Re: [gmx-users] Re: Membrane Runs Crashing

[Mirco Wahab]

Addendum:

On 19.06.2013 23:16, Mirco Wahab wrote:

...
MARTINI W is a strongly associating fluid and will freeze
trough your box in no time even when setting negative pressure
below 300K. In newer Gromacs versions (from 4.6) there seems
to be additional shift (?) in the potential, so the water phase
transition took another hit and went up to over 320K (with
verlet) and to about 315K (with shift).
...


I can't let this without further comment. After reading my own post
(and staring to thinking about it), I *checked back the results* of
"freezing MARTINI water" that allegedly changed it's freezing point
along different Gromacs versions.

These "freezings" really did occur - but were exclusively related
to equilibration problems, where "untercooled" (unequilibrated)
membrane patches caused violent density fluctuations in the coarse
grained water (W) on expanding on the way to their target temperature.

These high local densitiy fluctuations probably caused the Martini W
to freeze instantaneously at contact with the membrane and "blocked"
the further membrane expansion. This could be averted by choosing
higher temperatures (+20K).

**
 Checked again with well-equilibrated membranes in water, the Martini
 water (W) *does not freeze* above 300K with Gromacs 4.6.x.  The mem-
 brane properties  are in accord with expectations from the model do-
 cumentation.  Even with verlet integration and GPU usage.  The only
 significant difference is the speed, which is now *much* higher.
**

Sorry about my rant from the former posting, my information was
not correct/complete when I wrote the posting.

M.

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Re: [gmx-users] Re: Membrane Runs Crashing

[Mirco Wahab]

On 19.06.2013 15:25, Neha wrote:

Here's the full mdp file. Please let me know if you need anymore information
and thank you so much for helping!

dt   = 0.02


Should be 0.03 according to S. Marrinks own remarks
(but wouldn't change your experience)


nstcomm  = 1


This looks much too conservative ;-)


Pcoupltype   = semiisotropic
tau_p= 1.0  1.0
compressibility  = 5e-6 0.0
ref_p= 0.0  0.0


This (compressibility = XY  Z) means, the "height" of your
box is not allowed to change? Is this the intended behaviour?

The ref_p of zero should not pose any real problem here,
MARTINI W is a strongly associating fluid and will freeze
trough your box in no time even when setting negative pressure
below 300K. In newer Gromacs versions (from 4.6) there seems
to be additional shift (?) in the potential, so the water phase
transition took another hit and went up to over 320K (with
verlet) and to about 315K (with shift).

I could provide you (*) a large Martini-DPPC-bilayer (~25nm²,
2 x 1330 DPPC), fully solvated in W (98654 W) which is
stable at 0.03ps even with verlet integration, and
semiisotropic Parinello-Rahman coupling at ref_p of { 0, 0},
or {1, 1} or whatever you like. I made this some time ago for
a student's experiment.

It's (at least for me) remarkably complicated to get such a
simple thing like a Martini-bilayer right. You have to
equilibrate the pure-water box (exactly the same box size
as your target system), you have to make sure there are NO
waters later within the bilayer left (after genbox solvation)
 - (I had to write a script to remove the waters at the bilayer
core expicitly).

Regards

M.



(*) drop me a e-mail


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[gmx-users] Re: Your Response to my GROMACS question

[Justin Lemkul]

Please keep the discussion on the gmx-users mailing list.

On 6/19/13 12:14 PM, Raji Viswanathan wrote:

Dear Justin,

Thanks for your response regarding running demo with gromacs.  Do I need to have
ngmx installed or can I use most functionalities of gromacs without installing
gromacs?



I have never really used ngmx, and it certainly does not carry out any essential 
function.  Better visualization software certainly exists; ngmx was just created 
as a quick visualizer that interfaced with Gromacs file formats.  Most external 
visualization programs handle Gromacs files just fine.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Running a Demo Calculation

[Justin Lemkul]

On 6/19/13 11:26 AM, Raji Viswanathan wrote:

I recently installed gromacs-4.5.5 and attempted to run the demo calculation.  
I did not get new xterm windows opened and also get the following error:

Starting Trajectory viewer...
ngmx: Command not found.
[1] 23192
[1]Exit 1ngmx -f cpeptide_md -s cpeptide_md

I would appreciate your help in solving this.



Apparently your computer does not have the X window libraries necessary to 
install ngmx, and thus it was skipped during installation.


Note that there are vastly better tutorials available for learning Gromacs.  The 
demo doesn't teach much of anything, it just runs through some commands.  It was 
for that reason that the demo was removed for version 4.6.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] how to describe the change of channel in the MD

[Justin Lemkul]

On 6/19/13 11:21 AM, aixintiankong wrote:



  Dear,
  In the MD, I find that when the ligand keep in the active site , the 
channel formed by two loops is closed. without the ligand the channel is 
opened. I don't know how to describe the change of channel. could i describe 
the channel by calculating the the most narrow distance(mass center) between 
the residues on the two loops? please give me some adviece. thank you very much!



This question was answered already:

http://lists.gromacs.org/pipermail/gmx-users/2013-June/082350.html

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] cholesteryl oleate parameters-reg

[Justin Lemkul]

On 6/19/13 9:46 AM, Revthi Sanker wrote:

​Dear all,

  I found a paper where they have updated
the c36 forcefield to include cholesterol parameters ( to which I should be 
able to modify by adding an oleate chain to get my cholesteryl oleate
moiety) :

http://pubs.acs.org/doi/pdf/10.1021/jp207925m

and I found this link:

http://lists.gromacs.org/pipermail/gmx-users/2010-October/054515.html  and 
further obtained the file:  toppar_all36_lipid_cholesterol.str
file. Should I try converting *.str file to an itp file that is compatible with
gromacs or can I add this as a new molecule to the existing lipids.rtp
in the charmm36.ff folder? Which would be a cleaner way of doing it? I
am unable to decide in this regard. Kindly provide me your valuable
suggestions.



It doesn't really matter which way you go.  The "cleaner" way depends on what 
type of coordinate file you have already.  If you have a pre-built configuration 
with molecules whose atoms conform to the force field expectations (atom names 
and presence of hydrogens), I'd say just make an .itp file.  If you need to 
construct hydrogen positions, build .rtp and .hdb files.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Re: Membrane Runs Crashing

[Justin Lemkul]

On 6/19/13 9:25 AM, Neha wrote:

Here's the full mdp file. Please let me know if you need anymore information
and thank you so much for helping!

; RUN CONTROL PARAMETERS =
integrator   = md
; start time and timestep in ps =
tinit= 0.0
dt   = 0.02
nsteps   = 5000
; number of steps for center of mass motion removal =
nstcomm  = 1
comm-grps= DPPC W

; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout  = 5
nstvout  = 5
nstfout  = 0
; Output frequency for energies to log file and energy file =
nstlog   = 1
nstenergy= 500
; Output frequency and precision for xtc file =
nstxtcout= 1
xtc_precision= 1000
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =xtc-grps
=
; Selection of energy groups =
energygrps   = DPPC W

; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist  = 10
; ns algorithm (simple or grid) =
ns_type  = grid
; Periodic boundary conditions: xyz or none =
pbc  = xyz
; nblist cut-off =
rlist= 1.2

; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype  = Shift
rcoulomb_switch  = 0.0
rcoulomb = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r= 15
; Method for doing Van der Waals =
vdw_type = Shift
; cut-off lengths=
rvdw_switch  = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No

; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling   =
tcoupl   = Berendsen
; Groups to couple separately =
tc-grps  = DPPC W
; Time constant (ps) and reference temperature (K) =
tau_t= 1.0 1.0
ref_t= 325 325
; Pressure coupling  =
Pcoupl   = berendsen
Pcoupltype   = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p= 1.0  1.0
compressibility  = 5e-6 0.0
ref_p= 0.0  0.0

; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel  = yes
gen_temp = 325
gen_seed = 473529

; OPTIONS FOR BONDS =
constraints  = none
; Type of constraint algorithm =
constraint_algorithm = Lincs
; Do not constrain the start configuration =
unconstrained_start  = no
; Highest order in the expansion of the constraint coupling matrix =
lincs_order  = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs_warnangle  = 30



What was the outcome of EM before this?  What if you try NVT before NPT?  Have 
you tried reducing the timestep or the value of nstlist?


