Re: [gmx-users] strange behaviout in 5.1.2

[Mark Abraham]

Hi,

Thanks. I did make a config change yesterday that might be the cause. I'll
revert the config if the issues persist tomorrow.

Mark

On Fri, Feb 5, 2016 at 11:12 PM Erik Marklund 
wrote:

> Never mind. My review went through anyway.
>
> > On 5 Feb 2016, at 22:11, Erik Marklund 
> wrote:
> >
> > Am trying to review this, but the gerrit interface keeps complaining
> about a “500 Internal server error”.
> >
> > Kind regards,
> > Erik
> >
> >> On 5 Feb 2016, at 17:59, Mark Abraham  wrote:
> >>
> >> Hi,
> >>
> >> Docs amended at https://gerrit.gromacs.org/5618 :-)
> >>
> >> Mark
> >>
> >> On Fri, Feb 5, 2016 at 6:26 PM Mark Abraham 
> >> wrote:
> >>
> >>> Hi,
> >>>
> >>> You're reading readir.c correctly, and it is correct also. I was
> >>> mis-reading
> >>>
> http://manual.gromacs.org/documentation/5.1.2/user-guide/mdp-options.html
> about
> >>> semiisotropic coupling. (I guess you could imagine that you might want
> >>> different tau-p for semiisotropic coupling, but it's definitely not
> >>> implemented.)
> >>>
> >>> I agree that it is irritating that grompp now warns that "tau-p = 5 5"
> >>> isn't valid, but I think that's better than users thinking two values
> are
> >>> required for semiisotropic, or silently not getting what you might
> think
> >>> "tau-p = 5 10" might implement.
> >>>
> >>> I'll amend those docs to clarify this point.
> >>>
> >>> Mark
> >>>
> >>> On Fri, Feb 5, 2016 at 6:13 PM Justin Lemkul  wrote:
> >>>
> 
> 
>  On 2/5/16 12:07 PM, Mark Abraham wrote:
> > Hi,
> >
> > Yes,
> >
> 
> http://manual.gromacs.org/documentation/5.1.2/ReleaseNotes/release-notes.html#fix-grompp-not-warning-when-mdp-values-have-wrong-types
> > is
> > the fix for another bug that could in principle produce this
> behaviour,
>  but
> > semiisotropic is supposed to take two real values, so something may
> be
> > amiss here.
> >
> 
>  tau-p should only read one value, unless I'm missing something in
>  readir.c.
>  Semiisotropic coupling requires two values of ref_p and
> compressibility,
>  but
>  tau-p is read as RTYPE, not STYPE.
> 
>  -Justin
> 
> > Mark
> >
> > On Fri, Feb 5, 2016 at 5:41 PM Justin Lemkul 
> wrote:
> >
> >>
> >>
> >> On 2/5/16 11:37 AM, Kortzak, Daniel wrote:
> >>> Dear All,
> >>>
> >>> when using gmx-5.1.2 with a mdp file with the following pressure
> >> coupling parameters:
> >>>
> >>> ; pressure coupling
> >>> Pcoupl   = berendsen
> >>> Pcoupltype   = semiisotropic
> >>> nstpcouple   = -1
> >>> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> >>> tau_p= 5 5
> >>> compressibility  = 4.5e-5 4.5e-5
> >>> ref_p= 1.0 1.0
> >>> ; Scaling of reference coordinates, No, All or COM
> >>> refcoord_scaling = all
> >>>
> >>>
> >>> grompp gives the error message:
> >>>
> >>>
> >>> ERROR 1 [file parameter.mdp, line 387]:
> >>>   Right hand side '5 5' for parameter 'tau_p' in parameter file is
>  not a
> >>>   real value
> >>>
> >>>
> >>> With versions below 5.1.2 everything seems to be fine. Are there
> >> additional changes beyond what is mentioned in the release notes or
> am
>  I to
> >> blind to find the right section?
> >>>
> >>
> >> tau_p only takes one value (unlike tau_t, which needs one per
>  thermostat
> >> group).
> >>  The issue that was fixed was grompp silently ignoring extraneous
>  input
> >> values,
> >> so previous versions carry on happily ignoring the stuff it doesn't
>  need.
> >>
> >>
> >>
> 
> http://manual.gromacs.org/documentation/5.1.2/ReleaseNotes/release-notes.html#fix-grompp-not-warning-when-mdp-values-have-wrong-types
> >>
> >> -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
> >>
> >> ==
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe 

[gmx-users] Can we expect Gromacs- non bonded energy calculation in GPU in near future?

[Nikhil Maroli]

Can we expect Gromacs- non bonded energy calculation in GPU in near future?


-- 
Ragards,
Nikhil Maroli
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Re: [gmx-users] strange behaviout in 5.1.2

[Mark Abraham]

Hi,

Yes,
http://manual.gromacs.org/documentation/5.1.2/ReleaseNotes/release-notes.html#fix-grompp-not-warning-when-mdp-values-have-wrong-types
is
the fix for another bug that could in principle produce this behaviour, but
semiisotropic is supposed to take two real values, so something may be
amiss here.

Mark

On Fri, Feb 5, 2016 at 5:41 PM Justin Lemkul  wrote:

>
>
> On 2/5/16 11:37 AM, Kortzak, Daniel wrote:
> > Dear All,
> >
> > when using gmx-5.1.2 with a mdp file with the following pressure
> coupling parameters:
> >
> > ; pressure coupling
> > Pcoupl   = berendsen
> > Pcoupltype   = semiisotropic
> > nstpcouple   = -1
> > ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> > tau_p= 5 5
> > compressibility  = 4.5e-5 4.5e-5
> > ref_p= 1.0 1.0
> > ; Scaling of reference coordinates, No, All or COM
> > refcoord_scaling = all
> >
> >
> > grompp gives the error message:
> >
> >
> > ERROR 1 [file parameter.mdp, line 387]:
> >Right hand side '5 5' for parameter 'tau_p' in parameter file is not a
> >real value
> >
> >
> > With versions below 5.1.2 everything seems to be fine. Are there
> additional changes beyond what is mentioned in the release notes or am I to
> blind to find the right section?
> >
>
> tau_p only takes one value (unlike tau_t, which needs one per thermostat
> group).
>   The issue that was fixed was grompp silently ignoring extraneous input
> values,
> so previous versions carry on happily ignoring the stuff it doesn't need.
>
>
> http://manual.gromacs.org/documentation/5.1.2/ReleaseNotes/release-notes.html#fix-grompp-not-warning-when-mdp-values-have-wrong-types
>
> -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
>
> ==
> --
> Gromacs Users mailing list
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[gmx-users] strange behaviout in 5.1.2

[Kortzak, Daniel]

Dear All,

when using gmx-5.1.2 with a mdp file with the following pressure coupling 
parameters:

; pressure coupling
Pcoupl   = berendsen
Pcoupltype   = semiisotropic
nstpcouple   = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p= 5 5
compressibility  = 4.5e-5 4.5e-5
ref_p= 1.0 1.0
; Scaling of reference coordinates, No, All or COM
refcoord_scaling = all


grompp gives the error message:


ERROR 1 [file parameter.mdp, line 387]:
  Right hand side '5 5' for parameter 'tau_p' in parameter file is not a
  real value


With versions below 5.1.2 everything seems to be fine. Are there additional 
changes beyond what is mentioned in the release notes or am I to blind to find 
the right section?

