters in the ATB topology do exist in
ffbonded.itp file
but are not supposed to be applied for this kind of bond
(example: O - S
bond parameters are written for a C (involved in a double
bond) - CH2 bond)
My "instinctive" behavior would be to:
1) Put a 0 charge to these methyl groups since they should
not be charged
imo
2) Look for another gromos53a6 topology that includes a
double bond (like
this one https://lipidbook.bioch.ox.ac.uk/package/show/id/16.html)
and take
the double bond parameters from it
3) Replace those bonds by correct "default parameters" found
in
ffbonded.itp file, in this case by a "C, CHn - C, CHn"
bonded parameter.
However, I don't wish to break an "equilibrium" that ATB
could have built
with some apparently weird parameters.
Hence, is it better to take the ATB topology as it comes, or
to try to
refine it ? If the latter, how far should we go ? Isn't it
risky or
complicated to justify (in a reviewing process, for example
:)) ?
Thank you !
------------------------------
Message: 2
Date: Fri, 16 Dec 2016 12:59:29 +0000
From: "Nash, Anthony" <a.nash at ucl.ac.uk>
To: "gmx-users at gromacs.org"
<gmx-users at gromacs.org>
Subject: Re: [gmx-users] CG Lincs errors
Message-ID: <D479947E.15F3F%uccaja0 at ucl.ac.uk>
Content-Type: text/plain; charset="utf-8"
Hi Peter,
Thanks for the reply, I know we spoke in length on this
mater only just
recently. Many thanks for that.
I?ve taken the time step of collagen in vacu down to 0.0001
and I?ve
dropped the temp down to 280. I hope, running over 16 cores
for two days
that this should relieve any tension in the backdone before
in gradually
increase to 20-40fs. Again, all in vacu with no solvent.
I?ve actually thought about writing a script to modify the
equilibrium
bond angles in the CG.itp file for the backbone, using the
atomistic
structure as a template. After all, true collagen does not
replicate
?ideal? collagen along the stretch of the protein e.g., the
MMP1 binding
site is not very tightly coiled. Perhaps, there lies my
problem.
I haven?t thought too much of the actual full fibril
structure, I want to
capture the D-band gap in type I collagen. When I give
it some more
thought I will probably look into semi-isotropic pressure
coupling first.
Thanks
Anthony
Dr Anthony Nash
Department of Chemistry
University College London
Skeletal Tissue Dynamics Group
Committee member of London Matrix Group @LondonMatrixGrp
On 16/12/2016 09:02, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se
on
behalf of Peter Kroon" <gromacs.org_gmx-users-bounces at maillist.sys.kth.se
on behalf of p.c.kroon at rug.nl>
wrote:
>As a note to Alex (and the rest of the list), the
coarse-grained Martini
>forcefield is usually run with timesteps between 20-40
fs. 15fs is
>already rather low. I do agree that longer equilibration
at low timestep
>(5 or 10) might help.
>
>Alternatively, Do you think a semiisotropic pressure
coupling might be
>applicable in this case, since it's an infinite collagen
polymer?
>
>
>Peter (PhD in the Martini group)
>
>
>On 16-12-16 00:21, Nash, Anthony wrote:
>> Alex and Mark, thanks for the information. I?ll
drop dt down,
>> significantly, drop the temperature, and run it for
a long time.
>>
>> Thanks for the ideas.
>> Anthony
>>
>>
>> On 15/12/2016 21:54, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se
>>on
>> behalf of Alex" <gromacs.org_gmx-users-bounces at maillist.sys.kth.se
on
>> behalf of nedomacho at gmail.com>
wrote:
>>
>>> Mark is right, no two ways about it. For
initial equilibration and
>>> assessing preexisting structural strains try
vacuum, _much_ smaller
>>> timesteps and possibly low temperatures in
vacuum, only then transfer
>>>to
>>> solvent, etc. Algorithmically, LINCS requires
convergence and you
>>>already
>>> are using a pretty high LINCS order... From
what I see, dt = 15 fs at
>>>310K
>>> looks like a cowboy mode simulation in this
case.
>>>
>>> Alex
>>>
>>> On Thu, Dec 15, 2016 at 2:32 PM, Mark Abraham
>>><mark.j.abraham at gmail.com>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> If a simulation isn't stable with a small
time step (as I think you
>>>>are
>>>> saying) then moving to a larger time step
is guaranteed to make that
>>>> worse.
>>>> Try an even smaller time step, for a long
time, and see what happens.
>>>>Or
>>>> take a subset of your protein and see what
happens. Or simulate in
>>>>vacuo
>>>> for a while. Your topology could be
unsuited to your starting
>>>>structure,
>>>> e.g. some part is under a lot of tension
that gets released at some
>>>> point
>>>> and no finite time step can in practice
deal with the velocity of the
>>>> recoil...
>>>>
>>>> Mark
>>>>
>>>> On Thu, 15 Dec 2016 23:06 Nash, Anthony
<a.nash at ucl.ac.uk>
wrote:
>>>>
>>>>> Hi all,
>>>>>
>>>>> I?m hoping for some help. I?m very
sorry, this is a bit of a long
>>>>>one.
