Re: [gmx-users] gromos force field

2019-11-05 Thread Patrick Fuchs 

Hi,
I'm coming late, but I may add a few words. The GROMOS force fields have 
been parameterized with the GROMOS software using a twin-range cutoff 
(0.8/1.4), but this option is no longer available in recent versions of 
GROMACS. However, in a recent study 
(https://doi.org/10.1021/acs.jctc.8b00758), it was showed that using a 
single range cutoff (rlist = rcoulomb = rvdw = 1.4 and nstlist = 1) + 
reaction field (coulombtype = Generalized-Reaction-Field) together with 
the group scheme for neighbor searching (cutoff-scheme=group, even if 
this is deprecated since version 5.1, it is still usable) reproduces 
results generated with the GROMOS software and FF. One other study on 
lipids points to the same conclusion regarding the use of single range 
cutoff (https://doi.org/10.1021/acs.jctc.7b00178) as an alternative to 
twin-range cutoff. That was also tested in this redmine issue: 
https://redmine.gromacs.org/issues/1400. This solution increases 
significantly the computational cost compared to former twin-range 
cutoff, but it is probably the one which gives the closest results to 
the original GROMOS FF.
Alternatively, it was found in a recent paper 
(https://pubs.acs.org/doi/10.1021/acs.jctc.8b00425) that it is possible 
to use the Verlet scheme for neighbour searching with rvdw = 1.2 and PME 
for electrostatics (with rcoulomb = 1.2 since it has to equal rvdw) as 
an acceptable option to reproduce some liquid properties calculated with 
the GROMOS software.
Regarding the remark about the GROMOS software, I'm not aware of any 
"problems".

Best,

Patrick

Le 23/09/2019 à 12:49, Justin Lemkul a écrit :



On 9/21/19 12:44 PM, p buscemi wrote:

Dear Users,
I often use Gromos force field because ATB provides top files for 
reasonably large molecules - 1000 atoms. With Gromacs 2019.3 the 
error now appears:

The GROMOS force fields have been parametrized with a physically
incorrect multiple-time-stepping scheme for a twin-range cut-off. When
used with a single-range cut-off (or a correct Trotter
multiple-time-stepping scheme), physical properties, such as the 
density,

might differ from the intended values. Check if molecules in your system
are affected by such issues before proceeding. Further information 
may be

available at https://redmine.gromacs.org/issues/2884.

while message is clear enough, just how large an error in density is 
anticipated ? A 10 % error in polymer solution may be tolerable. A 2 
% error in a crystal or binding site may be a concern.
Gromacs indicated that Gromos may be dropped for v 2020. Is there no 
other option - llike fixing the time-stepping-scheme. Or must I not 
use the twin-cutoff typically presented in the mpd files ?
There is a conversion from Gromos top to Amber, but would not the 
error be translated as well ?


The problem is that the GROMOS force fields were derived using 
software that has problems, therefore rendering all of the behaviors 
of this force field in other software questionable. There should be a 
paper forthcoming from the core developers that describes the 
situation sometime soon.


-Justin



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Re: [gmx-users] download GROMOS54a6oxy

2018-12-11 Thread Patrick Fuchs 

Hi Tushar,
all parameters from GROMOS 53A6_OXY along with other improvements have 
been merged into a new parameter set called 2016H66 (see 
https://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b00187).
Philippe Hünenberger put some files for GROMACS on his website: 
http://www.csms.ethz.ch/files_and_links/GROMOS/2016H66.html.
For the time being, the parameters within these files are only available 
for 62 organic molecules. Some tests are currently being conducted for 
proteins, but the parameters are not ready yet.
Note also, that if you want to use the reaction field (as used in the 
paper cited above), you'll have to use GROMACS 4.0.7 (or lower). If you 
want to use GROMACS 4.6.6 (or higher), you'll have to use nstlist = 2 
(not more than 2!), see https://redmine.gromacs.org/issues/1400. We are 
actually testing some new PME parameters with this set, and we should be 
able to come with new recommandations pretty soon.