Best,
Daniel





Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt



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Re: [gmx-users] strange behaviout in 5.1.2

[Justin Lemkul]

On 2/5/16 11:37 AM, Kortzak, Daniel wrote:

Dear All,

when using gmx-5.1.2 with a mdp file with the following pressure coupling 
parameters:

; pressure coupling
Pcoupl   = berendsen
Pcoupltype   = semiisotropic
nstpcouple   = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p= 5 5
compressibility  = 4.5e-5 4.5e-5
ref_p= 1.0 1.0
; Scaling of reference coordinates, No, All or COM
refcoord_scaling = all


grompp gives the error message:


ERROR 1 [file parameter.mdp, line 387]:
   Right hand side '5 5' for parameter 'tau_p' in parameter file is not a
   real value


With versions below 5.1.2 everything seems to be fine. Are there additional 
changes beyond what is mentioned in the release notes or am I to blind to find 
the right section?



tau_p only takes one value (unlike tau_t, which needs one per thermostat group). 
 The issue that was fixed was grompp silently ignoring extraneous input values, 
so previous versions carry on happily ignoring the stuff it doesn't need.


http://manual.gromacs.org/documentation/5.1.2/ReleaseNotes/release-notes.html#fix-grompp-not-warning-when-mdp-values-have-wrong-types

-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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Re: [gmx-users] Laptop features for MD simulations - recommendations

[Björn Sommer]

Hi all,

I want to buy a laptop suitable and powerful enough for MD simulations
with GROMACS (mostly membrane/protein systems). Could you recommend
optimal features for this goal?

Thanks

Yasser


Hi Yasser,

just an extension to the previous answers. In case, money is not the 
problem, I can propose you a very nice laptop. I made a short review at 
LinkedIn about it, the EUROCOM Scorpius 3D2:


https://www.linkedin.com/grp/post/1945944-6066123861391335424

I compiled Gromacs with CPU and GPU support on Ubuntu 14, and it runs 
very fast for a laptop! I have a system with a 100X100 Angstrom membrane 
(modelled with the MembraneEditor ;) and a small polypeptide, and it 
requires less than 1 week for 100ns. This laptop in the configuration I 
discussed at LinkedIn, comes with an NVIDIA Quadro 5100M and a 3D 
monitor based on NVIDIA 3D Vision 2. So this means, you can do your 
simulation, and afterwards evaluate the 3D structures in VMD in full 
Stereo 3D! Aha, there is a small disadvantage: the laptop is huge (17" 
monitor) and heavy ;-)


However, please keep in mind, that you do not have to buy a Quadro card 
if you just need much power. You can buy then a top class GTX card. Some 
EUROCOM laptops can even be equipped with 2 cards! But if you want to 
combine it with Stereo 3D in VMD (you need windowed stereo mode OpenGL - 
as far as I know still not possible with 3D Vision and GTX cards), you 
have to go for a professional card like the Quadro.


Cheers,
Bjorn

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Re: [gmx-users] strange behaviout in 5.1.2

[Justin Lemkul]

On 2/5/16 12:07 PM, Mark Abraham wrote:

Hi,

Yes,
http://manual.gromacs.org/documentation/5.1.2/ReleaseNotes/release-notes.html#fix-grompp-not-warning-when-mdp-values-have-wrong-types
is
the fix for another bug that could in principle produce this behaviour, but
semiisotropic is supposed to take two real values, so something may be
amiss here.



tau-p should only read one value, unless I'm missing something in readir.c. 
Semiisotropic coupling requires two values of ref_p and compressibility, but 
tau-p is read as RTYPE, not STYPE.


-Justin


Mark

On Fri, Feb 5, 2016 at 5:41 PM Justin Lemkul  wrote:




On 2/5/16 11:37 AM, Kortzak, Daniel wrote:

Dear All,

when using gmx-5.1.2 with a mdp file with the following pressure

coupling parameters:


; pressure coupling
Pcoupl   = berendsen
Pcoupltype   = semiisotropic
nstpcouple   = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p= 5 5
compressibility  = 4.5e-5 4.5e-5
ref_p= 1.0 1.0
; Scaling of reference coordinates, No, All or COM
refcoord_scaling = all


grompp gives the error message:


ERROR 1 [file parameter.mdp, line 387]:
Right hand side '5 5' for parameter 'tau_p' in parameter file is not a
real value


With versions below 5.1.2 everything seems to be fine. Are there

additional changes beyond what is mentioned in the release notes or am I to
blind to find the right section?




tau_p only takes one value (unlike tau_t, which needs one per thermostat
group).
   The issue that was fixed was grompp silently ignoring extraneous input
values,
so previous versions carry on happily ignoring the stuff it doesn't need.


http://manual.gromacs.org/documentation/5.1.2/ReleaseNotes/release-notes.html#fix-grompp-not-warning-when-mdp-values-have-wrong-types

-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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--
==

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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[gmx-users] lipid pressure flucuations

[xy21hb]

Dear all,

I have followed the tutorial for the lipid  
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/
However, I see a large ~200 bar fluctuations in my system pressure, I wonder if 
someone has met this before.

Best,

Y 
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Re: [gmx-users] lipid pressure flucuations

[Justin Lemkul]

On 2/5/16 11:20 AM, xy21hb wrote:

Dear all,

I have followed the tutorial for the lipid  
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/
However, I see a large ~200 bar fluctuations in my system pressure, I wonder if 
someone has met this before.