I would try everything with ref_p = 1.0 instead of zero to make sure you can get 
a "normal" setup to work.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Running a Demo Calculation

[Raji Viswanathan]

I recently installed gromacs-4.5.5 and attempted to run the demo calculation.  
I did not get new xterm windows opened and also get the following error:

Starting Trajectory viewer...
ngmx: Command not found.
[1] 23192
[1]Exit 1ngmx -f cpeptide_md -s cpeptide_md

I would appreciate your help in solving this.

Thanks.
Raji
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[gmx-users] how to describe the change of channel in the MD

[aixintiankong]

 Dear,
 In the MD, I find that when the ligand keep in the active site , the 
channel formed by two loops is closed. without the ligand the channel is 
opened. I don't know how to describe the change of channel. could i describe 
the channel by calculating the the most narrow distance(mass center) between 
the residues on the two loops? please give me some adviece. thank you very much!
   


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[gmx-users] cholesteryl oleate parameters-reg

[Revthi Sanker]

​Dear all,

 I found a paper where they have updated 
the c36 forcefield to include cholesterol parameters ( to which I should be 
able to modify by adding an oleate chain to get my cholesteryl oleate 
moiety) :

http://pubs.acs.org/doi/pdf/10.1021/jp207925m

and I found this link:

http://lists.gromacs.org/pipermail/gmx-users/2010-October/054515.html  and 
further obtained the file:  toppar_all36_lipid_cholesterol.str 
file. Should I try converting *.str file to an itp file that is compatible with 
gromacs or can I add this as a new molecule to the existing lipids.rtp 
in the charmm36.ff folder? Which would be a cleaner way of doing it? I 
am unable to decide in this regard. Kindly provide me your valuable 
suggestions.

Thank you in advance.

Yours sincerely,

​Revathi.S
M.S. Research Scholar
Indian Institute Of Technology, Madras
India
__ 

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[gmx-users] Re: Membrane Runs Crashing

[Neha]

Here's the full mdp file. Please let me know if you need anymore information
and thank you so much for helping!

; RUN CONTROL PARAMETERS =
integrator   = md
; start time and timestep in ps =
tinit= 0.0
dt   = 0.02
nsteps   = 5000
; number of steps for center of mass motion removal =
nstcomm  = 1
comm-grps= DPPC W

; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout  = 5
nstvout  = 5
nstfout  = 0
; Output frequency for energies to log file and energy file =
nstlog   = 1
nstenergy= 500
; Output frequency and precision for xtc file =
nstxtcout= 1
xtc_precision= 1000
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =xtc-grps   
 
=
; Selection of energy groups =
energygrps   = DPPC W

; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist  = 10
; ns algorithm (simple or grid) =
ns_type  = grid
; Periodic boundary conditions: xyz or none =
pbc  = xyz
; nblist cut-off =
rlist= 1.2

; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype  = Shift
rcoulomb_switch  = 0.0
rcoulomb = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r= 15
; Method for doing Van der Waals =
vdw_type = Shift
; cut-off lengths=
rvdw_switch  = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No

; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling   =
tcoupl   = Berendsen
; Groups to couple separately =
tc-grps  = DPPC W
; Time constant (ps) and reference temperature (K) =
tau_t= 1.0 1.0
ref_t= 325 325
; Pressure coupling  =
Pcoupl   = berendsen
Pcoupltype   = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p= 1.0  1.0
compressibility  = 5e-6 0.0
ref_p= 0.0  0.0

; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel  = yes
gen_temp = 325
gen_seed = 473529

; OPTIONS FOR BONDS =
constraints  = none
; Type of constraint algorithm =
constraint_algorithm = Lincs
; Do not constrain the start configuration =
unconstrained_start  = no
; Highest order in the expansion of the constraint coupling matrix =
lincs_order  = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs_warnangle  = 30



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Re: [gmx-users] Quartic angle potential - how to use?

[Mark Abraham]

On Wed, Jun 19, 2013 at 10:30 AM, Steven Neumann wrote:

> Why? To avoid refining and extrapolating 100 tables for a Coarse grained
> run and use constants instead...


I'd still think writing the script in your language of choice to write out
the tables is a much lighter weight proposition than setting up the
machinery to build and read the equivalent [angletypes] database. And a
table is much easier to drop in a graph in a publication to show the
reviewer you did it right.

And to make it faster obviously.
>

That doesn't matter until you know the functional form is a good one to
use. So we'll assume that for here and now. Then you'd want to know that an
existing equivalent coarse-grained simulation spends at least 10% of its
time on its bonded interactions. Because unless that's true, even if half
the interactions are angles that now take twice the time because they're
tabulated, one is still not optimizing anything important.

Mark

>
> On Wed, Jun 19, 2013 at 9:22 AM, Mark Abraham  >wrote:
>
> > No. You're modifying the C code, so you will have to learn to maintain
> > a GROMACS installation. Yet another reason to avoid modifying the C
> > code :-)
> >
> > Mark
> >
> > On Wed, Jun 19, 2013 at 10:06 AM, Steven Neumann 
> > wrote:
> > > I will speak to someone who is familiar with the code. However, my
> > Gromacs
> > > version is installed on the cluster, can I create a file in my
> directory
> > > which will use this code with a given potential?
> > >
> > >
> > > On Wed, Jun 19, 2013 at 8:41 AM, Steven Neumann  > >wrote:
> > >
> > >>
> > >>
> > >>
> > >> On Tue, Jun 18, 2013 at 6:07 PM, Mark Abraham <
> mark.j.abra...@gmail.com
> > >wrote:
> > >>
> > >>> On Tue, Jun 18, 2013 at 5:39 PM, Steven Neumann <
> s.neuman...@gmail.com
> > >>> >wrote:
> > >>>
> > >>> > On Mon, Jun 10, 2013 at 1:22 PM, Justin Lemkul 
> > wrote:
> > >>> >
> > >>> > >
> > >>> > >
> > >>> > > On 6/10/13 5:16 AM, Steven Neumann wrote:
> > >>> > >
> > >>> > >> Thank you.
> > >>> > >> Do you know whether it is possible to use the 5th order
> polynomial
> > >>> for
> > >>> > >> angles in Gromacs? I know I can use tables but wish to fit my
> data
> > >>> into
> > >>> > >> such a function.
> > >>> > >>
> > >>> > >>
> > >>> > > Nothing in the manual seems to suggest that such a form is
> > supported.
> > >>> > >
> > >>> > > -Justin
> > >>> > >
> > >>> >
> > >>> > Would that be difficult to implement it into the code?
> > >>> >
> > >>>
> > >>> Not really, but since you can use a table to describe the functional
> > form
> > >>> even for a bonded interaction (see manual) then you should do that.
> > It's
> > >>> much better to prove the functional form is useful and works when you
> > >>> haven't touched the C code, and only touch the C code when it is
> clear
> > >>> that
> > >>> performance is an issue (which it probably isn't for any bonded
> > >>> interaction).
> > >>>
> > >>> Mark
> > >>>
> > >>
> > >> Thank you. I am trying to avoid tabulated potentials as much as I can
> so
> > >> hence my question. Can you please write me where in Gromacs direcotry
> I
> > >> could possibly modify it to see the code?
> > >>
> > >> Steven
> > >>
> > >>
> > >>>
> > >>> >
> > >>> > >  On Wed, Jun 5, 2013 at 5:55 PM, Justin Lemkul 
> > >>> wrote:
> > >>> > >>
> > >>> > >>
> > >>> > >>>
> > >>> > >>> On 6/5/13 8:40 AM, Steven Neumann wrote:
> > >>> > >>>
> > >>> > >>>  Dear Gmx Users,
> > >>> > 
> > >>> >  I wish to use quartic angle potential and specify all
> > constants. I
> > >>> > know
> > >>> >  it
> > >>> >  is a function 6 of [ angles ] but do not know how to place my
> > >>> > polynomial
> > >>> >  constants?
> > >>> > 
> > >>> > 
> > >>> >   As table 5.5 in the manual indicates, list the equilibrium
> > angle
> > >>> > >>> followed
> > >>> > >>> by all of the constants, in order.
> > >>> > >>>
> > >>> > >>> -Justin
> > >>> > >>>
> > >>> > >>> --
> > >>> > >>> ====
> > >>> > >>>
> > >>> > >>>
> > >>> > >>> Justin A. Lemkul, Ph.D.
> > >>> > >>> Research Scientist
> > >>> > >>> Department of Biochemistry
> > >>> > >>> Virginia Tech
> > >>> > >>> Blacksburg, VA
> > >>> > >>> jalemkul[at]vt.edu | (540) 231-9080
> > >>> > >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<
> > >>> > http://vt.edu/Pages/Personal/justin>
> > >>> > >>>  > >>> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> > >>> > >>> >
> > >>> > >>>
> > >>> > >>> ====
> > >>> > >>>
> > >>> > >>> --
> > >>> > >>> gmx-users mailing listgmx-users@gromacs.org
> > >>> > >>> http://lists.gromacs.org/mailman/listinfo/gmx-users<
> > >>> > http://lists.gromacs.org/**mailman/listinfo/gmx-users>
> > >>> > >>>  > >>> > http://lists.gromacs.org/mailman/listinfo/gmx-users>
> > >>> > >>> >
> > >>> > >>> * Please search the archive at http://www.gromacs.org/**
> > >>> > >>> Support/Mailing_Lists/Search www.gromacs.org/Support/**
> > >>> > >>> Mailing_List