Best,

Patrick

Le 08/12/2018 à 11:55, Dr Tushar Ranjan Moharana a écrit :

Hi all,

I wish to use GROMOS54a6oxy forcefield parameterized by Horta et. al.
However, I am unable to find any link to download the same. It will be a
great help if any one send me the link or the forcefield.

Thanks a lot.
Tushar


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Re: [gmx-users] 2016H66 force field

2018-02-18 Thread Patrick Fuchs 

Hi Anjana,
if you use the files from 2016H66 (see my previous message) and the 
statement #include "ffG2016h66.itp" in your top file, no need to change 
anything (provided you use a correct itp file for your molecule, e.g. 
the CiEj on my github website). All the parameters that were changed 
from 53A6 to 53A6_OXY are properly included in the 2016H66 files.

Best,

Patrick

Le 18/02/2018 à 04:55, Anjana Jayasinghe a écrit :

Dear All,
I would like to know that do we need to change bond lengths and bond angles 
such as gb_1, gb_18, ga_12 and ga_15 (according to OXY) for MD simulations of 
CiEj or PEO molecules when we use 2016H66 force field?
Thank you.


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Re: [gmx-users] Dihedral parameters in Gromos53A6OXY+D

2018-02-10 Thread Patrick Fuchs 

Hi Anjana,
you can add several dihedral functions for the same quadruplet of atoms. 
They will add up when you calculate the potential energy for that dihedral.
As for the 53A6OXY+D, the parameters have been merged recently, together 
with other improvements, into a new set called 2016H66 
(10.1021/acs.jctc.6b00187). You can find the FF files for some liquids 
on the web-page of Philippe Hünenberger 
(http://www.csms.ethz.ch/files_and_links/GROMOS/2016H66.html). 
Alternatively, I also put these parameters on my github web page 
(https://github.com/patrickfuchs/CiEj_2016H66), where there is a copy of 
Philippe's file, as well as the topology for non ionic CiEj surfactants 
(coming from this paper 10.1021/acs.langmuir.7b01348). Since these CiEj 
surfactants have a PEG polar head group, it might be convenient for you 
to start from those. For the time being, those files were tested within 
GROMACS 4 versions, but I plan to add other versions for GROMACS 5 and 
2016 in the near future. I realize it would be convenient to also add 
some PEG topologies there (will try to do that before summer).

Best,

Patrick

Le 10/02/2018 à 11:18, Anjana Jayasinghe a écrit :

Dear All,
I am trying to change the parameters for a PEG molecule using OXY+D ( 
https://pubs.acs.org/doi/abs/10.1021/ct300245h) parameters. When I tried to 
change the dihedral angles of C-C-O-C and O-C-C-O,  there are three new defined 
dihedral angles for each mentioned types. But in original 53A6, there is only 
one dihedral type available for those categories. I'm bit confused with OXY+D 
dihedral parameters for C-C-O-C and O-C-C-O.
Appreciate, if anyone can help me.
Thank you.


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Re: [gmx-users] Gromacs simulation with PEG

2017-11-26 Thread Patrick Fuchs 
FYI, starting from GROMOS 53a6 parameters, we have refined them against 
the free energy of solvation of dimethoxyethane in water (and 
cyclohexane) (DOI: 10.1021/ct300245h). These new parameters are now part 
of the new 2016H66 force field (DOI: 10.1021/acs.jctc.6b00187).

Best,

Patrick

Le 12/11/2017 à 23:54, Dallas Warren a écrit :

You used the incorrect forcefield.

We have found that GROMOS53a6 and associated forcefields reproduce
poorly the interactions between PEG and water.  We have made
improvements on that, and will be publishing something soon.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 13 November 2017 at 09:51, Amali Guruge  wrote:

Dear Gromacs users,

I tried to simulate a system which contains PEG and water. According to the
phase diagram of PEG, it should form micells after the simulation. However,
after the simulation PEG doesn't form micells. What could be the reason for
this. Can anyone help me.