Normal behavior.

http://www.gromacs.org/Documentation/Terminology/Pressure

-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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Re: [gmx-users] Water removed from system and visualizing protein alone in VMD. But problem in visualization of all frames

[sun]

If I change the representation then the problem occurs actually. Its fine with 
trajectory, for 10ns, 1001 frames are loaded in VMD. But when I play to 
visualize, the protein does not move at all. I mean, only one conformation 
remains in all frames which is not possible, I believe. This error never 
occured before. One more thing, i have saved cluster.pdb, it goes nice in pymol 
and all different structures can be viewed. What happens when i change 
representation?

Sent from my iPhone

> On 05-Feb-2016, at 3:20 pm, Mark Abraham  wrote:
> 
> Hi,
> 
> That works, but only if your full trajectory is small enough to fit in
> memory!
> 
> Mark
> 
>> On Fri, 5 Feb 2016 09:05 Nikhil Maroli  wrote:
>> 
>> HI,
>> simple way is to load the full trajectory and gro file then  change the
>> water draw style and protein draw style,so that you can have a nice look
>> on the structure,separately ..no need to remove anything from the .gro and
>> tpr or xtc
>> Regards
>> Nikhil
>> 
>> 
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Re: [gmx-users] strange behaviout in 5.1.2

[Mark Abraham]

Hi,

You're reading readir.c correctly, and it is correct also. I was
mis-reading
http://manual.gromacs.org/documentation/5.1.2/user-guide/mdp-options.html about
semiisotropic coupling. (I guess you could imagine that you might want
different tau-p for semiisotropic coupling, but it's definitely not
implemented.)

I agree that it is irritating that grompp now warns that "tau-p = 5 5"
isn't valid, but I think that's better than users thinking two values are
required for semiisotropic, or silently not getting what you might think
"tau-p = 5 10" might implement.

I'll amend those docs to clarify this point.

Mark

On Fri, Feb 5, 2016 at 6:13 PM Justin Lemkul  wrote:

>
>
> On 2/5/16 12:07 PM, Mark Abraham wrote:
> > Hi,
> >
> > Yes,
> >
> http://manual.gromacs.org/documentation/5.1.2/ReleaseNotes/release-notes.html#fix-grompp-not-warning-when-mdp-values-have-wrong-types
> > is
> > the fix for another bug that could in principle produce this behaviour,
> but
> > semiisotropic is supposed to take two real values, so something may be
> > amiss here.
> >
>
> tau-p should only read one value, unless I'm missing something in readir.c.
> Semiisotropic coupling requires two values of ref_p and compressibility,
> but
> tau-p is read as RTYPE, not STYPE.
>
> -Justin
>
> > Mark
> >
> > On Fri, Feb 5, 2016 at 5:41 PM Justin Lemkul  wrote:
> >
> >>
> >>
> >> On 2/5/16 11:37 AM, Kortzak, Daniel wrote:
> >>> Dear All,
> >>>
> >>> when using gmx-5.1.2 with a mdp file with the following pressure
> >> coupling parameters:
> >>>
> >>> ; pressure coupling
> >>> Pcoupl   = berendsen
> >>> Pcoupltype   = semiisotropic
> >>> nstpcouple   = -1
> >>> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> >>> tau_p= 5 5
> >>> compressibility  = 4.5e-5 4.5e-5
> >>> ref_p= 1.0 1.0
> >>> ; Scaling of reference coordinates, No, All or COM
> >>> refcoord_scaling = all
> >>>
> >>>
> >>> grompp gives the error message:
> >>>
> >>>
> >>> ERROR 1 [file parameter.mdp, line 387]:
> >>> Right hand side '5 5' for parameter 'tau_p' in parameter file is
> not a
> >>> real value
> >>>
> >>>
> >>> With versions below 5.1.2 everything seems to be fine. Are there
> >> additional changes beyond what is mentioned in the release notes or am
> I to
> >> blind to find the right section?
> >>>
> >>
> >> tau_p only takes one value (unlike tau_t, which needs one per thermostat
> >> group).
> >>The issue that was fixed was grompp silently ignoring extraneous
> input
> >> values,
> >> so previous versions carry on happily ignoring the stuff it doesn't
> need.
> >>
> >>
> >>
> http://manual.gromacs.org/documentation/5.1.2/ReleaseNotes/release-notes.html#fix-grompp-not-warning-when-mdp-values-have-wrong-types
> >>
> >> -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
> >>
> >> ==
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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[gmx-users] Segmentation fault (core dumped) after grompp minimization

[Poncho Arvayo Zatarain]

Hello, i'm working with a 256 phospholipid membrane and i run grompp for 
minimization and to generate a .tpr file, so after run grompp i run the mdrun 
but instantly crushed with the legend: SSteepest Descents: Tolerance Fmax: 
1.e03. No. of steps: 50,000, nan Fmax: inf, atom: 30983. Segmentation fault 
(core dumped). It could be by the cluster i ' m using? These are the 
characteristics: 512 cores CPU, 8 GPU'S, 2 visualization notes. Or it is like a 
Gromacs bug? Iḿ running in Gromacs 5.0.4. Or i have an error at atom 30983? I 
attached my .mdp file that i used for grompp of miniization. How can i solve 
it?Thanks   -- 
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Re: [gmx-users] Segmentation fault (core dumped) after grompp minimization

[Justin Lemkul]

On 2/5/16 1:07 PM, Poncho Arvayo Zatarain wrote:

Hello, i'm working with a 256 phospholipid membrane and i run grompp for 
minimization and to generate a .tpr file, so after run grompp i run the mdrun 
but instantly crushed with the legend: SSteepest Descents: Tolerance Fmax: 
1.e03. No. of steps: 50,000, nan Fmax: inf, atom: 30983. Segmentation fault 
(core dumped). It could be by the cluster i ' m using? These are the 
characteristics: 512 cores CPU, 8 GPU'S, 2 visualization notes. Or it is like a 
Gromacs bug? Iḿ running in Gromacs 5.0.4. Or i have an error at atom 30983? I 
attached my .mdp file that i used for grompp of miniization. How can i solve 
it?Thanks 



The list does not accept attachments.

An infinite force means you have severely clashing coordinates or the topology 
is fundamentally broken.