[gmx-users] radial distribution function gAB (r, θ)

[neshat haq]

Gromacs manual explains "radial distribution function gAB (r, θ)"
but g_rdf donot have options to directly do this.
Can anyone elaborate this.

-- 
Best regards
Neshatul Haque
PhD, Dpt of Biotechnology
university of hyderabad
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Re: [gmx-users] Re: QM/MM simulations

[Justin Lemkul]

On 6/19/13 6:11 AM, DavidPO wrote:

Hello.

I followed your advice and tried different versions of GROMACS (4.5.6,
4.6.2). All of them  give one and the same error:

Program mdrun, VERSION 4.5.6 (or 4.6.2)
Source code file: /home/timofeev/GROMACS/gromacs-4.5.6/src/mdlib/qmmm.c,
line: 710
Fatal error:
Ab-initio calculation only supported with Gamess, Gaussian or ORCA.

If I understand right, it occur because the GROMACS doesn't receive a value
of qm/mm program.



I have posted a patch at https://gerrit.gromacs.org/#/c/2455/ that fixes the 
build system issue.  There may be other issues with the ORCA QM/MM interface, 
though, but that's a separate issue.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] InflateGRO methodology deletion radius

[Justin Lemkul]

On 6/19/13 7:23 AM, Shima Arasteh wrote:

Do you mean another published paper rather than published one in Methods 
Journal? Another one which explains the algorithm?



That's a useful one.  There is a lot of helpful information on the InflateGRO 
website (http://www.csb.bit.uni-bonn.de/inflategro.html), and there is a new 
version of InflateGRO that has new features and is explained very thoroughly in 
this paper:


Schmidt TH, Kandt C (2012): LAMBADA & InflateGRO2: Efficient Membrane Alignment 
and Insertion of Membrane Proteins for Molecular Dynamics Simulations Journal of 
Chemical Information and Modeling 52(10): 2657-2669


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] InflateGRO methodology deletion radius

[Shima Arasteh]

Do you mean another published paper rather than published one in Methods 
Journal? Another one which explains the algorithm?


 
Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Discussion list for GROMACS users 
Cc: 
Sent: Wednesday, June 19, 2013 3:45 PM
Subject: Re: [gmx-users] InflateGRO methodology deletion radius



On 6/19/13 12:39 AM, Shima Arasteh wrote:
> Do you mean the commands of inflateGRO controls the deletion radius?
>

Yes, that's its purpose.  There is a published paper about its algorithm; I 
would suggest you read and understand it.

>   The command which I use is what I got from tutorial:
> #perl inflategro.pl em.gro 0.95 POPC 0 em_shrink1.gro 5 area_shrink1.dat
>
> Am I supposed to decrease 5 as deletion radius?

The value of 5 is a grid spacing for the InflateGRO APL measurement.  The 
deletion radius is zero, which is correct for shrinking because you don't want 
to continue deleting lipids, or you will have no membrane left!

> Would you please give me a hint to go on?
>

If these concepts are not intuitive, you should absolutely stop and read the 
paper for InflateGRO and watch the demonstration video that is posted online.

-Justin

> Thanks for your suggestions in advance. Those are really kind of you.
> Sincerely,
> Shima
>
> - Original Message -
> From: Justin Lemkul 
> To: Shima Arasteh ; Discussion list for GROMACS
> users 
> Cc:
> Sent: Saturday, June 15, 2013 4:18 PM
> Subject: Re: [gmx-users] InflateGRO methodology deletion radius
>
>
>
> On 6/15/13 3:56 AM, Shima Arasteh wrote:
>  > Hi,
>  >
>  > In Kalp15_DPPC tutorial, when the InflateGRO methodology is applied to pack
> the lipids, I need to follow the iteration while the cutoff value changed to 
> 0.
>  > I' d like to know what settings of EM.mdp file are suggested to get the 
>best
> results of doing shrinking steps?
>  > When I set the settings as follow, the lipids interfere the peptide however
> the APL doesn't get the experimental value. So the configuration is not ideal 
> to
> get through the equilibrium steps.
>  >
>  > define        = -DPOSRES
>  > integrator    = steep        ; Algorithm (steep = steepest descent 
>minimization)
>  > emtol        = 100.0      ; Stop minimization when the maximum force < 
>100.0
> kJ/mol/nm
>  > emstep            = 0.01      ; Energy step size
>  > nsteps        = 5          ; Maximum number of (minimization) steps to
> perform
>  > ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
>  > nstlist        = 1            ; Frequency to update the neighbor list and
> long range forces
>  > ns_type        = grid        ; Method to determine neighbor list (simple, 
>grid)
>  > rlist        = 0.4    ; Cut-off for making neighbor list (short range 
>forces)
>  > rlistlong      = 6.0
>  > coulombtype    = PME        ; Treatment of long range electrostatic 
>interactions
>  > rcoulomb    = 0.4     ; Short-range electrostatic cut-off
>  > rvdw        = 0.4        ; Short-range Van der Waals cut-off
>  > vdwtype        = switch
>  > rvdw_switch    = 0.2
>  > pbc        = xyz        ; Periodic Boundary Conditions
>  >
>  >
>  >
>  > Now, I am wondering if such a settings will serve a proper deletion radius?
>  >
>
> No.  These settings make no sense to me whatsoever.  Don't be confused by the
> "cutoff" used by InflateGRO and the cutoff values used in the .mdp file.
> InflateGRO uses a search radius to delete lipids, which is specified on the
> command line.  The cutoff values for the EM and MD runs are dictated by the
> force field you are using and are in no way connected to lipid deletion.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 

-- 


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Re: QM/MM simulations

[Justin Lemkul]

On 6/19/13 6:11 AM, DavidPO wrote:

Hello.