Thank you.
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Re: [gmx-users] read trr file

2014-12-02 Thread Patrick Fuchs 

Hi Tsjerk,
thanks for that, but I can't find anything attached.
Best,

Patrick

Le 02/12/2014 09:25, Tsjerk Wassenaar a écrit :

Hi Patrick,

Please find the code for reading TRR files attached. The neatest bit is
that it doesn't read the coordinates/velocities/forces for a frame, unless
you want them. That allows to do a quick indexing of frames first. The
offset argument to the TRR reader allows jumping to a specific (frame)
position.

If you have any issues or suggestions, please let me know. I'd also be
interested to hear about cool things that are achieved with the code :)

Cheers,

Tsjerk

On Wed, Nov 26, 2014 at 8:58 PM, Patrick Fuchs 
patrick.fu...@univ-paris-diderot.fr wrote:


Thanks Tsjerk, I'm interested in having a routine that needs as less
external library as possible. Pure python and numpy is perfect.
Best,

Patrick

Le 26/11/2014 18:15, Tsjerk Wassenaar a écrit :

  Hi Patrick,


TRR files are rather simple in structure and are quite easy to parse with
pure python/numpy. That's not the case for XTC files.

I'll make a few changes to the TRR reader, polishing a bit, and send it.
Probably next week, as I'll be occupied this weekend.

Cheers,

Tsjerk
On Nov 26, 2014 6:05 PM, Patrick Fuchs 
patrick.fu...@univ-paris-diderot.fr wrote:

  Hi Tsjerk,

I would be very interested by your python code. Does it also read xtc
files? Shall I contact you off-list? Thanks.
Best,

Patrick

Le 26/11/2014 06:26, Tsjerk Wassenaar a écrit :

  I also have Python code to read TRR files directly. Contact me if you're

interested.

Cheers,

Tsjerk
On Nov 26, 2014 5:44 AM, RINU KHATTRI nickname.mi...@gmail.com
wrote:

   you can also  read .trr file by the use of matlab code



On Wed, Nov 26, 2014 at 9:01 AM, Justin Lemkul jalem...@vt.edu
wrote:




On 11/25/14 9:04 PM, 石锐 wrote:



Hi all,

I have generated a large .trr file (~500 G) from a simulation. To
save

  the




  space, I just want to write a C/C++ code to read and manipulate the




  binary




  .trr file directly rather than convert it to a readable .gro or .pdb




  file.




  However, I cannot find the format of .trr file from the manual. Is

there


anyone who knows how to read the .trr file ?


  The XDR library can be used to do this:


http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library

-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul


==
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Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot
Bâtiment Buffon, 15 rue Hélène Brion, 75013 Paris
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Dynamique des membranes et trafic intracellulaire
Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot
Bâtiment Buffon, 15 rue Hélène Brion, 75013 Paris
Tel :  +33 (0)1 57 27 80 05 - Fax : +33 (0)1 57 27 81 35
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Re: [gmx-users] read trr file

2014-11-26 Thread Patrick Fuchs 

Hi Tsjerk,
I would be very interested by your python code. Does it also read xtc 
files? Shall I contact you off-list? Thanks.

Best,

Patrick

Le 26/11/2014 06:26, Tsjerk Wassenaar a écrit :

I also have Python code to read TRR files directly. Contact me if you're
interested.

Cheers,

Tsjerk
On Nov 26, 2014 5:44 AM, RINU KHATTRI nickname.mi...@gmail.com wrote:


you can also  read .trr file by the use of matlab code

On Wed, Nov 26, 2014 at 9:01 AM, Justin Lemkul jalem...@vt.edu wrote:



On 11/25/14 9:04 PM, 石锐 wrote:


Hi all,

I have generated a large .trr file (~500 G) from a simulation. To save

the

space, I just want to write a C/C++ code to read and manipulate the

binary

.trr file directly rather than convert it to a readable .gro or .pdb

file.

However, I cannot find the format of .trr file from the manual. Is there
anyone who knows how to read the .trr file ?



The XDR library can be used to do this:

http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library

-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul


==
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Dynamique des membranes et trafic intracellulaire
Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot
Bâtiment Buffon, 15 rue Hélène Brion, 75013 Paris
Tel :  +33 (0)1 57 27 80 05 - Fax : +33 (0)1 57 27 81 35
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Re: [gmx-users] read trr file

2014-11-26 Thread Patrick Fuchs 
Thanks Tsjerk, I'm interested in having a routine that needs as less 
external library as possible. Pure python and numpy is perfect.