-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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Re: [gmx-users] strange behaviout in 5.1.2

[Mark Abraham]

Hi,

Docs amended at https://gerrit.gromacs.org/5618 :-)

Mark

On Fri, Feb 5, 2016 at 6:26 PM Mark Abraham 
wrote:

> Hi,
>
> You're reading readir.c correctly, and it is correct also. I was
> mis-reading
> http://manual.gromacs.org/documentation/5.1.2/user-guide/mdp-options.html 
> about
> semiisotropic coupling. (I guess you could imagine that you might want
> different tau-p for semiisotropic coupling, but it's definitely not
> implemented.)
>
> I agree that it is irritating that grompp now warns that "tau-p = 5 5"
> isn't valid, but I think that's better than users thinking two values are
> required for semiisotropic, or silently not getting what you might think
> "tau-p = 5 10" might implement.
>
> I'll amend those docs to clarify this point.
>
> Mark
>
> On Fri, Feb 5, 2016 at 6:13 PM Justin Lemkul  wrote:
>
>>
>>
>> On 2/5/16 12:07 PM, Mark Abraham wrote:
>> > Hi,
>> >
>> > Yes,
>> >
>> http://manual.gromacs.org/documentation/5.1.2/ReleaseNotes/release-notes.html#fix-grompp-not-warning-when-mdp-values-have-wrong-types
>> > is
>> > the fix for another bug that could in principle produce this behaviour,
>> but
>> > semiisotropic is supposed to take two real values, so something may be
>> > amiss here.
>> >
>>
>> tau-p should only read one value, unless I'm missing something in
>> readir.c.
>> Semiisotropic coupling requires two values of ref_p and compressibility,
>> but
>> tau-p is read as RTYPE, not STYPE.
>>
>> -Justin
>>
>> > Mark
>> >
>> > On Fri, Feb 5, 2016 at 5:41 PM Justin Lemkul  wrote:
>> >
>> >>
>> >>
>> >> On 2/5/16 11:37 AM, Kortzak, Daniel wrote:
>> >>> Dear All,
>> >>>
>> >>> when using gmx-5.1.2 with a mdp file with the following pressure
>> >> coupling parameters:
>> >>>
>> >>> ; pressure coupling
>> >>> Pcoupl   = berendsen
>> >>> Pcoupltype   = semiisotropic
>> >>> nstpcouple   = -1
>> >>> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
>> >>> tau_p= 5 5
>> >>> compressibility  = 4.5e-5 4.5e-5
>> >>> ref_p= 1.0 1.0
>> >>> ; Scaling of reference coordinates, No, All or COM
>> >>> refcoord_scaling = all
>> >>>
>> >>>
>> >>> grompp gives the error message:
>> >>>
>> >>>
>> >>> ERROR 1 [file parameter.mdp, line 387]:
>> >>> Right hand side '5 5' for parameter 'tau_p' in parameter file is
>> not a
>> >>> real value
>> >>>
>> >>>
>> >>> With versions below 5.1.2 everything seems to be fine. Are there
>> >> additional changes beyond what is mentioned in the release notes or am
>> I to
>> >> blind to find the right section?
>> >>>
>> >>
>> >> tau_p only takes one value (unlike tau_t, which needs one per
>> thermostat
>> >> group).
>> >>The issue that was fixed was grompp silently ignoring extraneous
>> input
>> >> values,
>> >> so previous versions carry on happily ignoring the stuff it doesn't
>> need.
>> >>
>> >>
>> >>
>> http://manual.gromacs.org/documentation/5.1.2/ReleaseNotes/release-notes.html#fix-grompp-not-warning-when-mdp-values-have-wrong-types
>> >>
>> >> -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
>> >>
>> >> ==
>> >> --
>> >> Gromacs Users mailing list
>> >>
>> >> * Please search the archive at
>> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> >> posting!
>> >>
>> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >>
>> >> * For (un)subscribe requests visit
>> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> >> send a mail to gmx-users-requ...@gromacs.org.
>> >>
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
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>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
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Re: [gmx-users] Water removed from system and visualizing protein alone in VMD. But problem in visualization of all frames

[Nikhil Maroli]

HI,
simple way is to load the full trajectory and gro file then  change the 
water draw style and protein draw style,so that you can have a nice look 
on the structure,separately ..no need to remove anything from the .gro and 
tpr or xtc
Regards 
Nikhil


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[gmx-users] Sampling snapshots in arbitrary intervals of time

[Irem Altan]

Hi,

Is it possible to record snapshots in non-linear intervals? For instance, in 
logarithmic time. In that case we would not save the snapshots, say, once in 
every 1000 steps, but we would save the first one, then the 10th one, then the 
100th one, etc.

Also, if we save it in linear intervals, is it possible to get the coordinates 
with trjconv in non-linear intervals? In this case we would have saved every 
1000th step, but we would be sampling the first one, the 10th saved one 
(corresponding to the 1th step) etc.

Best,
Irem
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Re: [gmx-users] strange behaviout in 5.1.2

[Erik Marklund]

Never mind. My review went through anyway.

> On 5 Feb 2016, at 22:11, Erik Marklund  wrote:
> 
> Am trying to review this, but the gerrit interface keeps complaining about a 
> “500 Internal server error”.
> 
> Kind regards,
> Erik
> 
>> On 5 Feb 2016, at 17:59, Mark Abraham  wrote:
>> 
>> Hi,
>> 
>> Docs amended at https://gerrit.gromacs.org/5618 :-)
>> 
>> Mark
>> 
>> On Fri, Feb 5, 2016 at 6:26 PM Mark Abraham 
>> wrote:
>> 
>>> Hi,
>>> 
>>> You're reading readir.c correctly, and it is correct also. I was
>>> mis-reading
>>> http://manual.gromacs.org/documentation/5.1.2/user-guide/mdp-options.html 
>>> about
>>> semiisotropic coupling. (I guess you could imagine that you might want
>>> different tau-p for semiisotropic coupling, but it's definitely not
>>> implemented.)
>>> 
>>> I agree that it is irritating that grompp now warns that "tau-p = 5 5"
>>> isn't valid, but I think that's better than users thinking two values are
>>> required for semiisotropic, or silently not getting what you might think
>>> "tau-p = 5 10" might implement.
>>> 
>>> I'll amend those docs to clarify this point.
>>> 
>>> Mark
>>> 
>>> On Fri, Feb 5, 2016 at 6:13 PM Justin Lemkul  wrote:
>>> 
 
 
 On 2/5/16 12:07 PM, Mark Abraham wrote:
> Hi,
> 
> Yes,
> 
 http://manual.gromacs.org/documentation/5.1.2/ReleaseNotes/release-notes.html#fix-grompp-not-warning-when-mdp-values-have-wrong-types
> is
> the fix for another bug that could in principle produce this behaviour,
 but
> semiisotropic is supposed to take two real values, so something may be
> amiss here.
> 
 
 tau-p should only read one value, unless I'm missing something in
 readir.c.
 Semiisotropic coupling requires two values of ref_p and compressibility,
 but
 tau-p is read as RTYPE, not STYPE.
 