>>>>>
>>>>> I?ve 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
>>>>> using MD. I went on to use the latest
version of Martinize.py with
>>>>>the
>>>>> latest version of the MARTINI
forcefield fields.
>>>>>
>>>>> After a little tweaking (the way AMBER
names histidine residues), I
>>>>> successful converted the molecule
(approx 3100 amino acids) into a CG
>>>>> representation. I successfully energy
min the protein in vacuum to a
>>>>> threshold of 500, and in solvent to a
threshold of 750 using steepest
>>>>> descent. Looking for a system at an
energy min of a threshold around
>>>> 300
>>>> I
>>>>> begin to see LINCS warnings. Observing
the initial structure, there
>>>>>is
>>>>> nothing obviously wrong with the bond
network (both protein and
>>>> polarized
>>>>> CG water).
>>>>>
>>>>> I take the system that energy mins at
750 (protein-water mix, with no
>>>>> fault reported), and went straight to
NPT, 20fs step. Blew up. After
>>>>>a
>>>> bit
>>>>> of chatting with the MARTINI community,
I?ve started with an NVT
>>>> ensemble,
>>>>> beginning at 5s then through 10fs,
15fs, and 20fs. I only run for
>>>>>1000
>>>>> steps before switching. Keeping any of
the simulations running for
>>>> longer
>>>>> throws lincs warnings followed by a
segmentation fault from the
>>>> warning:
>>>>> "3 particles communicated to PME rank 7
are more than 2/3 times the
>>>>> cut-off out of the domain decomposition
cell of their charge group in
>>>>> dimension x."
>>>>>
>>>>> Observing the trajectories of any of
the extended simulations shows
>>>> the
>>>>> protein snapping like a rope, and
always at the same place. I have
>>>> watched
>>>>> every trajectory at this point, using
numerous energy min start
>>>> points,
>>>> to
>>>>> try and understand why it is blowing
up. I can?t see any obvious
>>>> reason.
>>>> I
>>>>> was told to consider how the
temperature is changing. Below is an
>>>> example
>>>>> of the temperature and pressure from an
NPT of 20fs step continued
>>>> from
>>>>> the very short 20fs step NVT simulation
(hoping that perhaps CG
>>>> without
>>>>> pressure just doesn?t behave happily; I
was wrong).
>>>>>
>>>>>
>>>>> TEMP:
>>>>> ?
>>>>> 6.630000 311.000336
>>>>> 6.645000
311.371643
>>>>> 6.660000
311.724213
>>>>> 6.675000
313.878693
>>>>> 6.690000
681558.937500
>>>>>
>>>>>
>>>>> PRESSURE:
>>>>> ?
>>>>> 6.630000 3.559879
>>>>> 6.645000
3.901433
>>>>> 6.660000
3.589078
>>>>> 6.675000
4.158611
>>>>> 6.690000
81762.437500
>>>>>
>>>>> The final LINCS warning from this same
run:
>>>>>
>>>>> Step 300, time 4.5 (ps) LINCS
WARNING
>>>>> relative constraint deviation after
LINCS:
>>>>> rms 0.000035, max 0.003386 (between
atoms 2125 and 2126)
>>>>> bonds that rotated more than 45
degrees:
>>>>> atom 1 atom 2 angle
previous, current, constraint length
>>>>>
2125 2126 68.3
0.2781 0.2691
0.2700
>>>>>
2125 2127 45.9
0.2789 0.2701
0.2700
>>>>>
>>>>>
>>>>> At this stage the structure ruptures as
described above.
>>>>>
>>>>>
>>>>> My NVT settings (with NPT included to
save space) are:
>>>>>
>>>>> -----------------
>>>>> title
= Martini
>>>>>
>>>>> integrator
= md
>>>>> dt
=
0.015
>>>>> nsteps
= 1000
>>>>> nstcomm
= 100
>>>>> ;comm-grps
=
>>>>>
>>>>> nstxout
= 1000
>>>>> nstvout
= 1000
>>>>> nstfout
= 0
>>>>> nstlog
= 1
>>>>> nstenergy
= 1
>>>>> nstxout-compressed
= 0
>>>>>
compressed-x-precision = 0
>>>>> ;compressed-x-grps
=
>>>>> energygrps
= collagen solvent
>>>>>
>>>>> cutoff-scheme
= Verlet
>>>>> nstlist
= 20
>>>>> ns_type
= grid
>>>>>
>>>>> pbc
= xyz
>>>>> verlet-buffer-tolerance = 0.005
>>>>>
>>>>> coulombtype
= PME ;reaction-field
>>>>> rcoulomb
= 1.1
>>>>> fourierspacing
= 0.16 ;0.2 ;0.12
>>>>>
>>>>> epsilon_r
= 2.5 ;15 ;
2.5 (with polarizable
>>>>>water)
>>>>> epsilon_rf
= 0
>>>>> vdw_type
= cutoff
>>>>> vdw-modifier
= Potential-shift-verlet
>>>>> rvdw
= 1.1
>>>>>
>>>>> tcoupl
= v-rescale
;berendsen ;v-rescale
>>>>> tc-grps
= collagen solvent
>>>>> tau_t
= 0.5 0.5 ;1.0 1.0
>>>>> ref_t
= 310 310
>>>>>
>>>>> Pcoupl
=
berendsen ;parrinello-rahman
>>>>> Pcoupltype
= isotropic
>>>>> tau_p
= 12.0 ;
parrinello-rahman is more stable
>>>> with
>>>>> larger tau-p, DdJ, 20130422
>>>>> compressibility
= 10e-4
>>>>> ref_p
= 1.0
>>>>> refcoord_scaling
= com
>>>>>
>>>>> gen_vel
= no
>>>>> gen_temp
= 310
>>>>> gen_seed
= 473529
>>>>>
>>>>> continuation = yes
>>>>> constraints
= none
>>>>> constraint_algorithm
= lincs
>>>>> lincs-warnangle = 45
>>>>> lincs-order=8
>>>>> lincs-iter=4
>>>>>
>>>>>
>>>>> ??????????