I followed your advice and tried different versions of GROMACS (4.5.6,
4.6.2). All of them  give one and the same error:



OK, good to know.


Program mdrun, VERSION 4.5.6 (or 4.6.2)
Source code file: /home/timofeev/GROMACS/gromacs-4.5.6/src/mdlib/qmmm.c,
line: 710
Fatal error:
Ab-initio calculation only supported with Gamess, Gaussian or ORCA.

If I understand right, it occur because the GROMACS doesn't receive a value
of qm/mm program.



Yes, it appears that the installation process completes without error, but the 
QM program is not actually linked to mdrun in any useful way.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] InflateGRO methodology deletion radius

[Justin Lemkul]

On 6/19/13 12:39 AM, Shima Arasteh wrote:

Do you mean the commands of inflateGRO controls the deletion radius?



Yes, that's its purpose.  There is a published paper about its algorithm; I 
would suggest you read and understand it.



  The command which I use is what I got from tutorial:
#perl inflategro.pl em.gro 0.95 POPC 0 em_shrink1.gro 5 area_shrink1.dat

Am I supposed to decrease 5 as deletion radius?


The value of 5 is a grid spacing for the InflateGRO APL measurement.  The 
deletion radius is zero, which is correct for shrinking because you don't want 
to continue deleting lipids, or you will have no membrane left!



Would you please give me a hint to go on?



If these concepts are not intuitive, you should absolutely stop and read the 
paper for InflateGRO and watch the demonstration video that is posted online.


-Justin


Thanks for your suggestions in advance. Those are really kind of you.
Sincerely,
Shima

- Original Message -
From: Justin Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS
users 
Cc:
Sent: Saturday, June 15, 2013 4:18 PM
Subject: Re: [gmx-users] InflateGRO methodology deletion radius



On 6/15/13 3:56 AM, Shima Arasteh wrote:
 > Hi,
 >
 > In Kalp15_DPPC tutorial, when the InflateGRO methodology is applied to pack
the lipids, I need to follow the iteration while the cutoff value changed to 0.
 > I' d like to know what settings of EM.mdp file are suggested to get the best
results of doing shrinking steps?
 > When I set the settings as follow, the lipids interfere the peptide however
the APL doesn't get the experimental value. So the configuration is not ideal to
get through the equilibrium steps.
 >
 > define= -DPOSRES
 > integrator= steep; Algorithm (steep = steepest descent 
minimization)
 > emtol= 100.0  ; Stop minimization when the maximum force < 100.0
kJ/mol/nm
 > emstep= 0.01  ; Energy step size
 > nsteps= 5  ; Maximum number of (minimization) steps to
perform
 > ; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
 > nstlist= 1; Frequency to update the neighbor list and
long range forces
 > ns_type= grid; Method to determine neighbor list (simple, 
grid)
 > rlist= 0.4; Cut-off for making neighbor list (short range forces)
 > rlistlong  = 6.0
 > coulombtype= PME; Treatment of long range electrostatic 
interactions
 > rcoulomb= 0.4 ; Short-range electrostatic cut-off
 > rvdw= 0.4; Short-range Van der Waals cut-off
 > vdwtype= switch
 > rvdw_switch= 0.2
 > pbc= xyz; Periodic Boundary Conditions
 >
 >
 >
 > Now, I am wondering if such a settings will serve a proper deletion radius?
 >

No.  These settings make no sense to me whatsoever.  Don't be confused by the
"cutoff" used by InflateGRO and the cutoff values used in the .mdp file.
InflateGRO uses a search radius to delete lipids, which is specified on the
command line.  The cutoff values for the EM and MD runs are dictated by the
force field you are using and are in no way connected to lipid deletion.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Re: Membrane Runs Crashing

[Justin Lemkul]

On 6/18/13 10:12 PM, Neha wrote:

Hi,

Well, I tried running a simulation at ref_p to 1.0 and got the same error as
earlier, so it doesn't seem to be that. That was the only thing I changed in
the mdp file, so I am still not sure as to where the problem is.



Please post a full .mdp file; partial .mdp files are rarely useful.

-Justin



Justin Lemkul wrote

On 6/18/13 3:13 PM, Neha wrote:

Hi everybody!

I am trying to simulate a lipid membrane at zero pressure and at a range
of
temperatures. I am using a bilayer from the Martini website. I was having
a
problem with the Parinello-Rahman barostat so I switched to Berendsen and
am
also keeping the height of the box constant otherwise it grows
uncontrollably. However my runs keep crashing, giving the error of atoms
having moved too far beyond the cut-off distance. I have attached part of
my
mdp file, and would love any suggestions as to how to alter it to get
more
fruitful runs. I am still really new to Gromacs and want to make sure I
am
not doing something completely wrong.

; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype  = Shift
rcoulomb_switch  = 0.0
rcoulomb = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r= 15
; Method for doing Van der Waals =
vdw_type = Shift
; cut-off lengths=
rvdw_switch  = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No

; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling   =
tcoupl   = Berendsen
; Groups to couple separately =
tc-grps  = DPPC W
; Time constant (ps) and reference temperature (K) =
tau_t= 1.0 1.0
ref_t= 325 325
; Pressure coupling  =
Pcoupl   = berendsen
Pcoupltype   = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p= 1.0  1.0
compressibility  = 5e-6 0.0
ref_p= 0.0  0.0

; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel  = yes
gen_temp = 325
gen_seed = 473529

Please let me know!



What happens if you set ref_p to 1.0?  I don't understand the use of zero
pressure; your system is expanding out into a vacuum and that's likely why
the
z-dimension is expanding uncontrollably.  Water diffuses faster than the
lipids,
so the z-dimension expands faster than x-y does.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Re: QM/MM simulations

[DavidPO]

Hello.

I followed your advice and tried different versions of GROMACS (4.5.6,
4.6.2). All of them  give one and the same error:

Program mdrun, VERSION 4.5.6 (or 4.6.2) 
Source code file: /home/timofeev/GROMACS/gromacs-4.5.6/src/mdlib/qmmm.c,
line: 710
Fatal error:
Ab-initio calculation only supported with Gamess, Gaussian or ORCA.

If I understand right, it occur because the GROMACS doesn't receive a value
of qm/mm program.


David



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Re: [gmx-users] Quartic angle potential - how to use?

[Steven Neumann]

Why? To avoid refining and extrapolating 100 tables for a Coarse grained
run and use constants instead... And to make it faster obviously.


On Wed, Jun 19, 2013 at 9:22 AM, Mark Abraham wrote:

> No. You're modifying the C code, so you will have to learn to maintain
> a GROMACS installation. Yet another reason to avoid modifying the C
> code :-)
>
> Mark
>
> On Wed, Jun 19, 2013 at 10:06 AM, Steven Neumann 
> wrote:
> > I will speak to someone who is familiar with the code. However, my
> Gromacs
> > version is installed on the cluster, can I create a file in my directory
> > which will use this code with a given potential?
> >
> >
> > On Wed, Jun 19, 2013 at 8:41 AM, Steven Neumann  >wrote:
> >
> >>
> >>
> >>
> >> On Tue, Jun 18, 2013 at 6:07 PM, Mark Abraham  >wrote:
> >>
> >>> On Tue, Jun 18, 2013 at 5:39 PM, Steven Neumann  >>> >wrote:
> >>>
> >>> > On Mon, Jun 10, 2013 at 1:22 PM, Justin Lemkul 
> wrote:
> >>> >
> >>> > >
> >>> > >
> >>> > > On 6/10/13 5:16 AM, Steven Neumann wrote:
> >>> > >
> >>> > >> Thank you.
> >>> > >> Do you know whether it is possible to use the 5th order polynomial
> >>> for
> >>> > >> angles in Gromacs? I know I can use tables but wish to fit my data
> >>> into
> >>> > >> such a function.
> >>> > >>
> >>> > >>
> >>> > > Nothing in the manual seems to suggest that such a form is
> supported.
> >>> > >
> >>> > > -Justin
> >>> > >
> >>> >
> >>> > Would that be difficult to implement it into the code?
> >>> >
> >>>
> >>> Not really, but since you can use a table to describe the functional
> form
> >>> even for a bonded interaction (see manual) then you should do that.
> It's
> >>> much better to prove the functional form is useful and works when you
> >>> haven't touched the C code, and only touch the C code when it is clear
> >>> that
> >>> performance is an issue (which it probably isn't for any bonded
> >>> interaction).
> >>>
> >>> Mark
> >>>
> >>
> >> Thank you. I am trying to avoid tabulated potentials as much as I can so
> >> hence my question. Can you please write me where in Gromacs direcotry I
> >> could possibly modify it to see the code?
> >>
> >> Steven
> >>
> >>
> >>>
> >>> >
> >>> > >  On Wed, Jun 5, 2013 at 5:55 PM, Justin Lemkul 
> >>> wrote:
> >>> > >>
> >>> > >>
> >>> > >>>
> >>> > >>> On 6/5/13 8:40 AM, Steven Neumann wrote:
> >>> > >>>
> >>> > >>>  Dear Gmx Users,
> >>> > 
> >>> >  I wish to use quartic angle potential and specify all
> constants. I
> >>> > know
> >>> >  it
> >>> >  is a function 6 of [ angles ] but do not know how to place my
> >>> > polynomial
> >>> >  constants?
> >>> > 
> >>> > 
> >>> >   As table 5.5 in the manual indicates, list the equilibrium
> angle
> >>> > >>> followed
> >>> > >>> by all of the constants, in order.
> >>> > >>>
> >>> > >>> -Justin
> >>> > >>>
> >>> > >>> --
> >>> > >>> ====
> >>> > >>>
> >>> > >>>
> >>> > >>> Justin A. Lemkul, Ph.D.
> >>> > >>> Research Scientist
> >>> > >>> Department of Biochemistry
> >>> > >>> Virginia Tech
> >>> > >>> Blacksburg, VA
> >>> > >>> jalemkul[at]vt.edu | (540) 231-9080
> >>> > >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<
> >>> > http://vt.edu/Pages/Personal/justin>
> >>> > >>>  >>> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> >>> > >>> >
> >>> > >>>
> >>> > >>> ====
> >>> > >>>
> >>> > >>> --
> >>> > >>> gmx-users mailing listgmx-users@gromacs.org
> >>> > >>> http://lists.gromacs.org/mailman/listinfo/gmx-users<
> >>> > http://lists.gromacs.org/**mailman/listinfo/gmx-users>
> >>> > >>>  >>> > http://lists.gromacs.org/mailman/listinfo/gmx-users>
> >>> > >>> >
> >>> > >>> * Please search the archive at http://www.gromacs.org/**
> >>> > >>> Support/Mailing_Lists/Search >>> > >>> Mailing_Lists/Search<
> >>> > http://www.gromacs.org/Support/Mailing_Lists/Search>>before
> >>> > >>> posting!
> >>> > >>>
> >>> > >>> * Please don't post (un)subscribe requests to the list. Use the
> www
> >>> > >>> interface or send it to gmx-users-requ...@gromacs.org.
> >>> > >>> * Can't post? Read
> http://www.gromacs.org/Support/Mailing_Lists
> >>> <
> >>> > http://www.gromacs.org/**Support/Mailing_Lists>
> >>> > >>>  >>> > http://www.gromacs.org/Support/Mailing_Lists>
> >>> > >>> >
> >>> > >>>
> >>> > >>>
> >>> > > --
> >>> > > ==**==
> >>> > >
> >>> > > Justin A. Lemkul, Ph.D.
> >>> > > Research Scientist
> >>> > > Department of Biochemistry
> >>> > > Virginia Tech
> >>> > > Blacksburg, VA
> >>> > > jalemkul[at]vt.edu | (540) 231-9080
> >>> > > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
> >>> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> >>> > >
> >>> > > ==**==
> >>> > > --
> >>> > > gmx-users mailing listgmx-users@gromacs.org
> >>> > > http://lists.gromacs.org/**mailman/listinfo/gmx-users

Re: [gmx-users] Quartic angle potential - how to use?

[Mark Abraham]

No. You're modifying the C code, so you will have to learn to maintain
a GROMACS installation. Yet another reason to avoid modifying the C
code :-)

Mark

On Wed, Jun 19, 2013 at 10:06 AM, Steven Neumann  wrote:
> I will speak to someone who is familiar with the code. However, my Gromacs
> version is installed on the cluster, can I create a file in my directory
> which will use this code with a given potential?
>
>
> On Wed, Jun 19, 2013 at 8:41 AM, Steven Neumann wrote:
>
>>
>>
>>
>> On Tue, Jun 18, 2013 at 6:07 PM, Mark Abraham 
>> wrote:
>>
>>> On Tue, Jun 18, 2013 at 5:39 PM, Steven Neumann >> >wrote:
>>>
>>> > On Mon, Jun 10, 2013 at 1:22 PM, Justin Lemkul  wrote:
>>> >
>>> > >
>>> > >
>>> > > On 6/10/13 5:16 AM, Steven Neumann wrote:
>>> > >
>>> > >> Thank you.
>>> > >> Do you know whether it is possible to use the 5th order polynomial
>>> for
>>> > >> angles in Gromacs? I know I can use tables but wish to fit my data
>>> into
>>> > >> such a function.
>>> > >>
>>> > >>
>>> > > Nothing in the manual seems to suggest that such a form is supported.
>>> > >
>>> > > -Justin
>>> > >
>>> >
>>> > Would that be difficult to implement it into the code?
>>> >
>>>
>>> Not really, but since you can use a table to describe the functional form
>>> even for a bonded interaction (see manual) then you should do that. It's
>>> much better to prove the functional form is useful and works when you
>>> haven't touched the C code, and only touch the C code when it is clear
>>> that
>>> performance is an issue (which it probably isn't for any bonded
>>> interaction).
>>>
>>> Mark
>>>
>>
>> Thank you. I am trying to avoid tabulated potentials as much as I can so
>> hence my question. Can you please write me where in Gromacs direcotry I
>> could possibly modify it to see the code?
>>
>> Steven
>>
>>
>>>
>>> >
>>> > >  On Wed, Jun 5, 2013 at 5:55 PM, Justin Lemkul 
>>> wrote:
>>> > >>
>>> > >>
>>> > >>>
>>> > >>> On 6/5/13 8:40 AM, Steven Neumann wrote:
>>> > >>>
>>> > >>>  Dear Gmx Users,
>>> > 
>>> >  I wish to use quartic angle potential and specify all constants. I
>>> > know
>>> >  it
>>> >  is a function 6 of [ angles ] but do not know how to place my
>>> > polynomial
>>> >  constants?
>>> > 
>>> > 
>>> >   As table 5.5 in the manual indicates, list the equilibrium angle
>>> > >>> followed
>>> > >>> by all of the constants, in order.
>>> > >>>
>>> > >>> -Justin
>>> > >>>
>>> > >>> --
>>> > >>> ====
>>> > >>>
>>> > >>>
>>> > >>> Justin A. Lemkul, Ph.D.
>>> > >>> Research Scientist
>>> > >>> Department of Biochemistry
>>> > >>> Virginia Tech
>>> > >>> Blacksburg, VA
>>> > >>> jalemkul[at]vt.edu | (540) 231-9080
>>> > >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<
>>> > http://vt.edu/Pages/Personal/justin>
>>> > >>> >> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>> > >>> >
>>> > >>>
>>> > >>> ====
>>> > >>>
>>> > >>> --
>>> > >>> gmx-users mailing listgmx-users@gromacs.org
>>> > >>> http://lists.gromacs.org/mailman/listinfo/gmx-users<
>>> > http://lists.gromacs.org/**mailman/listinfo/gmx-users>
>>> > >>> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>> > >>> >
>>> > >>> * Please search the archive at http://www.gromacs.org/**
>>> > >>> Support/Mailing_Lists/Search>> > >>> Mailing_Lists/Search<
>>> > http://www.gromacs.org/Support/Mailing_Lists/Search>>before
>>> > >>> posting!
>>> > >>>
>>> > >>> * Please don't post (un)subscribe requests to the list. Use the www
>>> > >>> interface or send it to gmx-users-requ...@gromacs.org.
>>> > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>> <
>>> > http://www.gromacs.org/**Support/Mailing_Lists>
>>> > >>> >> > http://www.gromacs.org/Support/Mailing_Lists>
>>> > >>> >
>>> > >>>
>>> > >>>
>>> > > --
>>> > > ==**==
>>> > >
>>> > > Justin A. Lemkul, Ph.D.
>>> > > Research Scientist
>>> > > Department of Biochemistry
>>> > > Virginia Tech
>>> > > Blacksburg, VA
>>> > > jalemkul[at]vt.edu | (540) 231-9080
>>> > > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
>>> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>> > >
>>> > > ==**==
>>> > > --
>>> > > gmx-users mailing listgmx-users@gromacs.org
>>> > > http://lists.gromacs.org/**mailman/listinfo/gmx-users<
>>> > http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>> > > * Please search the archive at http://www.gromacs.org/**
>>> > > Support/Mailing_Lists/Search<
>>> > http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>>> > > * Please don't post (un)subscribe requests to the list. Use the www
>>> > > interface or send it to gmx-users-requ...@gromacs.org.
>>> > > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
>>> > http://www.gromacs.org/Support/Mailing_List