Best,

Patrick

Le 26/11/2014 18:15, Tsjerk Wassenaar a écrit :

Hi Patrick,

TRR files are rather simple in structure and are quite easy to parse with
pure python/numpy. That's not the case for XTC files.

I'll make a few changes to the TRR reader, polishing a bit, and send it.
Probably next week, as I'll be occupied this weekend.

Cheers,

Tsjerk
On Nov 26, 2014 6:05 PM, Patrick Fuchs 
patrick.fu...@univ-paris-diderot.fr wrote:


Hi Tsjerk,
I would be very interested by your python code. Does it also read xtc
files? Shall I contact you off-list? Thanks.
Best,

Patrick

Le 26/11/2014 06:26, Tsjerk Wassenaar a écrit :


I also have Python code to read TRR files directly. Contact me if you're
interested.

Cheers,

Tsjerk
On Nov 26, 2014 5:44 AM, RINU KHATTRI nickname.mi...@gmail.com wrote:

  you can also  read .trr file by the use of matlab code


On Wed, Nov 26, 2014 at 9:01 AM, Justin Lemkul jalem...@vt.edu wrote:




On 11/25/14 9:04 PM, 石锐 wrote:



Hi all,

I have generated a large .trr file (~500 G) from a simulation. To save


the



space, I just want to write a C/C++ code to read and manipulate the



binary



.trr file directly rather than convert it to a readable .gro or .pdb



file.



However, I cannot find the format of .trr file from the manual. Is there

anyone who knows how to read the .trr file ?



The XDR library can be used to do this:

http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library

-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul


==
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Dynamique des membranes et trafic intracellulaire
Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot
Bâtiment Buffon, 15 rue Hélène Brion, 75013 Paris
Tel :  +33 (0)1 57 27 80 05 - Fax : +33 (0)1 57 27 81 35
E-mail address: patrick.fu...@univ-paris-diderot.fr
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Dynamique des membranes et trafic intracellulaire
Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot
Bâtiment Buffon, 15 rue Hélène Brion, 75013 Paris
Tel :  +33 (0)1 57 27 80 05 - Fax : +33 (0)1 57 27 81 35
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Re: [gmx-users] Naughty Vacuum Bubble in our Vesicle

2014-10-29 Thread Patrick Fuchs 

Hi Björn,
my five cents. Did you consider constructing the system using MARTINI, 
equilibrating it with artificial pores and then back-map it to all-atom? 
Otherwise, I guess this artificial pore strategy could be applied to an 
all-atom system, but it'd be way more lengthy.

Ciao,

Patrick

Le 28/10/2014 12:32, Justin Lemkul a écrit :



On 10/28/14 6:23 AM, Björn Sommer wrote:

Dear Rajat,
Dear Andre,
Dear all,

thanks again for your help.
1) I'm simulating an united atoms model and isotropic pressure is
used, not
coarse-grained (this would be indeed more simple, because faster and
much more
examples are available).
2) Yes, I added additional water bubbles of different sizes only in
the vacuum
region.
3) I don't know the lateral tension yet, but I'll try to compute it
and hand in
this information later.

4) Do you have sufficient water outside the vesicle to hydrate all the
lipids in the outer leaflet?

4) Yes, there should be enough water. I think, that this is currently
not the
problem, but we will keep this in mind.

In addition, you find two snapshots, one of the vacuum bubble and one
of the
inner lipid layer coated by water:

http://www.CELLmicrocosmos.org/images/downloads/cm2/WANTED_vacuum_bubble.pdf


(Sorry, I just had to do this joke, Manuel! - Björn ;-)

In addition I'm running a minimization run right now with a lot more
water
inside and will continue to equillibrate soon, as far as I get an
useful result,
we will inform you.



Does the size of the vesicle itself change at all?  My thought is that
this could simply be a force field issue; if the surface tension in the
vesicle is wrong, then if it gets larger over time, there's only a
finite amount of water in the center of the vesicle, so bubbles develop.