 -Justin
 
> Mark
> 
> On Fri, Feb 5, 2016 at 5:41 PM Justin Lemkul  wrote:
> 
>> 
>> 
>> On 2/5/16 11:37 AM, Kortzak, Daniel wrote:
>>> Dear All,
>>> 
>>> when using gmx-5.1.2 with a mdp file with the following pressure
>> coupling parameters:
>>> 
>>> ; pressure coupling
>>> Pcoupl   = berendsen
>>> Pcoupltype   = semiisotropic
>>> nstpcouple   = -1
>>> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
>>> tau_p= 5 5
>>> compressibility  = 4.5e-5 4.5e-5
>>> ref_p= 1.0 1.0
>>> ; Scaling of reference coordinates, No, All or COM
>>> refcoord_scaling = all
>>> 
>>> 
>>> grompp gives the error message:
>>> 
>>> 
>>> ERROR 1 [file parameter.mdp, line 387]:
>>>   Right hand side '5 5' for parameter 'tau_p' in parameter file is
 not a
>>>   real value
>>> 
>>> 
>>> With versions below 5.1.2 everything seems to be fine. Are there
>> additional changes beyond what is mentioned in the release notes or am
 I to
>> blind to find the right section?
>>> 
>> 
>> tau_p only takes one value (unlike tau_t, which needs one per
 thermostat
>> group).
>>  The issue that was fixed was grompp silently ignoring extraneous
 input
>> values,
>> so previous versions carry on happily ignoring the stuff it doesn't
 need.
>> 
>> 
>> 
 http://manual.gromacs.org/documentation/5.1.2/ReleaseNotes/release-notes.html#fix-grompp-not-warning-when-mdp-values-have-wrong-types
>> 
>> -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
>> 
>> ==
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>> 
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>> 
 
 --
 ==
 
 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow
 
 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn 

[gmx-users] Fattal error in npt_umbrella : Umbrella Sampling Simulations tutorial

[Alexander Alexander]

Dear Gromacs user,

I am trying to do the Umbrella simulation following exactly the the
tutorial, everything is fine but I a fatal error happens in .tpr file
generation of npt_umbrella section warning about Pcoupl in npt_umbrella.mdp
file.
I used the suggested .mdp file in tutorial with Parrinello-Rahman pressure
coupling, but it complained that this type of coupling make the
equilibration unstable, and use Berendsen pressure coupling instead.
Then, I did, but again Fatal error by an warning stating that Berendsen
invalidates the true ensemble for the thermostat.

All the inputs and even the name are fully identical with the tutorial
samples.
The version of Gromacs is : VERSION 5.1-rc1

Any suggestion would be highly appreciated.

Best regards,
Alex
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 142, Issue 24

[Timofey Tyugashev]

Message: 4
Date: Thu, 4 Feb 2016 07:51:27 -0500
From: Justin Lemkul
To:gmx-us...@gromacs.org
Subject: Re: [gmx-users] trjconv options?
Message-ID:<56b3494f.4070...@vt.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed



On 2/4/16 4:27 AM, Timofey Tyugashev wrote:

>
>

>>Message: 2
>>Date: Wed, 3 Feb 2016 07:37:42 -0500
>>From: Justin Lemkul
>>To:gmx-us...@gromacs.org
>>Subject: Re: [gmx-users] trjconv options?
>>Message-ID:<56b1f496.5090...@vt.edu>
>>Content-Type: text/plain; charset=windows-1252; format=flowed
>>
>>
>>
>>On 2/3/16 6:34 AM, Timofey Tyugashev wrote:

>>> >Thank you for replies on my previous questions.
>>> >And now I have another one dealing with trjconv.
>>> >
>>> >I have a simulation of  a three-chain protein/nucleic acid complex. 
Naturally,
>>> >it gets broken in three separate strands by PBC.
>>> >After trying several, I settled on using options '-pbc mol' with '-ur 
compact'
>>> >which makes the complex look decent again and it looks like that does the 
job.
>>> >But I'm worried about a possibility of something getting unrepaired by this
>>> >option and getting unnoticed by me. What is the way to check for it?

>>Any molecules that appear to fly away suddenly will be a pretty dead giveaway.
>>
>>In general, for multimeric complexes, you need to do a lot more work, e.g.
>>centering on a single chain after making molecules whole and removing jumps.  
If
>>a simple -pbc mol -ur compact does the trick, probably nothing has actually
>>crossed a periodic boundary yet.
>>

>>> >Also it keeps tumbling around the cell during the trajectory. It's 
annoying. Is
>>> >there a way to pin down the cluster and stop it from rotating?

>>This is what trjconv -fit is for.
>>
>>-Justin

>Well, both vmd and pymol render .gro file (and trajectory files) with DNA
>strands and protein positioned in different corners of the box.
>Also, editconf -pbc has no effect on .gro file with the broken complex. How 
it's
>supposed to behave?
>
>So in this case I should at first run trjconv with '-pbc whole', make second 
run
>with '-pbc nojump', then make third run with '-pbc mol' to properly repair the
>trajectory?
>I guess for -fit I should pick 'progressive' option?

Complex systems require complex operations.  Start with
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow  
because that order of operations generally works well.  Then see posts in the

archive, because this comes up frequently.  Typically, after making molecules
whole and removing jumps, you can center on a custom index group that defines
some useful center.  Then you can do whatever fitting you like.
I've already looked at this page and it's not very helpful due to it's 
vague wording, so I guess trial and error is the only suitable way to 
get results. Due to the unstructured nature of mailing lists it's very 
hard to find relevant previous discussions. Probably that's why the 
topic comes up so frequently.

Anyway, thank you for your suggestions.
In your answer you suggest to go whole-jump-center route an the linked 
page says whole-cluster-jump-center. What is the difference between them?
How is centering done? Define a new group, like one aminoacid in the 
middle of a protein, use '-center' on it and it'll be put in the 
designated position in box (specified by '-boxcenter')?

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[gmx-users] ff99SB-ILDN and .mdp parameters

[Timofey Tyugashev]

Also I have some doubts about proper mdp parameters to use for AMBER 
ff99SB-ILDN. GROMACS site recently updated ones for CHARMM 
(http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM), 
but not for AMBER.