Re: [gmx-users] Quartic angle potential - how to use?

[Mark Abraham]

On Wed, Jun 19, 2013 at 9:41 AM, Steven Neumann  wrote:
> On Tue, Jun 18, 2013 at 6:07 PM, Mark Abraham wrote:
>
>> On Tue, Jun 18, 2013 at 5:39 PM, Steven Neumann > >wrote:
>>
>> > On Mon, Jun 10, 2013 at 1:22 PM, Justin Lemkul  wrote:
>> >
>> > >
>> > >
>> > > On 6/10/13 5:16 AM, Steven Neumann wrote:
>> > >
>> > >> Thank you.
>> > >> Do you know whether it is possible to use the 5th order polynomial for
>> > >> angles in Gromacs? I know I can use tables but wish to fit my data
>> into
>> > >> such a function.
>> > >>
>> > >>
>> > > Nothing in the manual seems to suggest that such a form is supported.
>> > >
>> > > -Justin
>> > >
>> >
>> > Would that be difficult to implement it into the code?
>> >
>>
>> Not really, but since you can use a table to describe the functional form
>> even for a bonded interaction (see manual) then you should do that. It's
>> much better to prove the functional form is useful and works when you
>> haven't touched the C code, and only touch the C code when it is clear that
>> performance is an issue (which it probably isn't for any bonded
>> interaction).
>>
>> Mark
>>
>
> Thank you. I am trying to avoid tabulated potentials as much as I can so
> hence my question.

Why? You're just making extra work.

> Can you please write me where in Gromacs direcotry I
> could possibly modify it to see the code?

See src/gmxlib/bondfree.c. And then work out how to get your
parameters read in from a .top file and written to an .tpr file and
maintained in different data structures accordingly.

Mark

>
> Steven
>
>
>>
>> >
>> > >  On Wed, Jun 5, 2013 at 5:55 PM, Justin Lemkul 
>> wrote:
>> > >>
>> > >>
>> > >>>
>> > >>> On 6/5/13 8:40 AM, Steven Neumann wrote:
>> > >>>
>> > >>>  Dear Gmx Users,
>> > 
>> >  I wish to use quartic angle potential and specify all constants. I
>> > know
>> >  it
>> >  is a function 6 of [ angles ] but do not know how to place my
>> > polynomial
>> >  constants?
>> > 
>> > 
>> >   As table 5.5 in the manual indicates, list the equilibrium angle
>> > >>> followed
>> > >>> by all of the constants, in order.
>> > >>>
>> > >>> -Justin
>> > >>>
>> > >>> --
>> > >>> ====
>> > >>>
>> > >>>
>> > >>> Justin A. Lemkul, Ph.D.
>> > >>> Research Scientist
>> > >>> Department of Biochemistry
>> > >>> Virginia Tech
>> > >>> Blacksburg, VA
>> > >>> jalemkul[at]vt.edu | (540) 231-9080
>> > >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<
>> > http://vt.edu/Pages/Personal/justin>
>> > >>> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> > >>> >
>> > >>>
>> > >>> ====
>> > >>>
>> > >>> --
>> > >>> gmx-users mailing listgmx-users@gromacs.org
>> > >>> http://lists.gromacs.org/mailman/listinfo/gmx-users<
>> > http://lists.gromacs.org/**mailman/listinfo/gmx-users>
>> > >>> > > http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> > >>> >
>> > >>> * Please search the archive at http://www.gromacs.org/**
>> > >>> Support/Mailing_Lists/Search> > >>> Mailing_Lists/Search<
>> > http://www.gromacs.org/Support/Mailing_Lists/Search>>before
>> > >>> posting!
>> > >>>
>> > >>> * Please don't post (un)subscribe requests to the list. Use the www
>> > >>> interface or send it to gmx-users-requ...@gromacs.org.
>> > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<
>> > http://www.gromacs.org/**Support/Mailing_Lists>
>> > >>> > > http://www.gromacs.org/Support/Mailing_Lists>
>> > >>> >
>> > >>>
>> > >>>
>> > > --
>> > > ==**==
>> > >
>> > > Justin A. Lemkul, Ph.D.
>> > > Research Scientist
>> > > Department of Biochemistry
>> > > Virginia Tech
>> > > Blacksburg, VA
>> > > jalemkul[at]vt.edu | (540) 231-9080
>> > > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
>> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> > >
>> > > ==**==
>> > > --
>> > > gmx-users mailing listgmx-users@gromacs.org
>> > > http://lists.gromacs.org/**mailman/listinfo/gmx-users<
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> > > * Please search the archive at http://www.gromacs.org/**
>> > > Support/Mailing_Lists/Search<
>> > http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>> > > * Please don't post (un)subscribe requests to the list. Use the www
>> > > interface or send it to gmx-users-requ...@gromacs.org.
>> > > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
>> > http://www.gromacs.org/Support/Mailing_Lists>
>> > >
>> > --
>> > gmx-users mailing listgmx-users@gromacs.org
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> > * Please don't post (un)subscribe requests to the list. Use the
>> > www interface or send it to gmx-users-r

Re: [gmx-users] Quartic angle potential - how to use?

[Steven Neumann]

I will speak to someone who is familiar with the code. However, my Gromacs
version is installed on the cluster, can I create a file in my directory
which will use this code with a given potential?


