Re: [gmx-users] To calculate temperture in a specific region

[Mark Abraham]

Hi,

If you're after such a group-wise temperature at a single point in time,
then you can e.g. use gmx select to make your selection, and then gmx traj
to get the velocities for those atoms (if you recorded them from mdrun with
nstvout).

Mark


On Tue, Sep 22, 2015 at 8:03 AM Krishna Mohan Gupta 
wrote:

> Dear Gromacs users,
>
> I need to calculate temperature of molecules in a particular region after
> equilibration run (NVT or NPT) but during simulation molecules will
> exchange from one region to another.
>
> Can anyone have any suggestion in this regards ?
> Thanks.
>
> Krishna
>
>
> 
>
> Important: This email is confidential and may be privileged. If you are
> not the intended recipient, please delete it and notify us immediately; you
> should not copy or use it for any purpose, nor disclose its contents to any
> other person. Thank you.
> --
> 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.
>
-- 
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.

[gmx-users] Crystallographic Ions

[Parker de Waal]

Hi Everyone,

I'm working with a protein which contains 2 crystallographic sodium ions and am 
experiencing trouble making the .gro file using pdb2gro using the Charmm36.ff 
parameters.

The two ions can be seen here:
ATOM  29009 NANA 1 -18.056 -14.113 -24.865  1.00  0.00  
ATOM  29010 NANA 2  27.831  26.294 -32.202  1.00  0.00 

Whenever I run pdb2gro the program complains that NA is not a valid atom type, 
however whenever I manually change the ions to atom and res type to SOD the 
resulting .top file does not count the molecules correctly. 
[ molecules ]
; Compound#mols
Other   1 (should be NA+ and 2?)

If anyone could help fix this problem I would greatly appreciate it.

Best,
Parker


-- 
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.

[gmx-users] PMF calculation_ Constraint

[Sepideh Kavousi]

Dear Gromacs users

I want to calculate the PMF of tocopherol in DMPC bilayer system. For this
means, I used Constraint method. the pull code in my .mdp file is :

pull = constraint
pull-geometry = distance;distance, direction, or cylinder
pull-dim = N N Y
pull-constr-tol = 1e-6
pull-start = yes;add current COM distance to pull_init?
pull-print-reference = no
pull-nstxout = 1
pull-nstfout = 5
pull-ngroups = 2
pull-ncoords = 1
pull-group1-name = DMPC
pull-group2-name = VIT
pull-coord1-groups = 1 2
pull-coord1-init = 0.0


In my output file which shows force over time, we have some sudden diverges
of force to a very high number.
I realized it is because of the boundary condition, one part of molecule
comes out of the box and enters from the other side of the box and it needs
a huge force to keep the molecule at the same position. Can you please help
me how to solve this problem
-- 
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.

Re: [gmx-users] Prospective research areas of GROMACS

[Mark Abraham]

Hi,

On Mon, Sep 21, 2015 at 7:10 PM Sabyasachi Sahoo 
wrote:

> Dear Gromacs users and developers,
>
> I am a parallel programming researcher and would like to contribute to
> Gromacs molecular dynamics software by helping to nail down any bottlenecks
> that occur in scaling of the software on multiple CPUs (and probably
> improved performance in exa-scale era.) I am already in process of
> collecting profiling results to identify the phases that can be improved
> (and also for few other MD softwares).
>

Welcome! (And good luck... optimizing software that's had over 10 years of
performance focussed effort is... challenging!)

Profiling is itself problematic. Assuming one can get GROMACS to build with
whatever constraints the tool adds, and can benchmark on a machine where
you do not suffer contention for network resources, one needs to produce
more useful information than can already be obtained at the end of the .log
file. Such data is most interesting only when near the strong scaling limit
(e.g. < 100 particles per CPU core) and thus at very short per-MD-step
times (several wallclock milliseconds). Neither function instrumentation,
nor sampling tend to work well in this regime. But we'd love to be
surprised :-)

Hence, I would request all of you to please suggest me some possible areas
> of research, on which we can work on, for better scaling of Gromacs,
> (and/or MD softwares in general.) Going through the official website
> documentation helps me realise that implementing a truly parallel FFT (or
> making it scale better) in Gromacs will be truly helpful.


Yes and no. The FFT is intrinsically global, and most of the time spent
doing the PME component of MD is organizing the data to go into the FFT,
rather than doing the computation. The current implementation of spreading
charges onto the FFT grid is known to scale poorly across increasing
numbers of OpenMP cores of an MPI rank. That would be a high-impact problem
to fix - but start by getting a thorough understanding of the algorithm
before looking at the code (because the form of the code will not help you
understand anything). Some profiling with well-targeted function
instrumentation could be worthwhile here.