Currently I use the following options for MD run:

continuation= yes   ; first dynamics run
constraint_algorithm = lincs
constraints = all-bonds
lincs_iter  = 1 ; default
lincs_order = 4 ; default
; Neighborsearching
cutoff-scheme   = Verlet
ns_type = grid
nstlist = 40
rcoulomb= 1.0   ; Short-range electrostatic cut-off
rvdw= 1.0   ; Short-range Van der Waals cut-off
rlist   = 1.0   ; Short-range neighbor list
rlistlong   = 1.05  ; Long-range neighbor list
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling
tcoupl  = V-rescale ; Berendsen-modified
tc-grps = Protein_DNA Water_and_ions; two groups
tau_t   = 0.1   0.1 ; time constant, in ps
ref_t   = 300   300 ; reference temperature, one for 
each group, in K
; Pressure coupling
pcoupl  = Parrinello-Rahman ; pressure coupling is on for NPT
pcoupltype  = isotropic ; uniform scaling of box vectors
tau_p   = 2.0   ; time constant, in ps
ref_p   = 1.0   ; reference pressure, in bar
compressibility = 4.5e-5; isothermal compressibility of 
water, bar^-1
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no; assign velocities from Maxwell distribution




Paper for this FF provides the following parameters for computation 
set-up and I tried to implement them in .mdp, but I'm not sure how 
correct my interpretation is.


   Each system was equilibrated at 300 K and 1 atm with 2.4 ns of MD
   simulation in the NPT ensemble. Then, MD simulations were carried
   out in the NVT ensemble for 720 ns using the Nosé-Hoover thermostat
   with a relaxation time of 1 ps. All simulations were performed using
   the Desmond MD program^16
    version
   2.1.1.0 and either the Amber ff99SB^7
    or the
   modified Amber ff99SB force field described herein, which we have
   termed ff99SB-ILDN. All bonds involving hydrogen atoms were
   constrained with the SHAKE algorithm.^17
    A cutoff
   of 10 Å was used for the Lennard-Jones interaction and the
   short-range electrostatic interactions. The smooth particle mesh
   Ewald method^18
    with a
   32 × 32 × 32 grid and a fourth-order interpolation scheme was used
   to compute the long-range electrostatic interactions. The pairlists
   were updated every 10 fs with a cutoff of 10.5 Å. We used a
   multistep RESPA scheme^19
    for the
   integration of the equations of motion with timesteps of 2.0, 2.0,
   and 6.0 fs for the bonded, short-range nonbonded, and long-range
   nonbonded interactions, respectively. To check for potential biases
   introduced by long-range interactions between peptides in periodic
   images, we repeated these simulations for four of the amino acids
   (Xaa: Ile, Leu, Asp, and Asn) using a larger box with side length 37
   Å. We found that the results of these control simulations were
   within error of those using the smaller box sizes.


If understand the manual correctly, the Verlet option for cut-off scheme 
overrides rlist settings anyway and autotunes it.

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Re: [gmx-users] Water removed from system and visualizing protein alone in VMD. But problem in visualization of all frames

[Mark Abraham]

Hi,

That works, but only if your full trajectory is small enough to fit in
memory!

Mark

On Fri, 5 Feb 2016 09:05 Nikhil Maroli  wrote:

> HI,
> simple way is to load the full trajectory and gro file then  change the
> water draw style and protein draw style,so that you can have a nice look
> on the structure,separately ..no need to remove anything from the .gro and
> tpr or xtc
> Regards
> Nikhil
>
>
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 142, Issue 24

[Mark Abraham]

Hi,

As that page says, part of the issue is that different people need and want
different things, so there is not one magic recipe we can give, nor for
someone to find in a search. For example, it does not make sense to use the
cluster stage if you are centering on a single-chain protein. So the
workflow there prompts you to make that decision!

The centering options are described in trjconv -h, which that page has
already encouraged you to read. ;-)

If you want a chef to cook exactly the dinner you want to eat, you're going
to have to know a little about food and cooking! ;-)

Mark

On Fri, 5 Feb 2016 10:47 Timofey Tyugashev  wrote:

>
> > Message: 4
> > Date: Thu, 4 Feb 2016 07:51:27 -0500
> > From: Justin Lemkul
> > To:gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] trjconv options?
> > Message-ID:<56b3494f.4070...@vt.edu>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> >
> >
> > On 2/4/16 4:27 AM, Timofey Tyugashev wrote:
> >> >
> >> >
> >>> >>Message: 2
> >>> >>Date: Wed, 3 Feb 2016 07:37:42 -0500
> >>> >>From: Justin Lemkul
> >>> >>To:gmx-us...@gromacs.org
> >>> >>Subject: Re: [gmx-users] trjconv options?
> >>> >>Message-ID:<56b1f496.5090...@vt.edu>
> >>> >>Content-Type: text/plain; charset=windows-1252; format=flowed
> >>> >>
> >>> >>
> >>> >>
> >>> >>On 2/3/16 6:34 AM, Timofey Tyugashev wrote:
> > >>> >Thank you for replies on my previous questions.
> > >>> >And now I have another one dealing with trjconv.
> > >>> >
> > >>> >I have a simulation of  a three-chain protein/nucleic acid
> complex. Naturally,
> > >>> >it gets broken in three separate strands by PBC.
> > >>> >After trying several, I settled on using options '-pbc mol'
> with '-ur compact'
> > >>> >which makes the complex look decent again and it looks like
> that does the job.
> > >>> >But I'm worried about a possibility of something getting
> unrepaired by this
> > >>> >option and getting unnoticed by me. What is the way to check
> for it?
> >>> >>Any molecules that appear to fly away suddenly will be a pretty dead
> giveaway.
> >>> >>
> >>> >>In general, for multimeric complexes, you need to do a lot more
> work, e.g.
> >>> >>centering on a single chain after making molecules whole and
> removing jumps.  If
> >>> >>a simple -pbc mol -ur compact does the trick, probably nothing has
> actually
> >>> >>crossed a periodic boundary yet.
> >>> >>
> > >>> >Also it keeps tumbling around the cell during the trajectory.
> It's annoying. Is
> > >>> >there a way to pin down the cluster and stop it from rotating?
> >>> >>This is what trjconv -fit is for.
> >>> >>
> >>> >>-Justin
> >> >Well, both vmd and pymol render .gro file (and trajectory files) with
> DNA
> >> >strands and protein positioned in different corners of the box.
> >> >Also, editconf -pbc has no effect on .gro file with the broken
> complex. How it's
> >> >supposed to behave?
> >> >
> >> >So in this case I should at first run trjconv with '-pbc whole', make
> second run
> >> >with '-pbc nojump', then make third run with '-pbc mol' to properly
> repair the
> >> >trajectory?
> >> >I guess for -fit I should pick 'progressive' option?
> > Complex systems require complex operations.  Start with
> >
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow
> > because that order of operations generally works well.  Then see posts
> in the
> > archive, because this comes up frequently.  Typically, after making
> molecules
> > whole and removing jumps, you can center on a custom index group that
> defines
> > some useful center.  Then you can do whatever fitting you like.
> I've already looked at this page and it's not very helpful due to it's
> vague wording, so I guess trial and error is the only suitable way to
> get results. Due to the unstructured nature of mailing lists it's very
> hard to find relevant previous discussions. Probably that's why the
> topic comes up so frequently.
> Anyway, thank you for your suggestions.
> In your answer you suggest to go whole-jump-center route an the linked
> page says whole-cluster-jump-center. What is the difference between them?
> How is centering done? Define a new group, like one aminoacid in the
> middle of a protein, use '-center' on it and it'll be put in the
> designated position in box (specified by '-boxcenter')?
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[gmx-users] Fwd: C_v and Temperature