Apologies if I've missed relevant information; I've been following the
thread but have not had time to study it very closely.

-Justin



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Dynamique des membranes et trafic intracellulaire
Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot
Bâtiment Buffon, 15 rue Hélène Brion, 75013 Paris
Tel :  +33 (0)1 57 27 80 05 - Fax : +33 (0)1 57 27 81 35
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Re: [gmx-users] Accelerated MD

2014-10-23 Thread Patrick Fuchs 

Hi Doug,
I recently read a good review on ABF 
http://pubs.acs.org/doi/abs/10.1021/jp506633n. It's focused on ABF but 
there's a section which compares ABF to other techniques.
While I'm at it, are there any plans from gromacs devs to implement ABF 
in gromacs?

Best,

Patrick

Le 20/10/2014 22:33, Douglas Houston a écrit :

Hi all,

Can anyone recommend a book or (preferably) review article summarising
the various accelerated MD methods commonly used in protein/peptide
simulation these days? e.g. ABF, PLUMED, REMD, aMD etc. etc. I can read
about each individually but I could use a comprehensive but concise
comparison of their pros/cons and most popular applications.

cheers,
Doug


_
Dr. Douglas R. Houston
Lecturer
Institute of Structural and Molecular Biology
Room 3.23, Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358
http://tinyurl.com/douglasrhouston





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___
Patrick FUCHS
Dynamique des membranes et trafic intracellulaire
Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot
Bâtiment Buffon, 15 rue Hélène Brion, 75013 Paris
Tel :  +33 (0)1 57 27 80 05 - Fax : +33 (0)1 57 27 81 35
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Re: [gmx-users] Gromos DPPC bilayer: different results for 4.0.7 and 4.6.5

2014-03-25 Thread Patrick Fuchs 

Hi,
I answer a long time after the last discussion of this thread, but I did 
some tests in between and discussed with some people. I would like to 
follow-up on this issue and sum-up what I found.


After digging into the mailing list, I finally found that the same type 
of issue was discussed in 2011 between Antonio Baptista/Miguel 
Machuqueiro and gromacs devs. There a typical GROMOS setup (twin-range 
cutoff 0.8/1.4 + RF) was giving LINCS crashes (protein simulations in 
water) in 4.5 whereas it was stable in 4.0. It looks like that what we 
see with the Poger lipids has the same origin (the new reversible 
algorithm introduced in 4.5). We don't have crashes because there are no 
explicit H in the lipids. So to sum up the situation, if we want a 
stable simulation with 4.5 and the GROMOS typical simulation parameters, 
that give similar results to 4.0 there seem to be 2 possibilies (maybe 
there are others, but at least these 2 have been tested):

1) reduce nstlist to 1 (2 seems to work according to Miguel)
2) increase rlist up to rlist=rcoulomb (I tried Samuli's suggestion 
rlist=rcoulomb and recover a correct area on the DPPC system, see 
http://redmine.gromacs.org/issues/1400 for the plot).
Both solutions increase a lot the computational cost. For example 2) 
gives 1.5 ns/h on my eight-core computer, whereas in 4.0 I had ~ 1.0 ns/h.


In the discussion of 2011 Berk proposed some other possible solutions to 
speed up with 4.6 
(https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2011-December/005506.html), 
but these were not tested to my knowledge.


My concern is that a twin-range/RF setup in version = 4.0 gives a given 
result, but does'nt give the same result in = 4.5 and possibly crashes. 
So I shall say that it would be nice to warn the users that they will 
encounter problems when using twin-range/RF with versions = 4.5. Maybe 
with a grompp warning? Section 3.4.7 in the manual may not be the first 
place a user will look at.
Anyhow, if for some reason someone wants to use the twin-range cut-off 
as it is done in the GROMOS software (with all versions of GROMOS force 
fields), one has to stick to 4.0.* or lower.