>>>>>
>>>>> Every setting bar the lincs iter,
order, warnangle were supplied with
>>>> the
>>>>> latest version of MARTINI. During many
NVT runs I have adjusted the
>>>> tau-t
>>>>> to try and keep the thermostat from
oscillating its way into
>>>>>infinity.
>>>>>
>>>>> I?m curious, will an out of control
thermostat break a structure, or
>>>> will
>>>>> a structure breaking (for what ever
reason this structure is
>>>>>breaking)
>>>>> cause the thermostat to go out of
control?
>>>>>
>>>>> My only thought thought is the initial
.itp file that Martinize
>>>> created.
>>>> I
>>>>> informed the script that this was
collagen, therefor it sets ?F? and
>>>> the
>>>>> corresponding bonded parameters. A
human collagen is not perfect in
>>>> its
>>>>> helical structure. Could there be
underlying forces contributed from
>>>> badly
>>>>> bonded backbone-backbone arrangements?
>>>>>
>>>>> [ atoms ]
>>>>> 1
N0 1 GLY
BB 1 0.0000 ; F
>>>>> 2
N0 2 LEU
BB 2 0.0000 ; F
>>>>> 3
C1
2 LEU SC1
3 0.0000 ; F
>>>>> 4
N0 3 SER
BB 4 0.0000 ; F
>>>>>
>>>>>
>>>>> Many thanks
>>>>> Anthony
>>>>>
>>>>> Thanks
>>>>> Anthony
>>>>>
>>>>> --
>>>>> 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.
>>>>>
>>>> --
>>>> 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.
>>> --
>>> 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: Fri, 16 Dec 2016 16:26:10 -0500
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Desolvation or hydration free
energy of an
ION
Message-ID: <5bc664fd-1288-bf34-b57f-68103f4bea88 at vt.edu>
Content-Type: text/plain; charset=windows-1252;
format=flowed
On 12/15/16 10:15 AM, Alex wrote:
> Thanks Justin for your response.
>
> Surly PMF is better, but the point is that via FEP I
have already calculate
> the binding free energy of a charged amino acid to a
solid surface while
> Na+ used as counter-ion where both "amino acid and Na+"
considered as a
> single "couple-moltype" to be decoupled both of them
simultaneously from
> the system. And of course by this I have desolvation
energy of Na+ into
> account which should not be. So, I want to calculate
the desolvation energy
> of only Na+ to remove its portion out from my original
calculation. That is
> why I want to keep the conditions as my original
simulations.
>
> With free energy of {amino acid and Na+} in both
bounded and unbounded to
> the solid slab, I mean DG_unbounded{AA and Na+} -
DG_bounded{AA and Na+},
> the portion of Na+ has been already removed partially,
but not completely.
>
Are there significant interactions between the amino acid
and Na+, and/or the
surface and Na+? If so, the only way to figure out the
extent of the
contribution is a full thermodynamic cycle in which the
amino acid and Na+ are
decoupled separately.
-Justin
> Regards,
> Alex
>
> On Thu, Dec 15, 2016 at 3:55 PM, Justin Lemkul <jalemkul at vt.edu>
wrote:
>
>>
>>
>> On 12/15/16 9:39 AM, Alex wrote:
>>
>>> Hello gromacs user,
>>>
>>> I was wondering if anybody has experience with
the hydration or
>>> desolvation
>>> free energy of an ION for example Na+, using
alchemical free energy
>>> perturbation method?
>>>
>>> Actually in my case, I would like to calculate
the difference between free
>>> energy of "Na+" when it is close to a solid
slab in aqueous solutions,
>>> and
>>> when it is far away from the slab inside bulk
water.
>>>
>>>
>> If it's a simple matter of Na+ partially
desolvating to bind to the
>> surface (with no intervening waters) then the
simple approach is a PMF.
>> Using a decoupling method requires additional
restraints that have to be
>> accounted for. This can of course be done done but
a PMF is trivial to set
>> up.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu
| (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
>> --
>> 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.
>>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu
| (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
------------------------------
--
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.
End of gromacs.org_gmx-users Digest, Vol 152, Issue 55
******************************************************
More information about the gromacs.org_gmx-users
mailing list