[Alexander Alexander]

No comment please?


-- Forwarded message --
From: Alexander Alexander 
Date: Thu, Feb 4, 2016 at 1:27 PM
Subject: Re: [gmx-users] C_v and Temperature
To: gmx-us...@gromacs.org


Thank you for your response.

I am trying to calculate the heat capacity at constant volume for a crystal
solid in different temperature; below are what "gmx energy -fluct_props
..." gives me in 4 different temperatures:

T = 29.9Cv = 24.4681 J/mol K

T = 99.9Cv = 24.6643 J/mol K

T = 297.9  Cv = 24.4926 J/mol K

T = 799.9  Cv = 24.5054 J/mol K

And "gmx dos" gives something around "Heat capacity 0.000683396 (J/mol K)"
as quantum correction for all the simulation temperature I have tried.

The result for the two last temperature is fascinating and agree well with
my DFPT and phonon calculations as well as all the heat capacity laws in
higher temperatures.
Also, I was expecting that the C_v reduces to around 2 or 3 J/mol K  in
lower temperatures, but I do not know why the C_v in lower temperature is
the same as higher temperature, although I had a well prepared and
converged calculations. So, I would be so thankful if one could comment on
this.

By the way, this is what I have in my dos.log file.

System = "A3B crystal Solid"
Nmol = 43904
Natom = 43904
dt = 0.2 ps
tmass = 2.05132e+06 amu
V = 415.228 nm^3
rho = 8203.43 g/l
T = 298.15 K
beta = 0.403395 mol/kJ

DoS parameters
Delta = 3.49303e-05
fluidicity = 0.00202656
hard sphere packing fraction = 441.911
hard sphere compressibility = 1.00454
ideal gas entropy = 0.0717008
hard sphere entropy = -0.762789
sigma_HS = 1.99851 nm
DoS0 = 2.3222
Dos2 = 627309
DoSTot = 6.19421
Diffusion coefficient from VACF 0.000169117 10^-5 cm^2/s
Diffusion coefficient from DoS 0.00023386 10^-5 cm^2/s
Heat capacity 0.000623269 J/mol K
--

Best regards,
Alex



On Thu, Feb 4, 2016 at 8:45 AM, David van der Spoel 
wrote:

> On 03/02/16 23:52, Alexander Alexander wrote:
>
>> Dear Gromacs user,
>>
>> Normally there is a "*ref-t" [K]  *in .mdp file as reference temperature
>> in
>> NVT calculation, in addition, yet another Temperature must be indicated in
>> "gmx dos *-T* XXX ..." for example in heat capacity (C_v) calculation with
>> quantum correction. So, I was wondering that which of these two
>> temperatures is the one that the heat capacity (C_v) has been calculated
>> in
>> to be reported later?
>>
> To get the simulation temperature run gmx energy
>
>
>> One more question:
>> In C_v calculation, would you please confirm me that the "gmx dos" would
>> give only the quantum correction for C_v? Not the total C_v including
>> quantum correction.
>> IF so, then, the Total C_v  would be:
>> Total C_v = "gmx energy -nmol -fluct_props" + "gmx dos -T ..."
>>
> Have you checked the output from gxm dos?
> It describes everything in quite some detail.
>
>
>> Thank you so much.
>>
>> Cheers,
>>
>> Alex
>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] Water removed from system and visualizing protein alone

[Björn Sommer]

On 5/02/2016 9:02 pm, gromacs.org_gmx-users-requ...@maillist.sys.kth.se 
wrote:

Hi,

That works, but only if your full trajectory is small enough to fit in
memory!

Mark

On Fri, 5 Feb 2016 09:05 Nikhil Maroli  wrote:


>HI,
>simple way is to load the full trajectory and gro file then  change the
>water draw style and protein draw style,so that you can have a nice look
>on the structure,separately ..no need to remove anything from the .gro and
>tpr or xtc
>Regards
>Nikhil
>
>

Mark, yes, but you know that you can just skip every Xth frame in VMD by 
defining in the "Molecule File Browser" Frames -> Stride. Yes, it will 
not be so smooth anymore, but you can check at least if the trajectory 
meets your expectations. And as I said before, if your memory is very 
limited, please 1) load the PDB, then 2) select the molecules/atoms to 
be visualized in the "Representations" window, and then 3) load the 
trajectory (see my previous email for details). Especially in case you 
are not interested in the water, this may safe a lot of your precious 
memory!

Bjorn
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Re: [gmx-users] sigma and epsilon values for C and H atoms in CNT

[soumadwip ghosh]

Hi,
   the atomtype descriptions for CNT in CHARMM27 force field are CA and HP
for carbon and hydrogen respectively( both of them aromatic). You will find
the sigma and epsilon values in the ffnonbonded.itp of the CHARMM27 ff
directory. Best of luck.