Best,

Patrick

Le 18/12/2013 21:26, Ollila Samuli a écrit :

Hi,


On Dec 18, 2013, at 8:50 AM, Sabine Reisser sabine.reis...@kit.edu wrote:
Up to Gromacs 4.0.7, the long rance forces, which are calculated at every 
nstlist'th step, were added constantly
to the short range force in the subsequent steps. Starting from Gromacs 4.5., 
the long range force is added
nstlist times to the short range force on the nstlist'th step, while there is 
nothing added to the short range force
on the subsequent steps. This creates some kind of impulse force which we 
believe is responsible for the
different behaviour of the membrane, although we haven't figured out the exact 
mechanism yet.



That's interesting. Now I see that this change is documented in the manual (Section 
3.4.7). Would that imply that this effect does not depend on the model for 
long-range electrostatics (Reaction Field or PME), but it comes from using twin 
range cutoffs?


I also noticed the same section in the manual today. I think that what possibly 
happens is that with the reaction field the forces between rlist and rcoulumb 
are not used in the steps between neighbour list update. However, in these 
steps the reaction field force calculation assumes the dielectric envinronment 
beoynd rcoulomb, not beoynd rlist even though the forces only up to rlist are 
used. I am not sure if this would have any practical relevance, though? I am 
also not sure how this is handled in the pressure calculation?

I think that the reason why Patrick did not get the difference in the PME results 
between versions might be that he probably used rcoulomb=rlist in those 
simulations. If I try to set rcoulombrlist with PME, I get error:

   With coulombtype = PME, rcoulomb must be equal to rlist
   If you want optimal energy conservation or exact integration use PME-Switch

If it is true what I am saying, then the area per molecules should be the same 
between versions also using RF and setting rlist=rcoulomb.

BR,
Samuli Ollila




I expect you to get the 'right' area per lipid if you use nstlist 1 as already 
suggested by Mirco, because in that
case the multistep algorithms give the same answer. This is also our experience 
with G54A7.



I started a run yesterday with nstlist=1, and so far (about 12 ns) the area per lipid indeed 
stays at the correct value of around 0.63 nm^2.


Thanks,

   Lutz

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Re: [gmx-users] Gromos DPPC bilayer: different results for 4.0.7 and 4.6.5

2013-12-16 Thread Patrick Fuchs 

Hi,
following Justin's suggestion on redmine (issue #1400), a simulation 
with Reaction-Field-nec using 4.5.3 is running. It hasn't completed 
yet but the mean area per lipid around 50 ns is 0.59  mean area  0.60 
nm^2. I will update on redmine once the simulation is completed 
(probably in a couple of days).

Best,

Patrick

Le 16/12/2013 22:30, Justin Lemkul a écrit :

On Mon, Dec 16, 2013 at 3:10 PM, Lutz Maibaum lutz.maib...@gmail.comwrote:


I am running MD simulations of DPPC bilayers with the Gromos force field,
and I am seeing some differences between using Gromacs 4.0.7 and
4.5.5/4.6.5 that I do not understand. It would be great if someone had any
insight into what's going on here.

When I use the Gromos 53A6-L force field, which is the default 53A6 force
field combined with improved lipid parameters that can be downloaded from
http://compbio.chemistry.uq.edu.au/~david/research/lipids.htm, I obtain
an average area per lipid of 0.627 nm^2, in good agreement with both the
paper that describes these new parameters (0.629 nm^2, obtained with
Gromacs 3.2.1, Ref. [1]) and another follow-up study (0.631 nm^2 and 0.623
nm^2, Gromacs 4.0.7, Ref. [2]).

Now, if I use the same force field and mdp file, and the same initial
configuration (which is a pre-equilibrated DPPC bilayer from
http://compbio.biosci.uq.edu.au/atb/system_download.py?boxid=32 and
randomly generated velocities), but use Gromacs 4.6.5 instread, I get a
lower value of about 0.59 nm^2.

I also tried the Gromos 54A7 force field, which is included with Gromacs
4.6.5 and that should be identical to 53A6-L (plus it has some other
improvements over 53A6 that shouldn't be relevant here), I also get the
lower area per lipid of ~0.59 nm^2.