On Wed, Jun 19, 2013 at 8:41 AM, Steven Neumann wrote:

>
>
>
> On Tue, Jun 18, 2013 at 6:07 PM, Mark Abraham wrote:
>
>> On Tue, Jun 18, 2013 at 5:39 PM, Steven Neumann > >wrote:
>>
>> > On Mon, Jun 10, 2013 at 1:22 PM, Justin Lemkul  wrote:
>> >
>> > >
>> > >
>> > > On 6/10/13 5:16 AM, Steven Neumann wrote:
>> > >
>> > >> Thank you.
>> > >> Do you know whether it is possible to use the 5th order polynomial
>> for
>> > >> angles in Gromacs? I know I can use tables but wish to fit my data
>> into
>> > >> such a function.
>> > >>
>> > >>
>> > > Nothing in the manual seems to suggest that such a form is supported.
>> > >
>> > > -Justin
>> > >
>> >
>> > Would that be difficult to implement it into the code?
>> >
>>
>> Not really, but since you can use a table to describe the functional form
>> even for a bonded interaction (see manual) then you should do that. It's
>> much better to prove the functional form is useful and works when you
>> haven't touched the C code, and only touch the C code when it is clear
>> that
>> performance is an issue (which it probably isn't for any bonded
>> interaction).
>>
>> Mark
>>
>
> Thank you. I am trying to avoid tabulated potentials as much as I can so
> hence my question. Can you please write me where in Gromacs direcotry I
> could possibly modify it to see the code?
>
> Steven
>
>
>>
>> >
>> > >  On Wed, Jun 5, 2013 at 5:55 PM, Justin Lemkul 
>> wrote:
>> > >>
>> > >>
>> > >>>
>> > >>> On 6/5/13 8:40 AM, Steven Neumann wrote:
>> > >>>
>> > >>>  Dear Gmx Users,
>> > 
>> >  I wish to use quartic angle potential and specify all constants. I
>> > know
>> >  it
>> >  is a function 6 of [ angles ] but do not know how to place my
>> > polynomial
>> >  constants?
>> > 
>> > 
>> >   As table 5.5 in the manual indicates, list the equilibrium angle
>> > >>> followed
>> > >>> by all of the constants, in order.
>> > >>>
>> > >>> -Justin
>> > >>>
>> > >>> --
>> > >>> ====
>> > >>>
>> > >>>
>> > >>> Justin A. Lemkul, Ph.D.
>> > >>> Research Scientist
>> > >>> Department of Biochemistry
>> > >>> Virginia Tech
>> > >>> Blacksburg, VA
>> > >>> jalemkul[at]vt.edu | (540) 231-9080
>> > >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<
>> > http://vt.edu/Pages/Personal/justin>
>> > >>> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> > >>> >
>> > >>>
>> > >>> ====
>> > >>>
>> > >>> --
>> > >>> gmx-users mailing listgmx-users@gromacs.org
>> > >>> http://lists.gromacs.org/mailman/listinfo/gmx-users<
>> > http://lists.gromacs.org/**mailman/listinfo/gmx-users>
>> > >>> > > http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> > >>> >
>> > >>> * Please search the archive at http://www.gromacs.org/**
>> > >>> Support/Mailing_Lists/Search> > >>> Mailing_Lists/Search<
>> > http://www.gromacs.org/Support/Mailing_Lists/Search>>before
>> > >>> posting!
>> > >>>
>> > >>> * Please don't post (un)subscribe requests to the list. Use the www
>> > >>> interface or send it to gmx-users-requ...@gromacs.org.
>> > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> <
>> > http://www.gromacs.org/**Support/Mailing_Lists>
>> > >>> > > http://www.gromacs.org/Support/Mailing_Lists>
>> > >>> >
>> > >>>
>> > >>>
>> > > --
>> > > ==**==
>> > >
>> > > Justin A. Lemkul, Ph.D.
>> > > Research Scientist
>> > > Department of Biochemistry
>> > > Virginia Tech
>> > > Blacksburg, VA
>> > > jalemkul[at]vt.edu | (540) 231-9080
>> > > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
>> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> > >
>> > > ==**==
>> > > --
>> > > gmx-users mailing listgmx-users@gromacs.org
>> > > http://lists.gromacs.org/**mailman/listinfo/gmx-users<
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> > > * Please search the archive at http://www.gromacs.org/**
>> > > Support/Mailing_Lists/Search<
>> > http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>> > > * Please don't post (un)subscribe requests to the list. Use the www
>> > > interface or send it to gmx-users-requ...@gromacs.org.
>> > > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
>> > http://www.gromacs.org/Support/Mailing_Lists>
>> > >
>> > --
>> > gmx-users mailing listgmx-users@gromacs.org
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> > * Please don't post (un)subscribe requests to the list. Use the
>> > www interface or send it to gmx-users-requ...@gromacs.

Re: [gmx-users] how to describe the change of channel in the MD

[francesco oteri]

Hi,
you can use CAVER (http://www.caver.cz/) to detect tunnels. In the first
case you should not see anything while in the second you shold see a
channel.An other program you can use i s MDPocket ( '
http://bioserv.rpbs.univ-paris-diderot.fr/fpocket/): It simply detects
cavities (either tunnels or closed cavitiies)  and outputs informations.

I successfully used these two software to characterize tunnels and cavities
in a MD simulation.


Francesco




2013/6/19 aixintiankong 

>
>
>  Dear,
>  In the MD, I find that when the ligand keep in the active site , the
> channel formed by two loops is closed. without the ligand the channel is
> opened. I don't know how to describe the change of channel. could i
> describe the channel by calculating the the most narrow distance(mass
> center) between the residues on the two loops? please give me some adviece.
> thank you very much!
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Oteri Francesco, PhD
https://sites.google.com/site/francescooteri
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Quartic angle potential - how to use?

[Steven Neumann]

On Tue, Jun 18, 2013 at 6:07 PM, Mark Abraham wrote:

> On Tue, Jun 18, 2013 at 5:39 PM, Steven Neumann  >wrote:
>
> > On Mon, Jun 10, 2013 at 1:22 PM, Justin Lemkul  wrote:
> >
> > >
> > >
> > > On 6/10/13 5:16 AM, Steven Neumann wrote:
> > >
> > >> Thank you.
> > >> Do you know whether it is possible to use the 5th order polynomial for
> > >> angles in Gromacs? I know I can use tables but wish to fit my data
> into
> > >> such a function.
> > >>
> > >>
> > > Nothing in the manual seems to suggest that such a form is supported.
> > >
> > > -Justin
> > >
> >
> > Would that be difficult to implement it into the code?
> >
>
> Not really, but since you can use a table to describe the functional form
> even for a bonded interaction (see manual) then you should do that. It's
> much better to prove the functional form is useful and works when you
> haven't touched the C code, and only touch the C code when it is clear that
> performance is an issue (which it probably isn't for any bonded
> interaction).
>
> Mark
>

Thank you. I am trying to avoid tabulated potentials as much as I can so
hence my question. Can you please write me where in Gromacs direcotry I
could possibly modify it to see the code?

Steven


>
> >
> > >  On Wed, Jun 5, 2013 at 5:55 PM, Justin Lemkul 
> wrote:
> > >>
> > >>
> > >>>
> > >>> On 6/5/13 8:40 AM, Steven Neumann wrote:
> > >>>
> > >>>  Dear Gmx Users,
> > 
> >  I wish to use quartic angle potential and specify all constants. I
> > know
> >  it
> >  is a function 6 of [ angles ] but do not know how to place my
> > polynomial
> >  constants?
> > 
> > 
> >   As table 5.5 in the manual indicates, list the equilibrium angle
> > >>> followed
> > >>> by all of the constants, in order.
> > >>>
> > >>> -Justin
> > >>>
> > >>> --
> > >>> ====
> > >>>
> > >>>
> > >>> Justin A. Lemkul, Ph.D.
> > >>> Research Scientist
> > >>> Department of Biochemistry
> > >>> Virginia Tech
> > >>> Blacksburg, VA
> > >>> jalemkul[at]vt.edu | (540) 231-9080
> > >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<
> > http://vt.edu/Pages/Personal/justin>
> > >>>  > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> > >>> >
> > >>>
> > >>> ====
> > >>>
> > >>> --
> > >>> gmx-users mailing listgmx-users@gromacs.org
> > >>> http://lists.gromacs.org/mailman/listinfo/gmx-users<
> > http://lists.gromacs.org/**mailman/listinfo/gmx-users>
> > >>>  > http://lists.gromacs.org/mailman/listinfo/gmx-users>
> > >>> >
> > >>> * Please search the archive at http://www.gromacs.org/**
> > >>> Support/Mailing_Lists/Search > >>> Mailing_Lists/Search<
> > http://www.gromacs.org/Support/Mailing_Lists/Search>>before
> > >>> posting!
> > >>>
> > >>> * Please don't post (un)subscribe requests to the list. Use the www
> > >>> interface or send it to gmx-users-requ...@gromacs.org.
> > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<
> > http://www.gromacs.org/**Support/Mailing_Lists>
> > >>>  > http://www.gromacs.org/Support/Mailing_Lists>
> > >>> >
> > >>>
> > >>>
> > > --
> > > ==**==
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Research Scientist
> > > Department of Biochemistry
> > > Virginia Tech
> > > Blacksburg, VA
> > > jalemkul[at]vt.edu | (540) 231-9080
> > > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> > >
> > > ==**==
> > > --
> > > gmx-users mailing listgmx-users@gromacs.org
> > > http://lists.gromacs.org/**mailman/listinfo/gmx-users<
> > http://lists.gromacs.org/mailman/listinfo/gmx-users>
> > > * Please search the archive at http://www.gromacs.org/**
> > > Support/Mailing_Lists/Search<
> > http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> > > * Please don't post (un)subscribe requests to the list. Use the www
> > > interface or send it to gmx-users-requ...@gromacs.org.
> > > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<
> > http://www.gromacs.org/Support/Mailing_Lists>
> > >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.