Soumadwip
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Re: [gmx-users] Fwd: FW: PME settings in free energy calculations

[Dries Van Rompaey]

Hi,

The corresponding mdp output section is:

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = PME
coulomb-modifier = Potential-shift-Verlet
rcoulomb-switch  = 0
rcoulomb = 1.0
; Relative dielectric constant for the medium and the reaction field
epsilon-r= 1
epsilon-rf   = 0
; Method for doing Van der Waals
vdwtype  = cutoff
vdw-modifier = Potential-switch
; cut-off lengths
rvdw-switch  = 0.9
rvdw = 1.0
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Separate tables between energy group pairs
energygrp-table  =
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.08
; FFT grid size, when a value is 0 fourierspacing will be used
fourier-nx   = 0
fourier-ny   = 0
fourier-nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 6
ewald_rtol   = 1e-06
ewald-rtol-lj= 0.001
lj-pme-comb-rule = Geometric
ewald-geometry   = 3d
epsilon_surface  = 0


I evaluated the energy with:

Verlet - settings above (with standard verlet-buffer-tolerance)
@ s0 legend "Coulomb-14"
@ s1 legend "Coulomb (SR)"
@ s2 legend "Coul. recip."
0.00  -2221.295898  -546205.25  9271.518555
Total - 539155.0273

Verlet - settings above - with verlet-buffer-tolerance -1
0.00  -2221.295898  -546205.25  9271.516602
Total   -539155.029296


Group - settings above
@ s0 legend "Coulomb-14"
@ s1 legend "Coulomb (SR)"
@ s2 legend "Coul. recip."
0.00  -2221.296387  -487993.593750  -48931.437500
Total -539146.3276


Verlet - 3 nm cutoffs, 2.9 vdwswitch, coulomb-modifier none
@ s0 legend "Coulomb-14"
@ s1 legend "Coulomb (SR)"
0.00  -2221.295898  -774817.875000
Total -777039.1709


Group - 3 nm cutoffs, 2.9 vdwswitch, coulomb-modifier none
@ s0 legend "Coulomb-14"
@ s1 legend "Coulomb (SR)"
0.00  -2221.296387  -553398.125000
Total -555619.4214

Thanks,

Dries

On 4 February 2016 at 14:48, Michael Shirts  wrote:

> Also, can you be more precise about the inconsistency in the outputs
> you are seeing (with numerical output from GROMACS and analysis code).
>
> On Thu, Feb 4, 2016 at 6:17 AM, Michael Shirts  wrote:
> > Hi, Dries-
> >
> > Can you print out what the corresponding section of mdout.mdp look like?
> >
> > Have you  tried using the cutoffs above with group cutoffs, and seen
> > what the difference is?
> >
> > On Thu, Feb 4, 2016 at 4:59 AM, Dries Van Rompaey
> >  wrote:
> >> Hi,
> >>
> >> I'm using PME with the default Potential-Shift-Verlet modifier. If I'm
> >> interpreting the manual and comments on the mailinglist correctly, the
> >> settings for rcoulomb-switch shouldn't affect this and PME-switching
> >> shouldn't be necessary (although there seems to have been some
> discussion
> >> about this, https://gerrit.gromacs.org/#/c/2220/). Has a consensus been
> >> reached elsewhere?
> >>
> >> Current nonbonded settings in my .mdp files are:
> >> ; Electrostatics
> >> coulombtype  = PME
> >> rcoulomb= 1.0
> >>
> >> ; van der Waals
> >> vdwtype= cutoff
> >> vdw-modifier= Potential-switch
> >> rvdw-switch  = 0.9
> >> rvdw = 1.0
> >>
> >> ; Apply long range dispersion corrections for Energy and Pressure
> >> DispCorr  = EnerPres
> >>
> >> ; Spacing for the PME/PPPM FFT grid
> >> fourierspacing   = 0.08
> >>
> >> ; EWALD/PME/PPPM parameters
> >> pme_order= 6
> >> ewald_rtol = 1e-06
> >> epsilon_surface= 0
> >>
> >> Thanks in advance,
> >>
> >> Dries
> >>
> >> On 4 February 2016 at 00:56, Michael Shirts  wrote:
> >>
> >>> Hi, Dries-
> >>>
> >>> Questions like this are probably best answered on the gmx-users list.
> >>> I can't say too much for the Verlet scheme -- I know that it was
> >>> relatively recently adapted for free energies, and there may be some
> >>> combinations of settings that could give unanticipated results.
> >>>
> >>> Pretty much all of our experience about nonbonded calculations and
> >>> free energies is collected in the following paper:
> >>> http://pubs.acs.org/doi/abs/10.1021/ct4005068. We used the group
> >>> cutoff scheme since that was the only one that was supported in
> >>> GROMACS at the time.
> >>>
> >>> Since you haven't sent any files, it's hard to tell what is actually
> >>> going on. The one thing that has a tendency to happen with the more
> >>> recent update schemes is if you set a potential modifier that is a
> >>> switch, but don't set the distance the switch starts at, then it is
> >>> 

Re: [gmx-users] Sampling snapshots in arbitrary intervals of time

[Mark Abraham]

Hi,

No. You'd have to use trjconv and trjcat to construct that after the fact.

Mark

On Fri, Feb 5, 2016 at 11:28 PM Irem Altan  wrote:

> Hi,
>
> Is it possible to record snapshots in non-linear intervals? For instance,
> in logarithmic time. In that case we would not save the snapshots, say,
> once in every 1000 steps, but we would save the first one, then the 10th
> one, then the 100th one, etc.
>
> Also, if we save it in linear intervals, is it possible to get the
> coordinates with trjconv in non-linear intervals? In this case we would
> have saved every 1000th step, but we would be sampling the first one, the
> 10th saved one (corresponding to the 1th step) etc.
>
> Best,
> Irem
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Re: [gmx-users] Fattal error in npt_umbrella : Umbrella Sampling Simulations tutorial

[Justin Lemkul]

On 2/5/16 2:50 PM, Alexander Alexander wrote:

Dear Gromacs user,

I am trying to do the Umbrella simulation following exactly the the
tutorial, everything is fine but I a fatal error happens in .tpr file
generation of npt_umbrella section warning about Pcoupl in npt_umbrella.mdp
file.
I used the suggested .mdp file in tutorial with Parrinello-Rahman pressure
coupling, but it complained that this type of coupling make the
equilibration unstable, and use Berendsen pressure coupling instead.
Then, I did, but again Fatal error by an warning stating that Berendsen
invalidates the true ensemble for the thermostat.



Use of the Berendsen weak coupling should not trigger a fatal error.  It should 
produce a note for the user.  Can you provide the exact output from the screen, 
copied and pasted?



All the inputs and even the name are fully identical with the tutorial
samples.
The version of Gromacs is : VERSION 5.1-rc1



Don't use release candidates for production work :)  Get the newest version 
(5.1.2).

-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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