If have attached a plot of the area per lipid for these three simulations,
each more than 100ns long. This looks to me like 4.6.5 give systematically
lower area per lipid than 4.0.7. Running additional simulations with
Gromacs 4.5.5 suggest that that also results in the lower area per lipid.
Does anyone know why this might be?  I have uploaded the relevant files in
case that is helpful:

http://faculty.washington.edu/maibaum/dppc_comparison/

To see if there are any differences between the energies that 4.0.7 and
4.6.5 compute, I picked a configuration, and used mdrun -rerun with the
three different gromacs / force field combinations. Here is what I get for
the sample.gro configuration (included in the link above):

Gromacs 4.0.7 + Gromos53A6-L:

Energies (kJ/mol)
 G96Bond   G96AngleProper Dih.  Improper Dih.  LJ-14
 1.76906e+021.29521e+049.57922e+034.97638e+02   -1.38126e+03
  Coulomb-14LJ (SR)LJ (LR)   Coulomb (SR)   Coulomb (LR)
 1.50791e+041.23533e+04   -7.49664e+03   -3.78489e+05   -8.97363e+02
RF excl.  PotentialKinetic En.   Total EnergyTemperature
-5.25414e+04   -3.90168e+056.47185e+04   -3.25449e+052.87013e+02
  Pressure (bar)
 2.00740e+02


Gromacs 4.6.5 + Gromos53A6-L:

Energies (kJ/mol)
 G96Bond   G96AngleProper Dih.  Improper Dih.  LJ-14
 1.76905e+021.29522e+049.57922e+034.97637e+02   -1.38126e+03
  Coulomb-14LJ (SR)LJ (LR)   Coulomb (SR)   Coulomb (LR)
 1.50791e+041.23533e+04   -7.49659e+03   -3.78489e+05   -8.97344e+02
RF excl.  PotentialKinetic En.   Total EnergyTemperature
-5.25414e+04   -3.90168e+056.47458e+04   -3.25422e+052.87134e+02
  Pressure (bar)
 2.15012e+02


Gromacs 4.6.5 + Gromos54A7:

Energies (kJ/mol)
 G96Bond   G96AngleProper Dih.  Improper Dih.  LJ-14
 1.76905e+021.30332e+049.57922e+034.97637e+02   -1.38126e+03
  Coulomb-14LJ (SR)LJ (LR)   Coulomb (SR)   Coulomb (LR)
 1.50791e+041.25510e+04   -7.32610e+03   -3.78489e+05   -8.97344e+02
RF excl.  PotentialKinetic En.   Total EnergyTemperature
-5.25414e+04   -3.89718e+056.47631e+04   -3.24955e+052.87211e+02
  Pressure (bar)
 2.89622e+02


I don't see any significant difference between what 4.0.7 and what 4.6.5
compute. I don't know if the somewhat higher pressure with the 4.6.5/54A7
combination is meaningful.

If anyone can shed any light on this, or has ideas for how to debug this
further, I'd be most grateful.



I suspect you're running into the same issue that has been reported here:
http://redmine.gromacs.org/issues/1400.

Can you check to see if Reaction-Field-nec fixes the issue?  We're still
waiting on feedback from the Redmine issue.  The RF methods changed
somewhere along the way, and we need to make sure that the appropriate
algorithms are being tested for an apples-to-apples comparison.

-Justin



--
___
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Dynamique des membranes et trafic intracellulaire
Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot
Bâtiment

[gmx-users] redmine account

2013-12-09 Thread Patrick Fuchs 

Hi all,
I tried to make an account on http://redmine.gromacs.org/ by filling the 
online form, but didn't receive any E-mail of confirmation. When I try 
to register again, it tells me my E-mail is already used, but when I ask 
for a forgotten passwd it tells me my E-mail doesn't correspond to any 
account. Who should I contact to fix this?

Thanks,

Patrick
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___
Patrick FUCHS
Dynamique des membranes et trafic intracellulaire
Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot
Bâtiment Buffon, 15 rue Hélène Brion, 75013 Paris
Tel :  +33 (0)1 57 27 80 05 - Fax : +33 (0)1 57 27 81 35
E-mail address: patrick.fu...@univ-paris-diderot.fr
Web Site: http://www.dsimb.inserm.fr/~fuchs
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