Re: [gmx-users] grompp error

[Hasni Arsad]

Thanks,
Finally I managed to run MD of protein-ligand complex after a few trial of
tutorial



On Tue, Jun 18, 2013 at 5:06 PM, Mark Abraham wrote:

> Please keep GROMACS usage questions on the gmx-users mailing list. Nobody
> here is a private tutor :-)
>
> The error messages you are getting are self-explanatory. You need to think
> about why they are arising. Perhaps do some tutorials to get a feel for
> normal workflows, and how best to modify them to suit your needs.
>
> Mark
>
>
> On Tue, Jun 18, 2013 at 10:57 AM, Hasni Arsad 
> wrote:
>
> >
> >
> > -- Forwarded message --
> > From: Hasni Arsad 
> > Date: Tue, Jun 18, 2013 at 4:55 PM
> > Subject: Re: [gmx-users] grompp error
> > To: Discussion list for GROMACS users 
> >
> >
> > What should i do with this error massage:
> >
> > Program grompp, VERSION 4.6.2
> > Source code file:
> > /home/hasni/Bioinformatics/gromacs-4.6.2/src/kernel/grompp.c, line: 563
> >
> > Fatal error:
> > number of coordinates in coordinate file (solv.gro, 16268)
> >  does not match topology (topol.top, 50816)
> >
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> >
> > __
> >
> > Attach is my topol.top and solv.gro.
> >
> >
> >
> >
> > On Tue, Jun 18, 2013 at 4:36 PM, Mark Abraham  >wrote:
> >
> >> GROMACS is not yet magic. You used an atom type not found in your force
> >> field. Over to you. :-)
> >>
> >> Mark
> >> On Jun 18, 2013 5:23 AM, "Hasni Arsad"  wrote:
> >>
> >> > Hi,
> >> >
> >> > I got this error massage when execute this command- grompp -f em.mdp
> -c
> >> > solvated.pdb -p topol.top
> >> >
> >> >
> >> >
> >> > Program grompp, VERSION 4.6.2
> >> > Source code file: /gromacs-4.6.2/src/kernel/toppush.c, line: 1336
> >> >
> >> > Fatal error:
> >> > Atomtype NPYL not found
> >> > For more information and tips for troubleshooting, please check the
> >> GROMACS
> >> > website at http://www.gromacs.org/Documentation/Errors
> >> >
> >> >
> >> > comment please!
> >> > --
> >> > gmx-users mailing listgmx-users@gromacs.org
> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> > * Please search the archive at
> >> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >> > * Please don't post (un)subscribe requests to the list. Use the
> >> > www interface or send it to gmx-users-requ...@gromacs.org.
> >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >> >
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >> * Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-requ...@gromacs.org.
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >
> >
> >
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] grompp error

[Hasni Arsad]

Thanks


On Tue, Jun 18, 2013 at 10:44 PM, massimo sandal wrote:

> 2013/6/18 Hasni Arsad 
>
> > What should i do with this error massage:
> >
>
> Google it.
>
>
> > Program grompp, VERSION 4.6.2
> > Source code file:
> > /home/hasni/Bioinformatics/gromacs-4.6.2/src/kernel/grompp.c, line: 563
> >
> > Fatal error:
> > number of coordinates in coordinate file (solv.gro, 50853)
> >  does not match topology (topol.top, 50816)
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > __
> >
> >
> >
> >  solv.gro file
> >
> > 16268
> > 1MET  N1   3.978   6.462   2.460
> > 1MET H12   3.894   6.415   2.435
> > 1MET H23   4.057   6.411   2.426
> > 1MET H34   3.983   6.470   2.560
> >
> > ..
> > .
> > .
> > .
> > .
> > 275UNK H2 2869   9.769   6.981   4.477
> >   275UNK N1 2870   9.733   7.084   4.303
> >   275UNK C6 2871   9.725   7.203   4.240
> >   275UNK N6 2872   9.693   7.205   4.110
> >   275UNKH62 2873   9.675   7.119   4.062
> >   275UNKH61 2874   9.686   7.292   4.061
> >   276SOL OW 2875   0.569   1.275   1.165
> >   276SOLHW1 2876   0.476   1.268   1.128
> >   276SOLHW2 2877   0.580   1.364   1.209
> >   277SOL OW 2878   1.555   1.511   0.703
> >   277SOLHW1 2879   1.498   1.495   0.784
> >   277SOLHW2 2880   1.496   1.521   0.623
> >   278SOL OW 2881   1.743   0.618   0.856
> >   278SOLHW1 2882   1.776   0.712   0.856
> > .
> > .
> >
> > 16267SOL OW50848   4.521   3.149   0.076
> > 16267SOLHW150849   4.437   3.148   0.130
> > 16267SOLHW250850   4.523   3.232   0.020
> > 16268SOL OW50851   7.487   8.525   5.886
> > 16268SOLHW150852   7.586   8.514   5.877
> > 16268SOLHW250853   7.447   8.439   5.918
> >
> >
> > topol.top file
> >
> > [ molecules ]
> > ; Compound#mols
> > Protein_chain_X 1
> > UNK1
> >
> > SOL 15993
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > On Tue, Jun 18, 2013 at 4:36 PM, Mark Abraham  > >wrote:
> >
> > > GROMACS is not yet magic. You used an atom type not found in your force
> > > field. Over to you. :-)
> > >
> > > Mark
> > > On Jun 18, 2013 5:23 AM, "Hasni Arsad"  wrote:
> > >
> > > > Hi,
> > > >
> > > > I got this error massage when execute this command- grompp -f em.mdp
> -c
> > > > solvated.pdb -p topol.top
> > > >
> > > >
> > > >
> > > > Program grompp, VERSION 4.6.2
> > > > Source code file: /gromacs-4.6.2/src/kernel/toppush.c, line: 1336
> > > >
> > > > Fatal error:
> > > > Atomtype NPYL not found
> > > > For more information and tips for troubleshooting, please check the
> > > GROMACS
> > > > website at http://www.gromacs.org/Documentation/Errors
> > > >
> > > >
> > > > comment please!
> > > > --
> > > > gmx-users mailing listgmx-users@gromacs.org
> > > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > > > * Please don't post (un)subscribe requests to the list. Use the
> > > > www interface or send it to gmx-users-requ...@gromacs.org.
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > --
> > > gmx-users mailing listgmx-users@gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > > * Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-requ...@gromacs.org.
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> >
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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-- 
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