Because of this, at scale it is often necessary to use a subset of the MPI
ranks to handle the PME part, MPMD style (see reference manual, and/or
GROMACS 4 paper). However, the implementation of that requires that the
user choose a division in advance, and without running some external
optimizer (like gmx tune_pme) that choice is difficult because there also
has to be a PME domain decomposition, and now an extra communication phase
mapping from one DD to the other, and that can't be efficient unless
various constraints are satisified... Approaches that would take variables
out of user space could be quite useful here. For a trivial example, it
might be best
* to interleave PME ranks with PP ranks, to spread them out over the
network to maximize communication bandwidth when doing the all-to-all for
the 3DFFT, and hopefully minimize communication latency when doing the
transformation from PP DD to PME DD by having ranks very close, or
* to pack PME ranks together on the network to minimize external network
contention during the all-to-all, but to do so in a way that doesn't lose
all the benefits by instead taking the latency hit at the PP<->PME stages...
Currently the user has to choose one of these "up front." The latter works
well only in the presence of knowledge about the network topology, which is
unavailable until someone adds (e.g.) netloc support.

Replacing our home-grown hardware detection support with hwloc support
would perhaps be higher reward for effort, however.

Avoiding PME entirely is another avenue (but there are two fast-multipole
projects running here already).

The latest paper
> on Gromacs 5.0 concludes saying an algorithm implementing preempting fine
> grained tasks based on priority can lead to improvements. I am also trying
> to look into it and would want to know your take on this.
>

We don't think the current approach of

1. spread this task over n threads per rank, then
2. do something serial
3. spread the next task over the same n threads per rank, then
4. do something serial
5. spread the next task over the same n threads per rank, then
... continue like this

is going to cut it in the long term. You need to be able e.g. to fire off
the necessary PME communication, then go back to doing bonded work, then 20
microseconds later when communication arrives drop everything to handle the
next phase of PME ASAP, then go back to the bondeds, but preferably don't
trash all your cache in the meantime, etc. But there's a lot of boring code
transformation that has to happen before we can do much about it. Current
thinking is that we want to move in the direction of encapsulated tasks
that we might be able to write a custom TBB thread scheduler to handle in a
way that's automatic and efficient.

Re: [gmx-users] distance dependent energy

[Mark Abraham]

Hi,

On Tue, Sep 22, 2015 at 5:47 PM Cuong Nguyen  wrote:

> Dear Gromacs users,
>
> I would like to work out the energy (total and kinetic) as a function of
> the distance from the center of mass of a droplet. However, using g_energy
> just gave me the values as a function of time. Could anyone tell me the way
> to get the distance dependent values?
>

First, you'd have to record them. mdrun doesn't work by first evaluating a
giant matrix of per-anything energies, and then adding them up. You can use
energy groups to break down the short-ranged non-bonded component of the
potential energy into intra- and inter-group terms, but you can only have
256 of them, and only with the group scheme, and only if you're not
concerned about diffusion (or are prepared to use dynamic selections and
mdrun -rerun creatively). And the work you have to put in to get that out
is not really worth thinking about unless you know exactly what you're
going to learn from the result.

Mark
-- 
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.

Re: [gmx-users] What's the practical effect of 'continuation = yes/no'?

[Mark Abraham]

Hi,

On Tue, Sep 22, 2015 at 8:22 AM Trayder Thomas 
wrote:

> What exactly does 'continuation = yes' do?
>

Tells mdrun to behave as though the simulation didn't stop :-) We need a
way to let people stop the simulation, perhaps change something, and
continue on with the minimum disruption necessary.

For better or worse, mdrun defaults to doing a call to the constraint code
before entering the MD loop, which perhaps helps with some cases of
starting new simulations from states that don't belong in the ensemble.
Thus this .mdp option.

My understanding thus far is that it will move particles in the first step
> (using the input velocities) before applying the constraints (LINCS bond
> lengths etc.). When continuing a simulation with 'continuation=no' you
> would apply constraints twice in a row.
>

Yes - per Fig 3.3 of the reference manual, except that constraints happen
either before the loop enters, or after the update.

So when using pull code, 'continuation=no' would give you a double-pull,
> which would be bad.
>
> But if you were dealing with, for example, only LINCS/SHAKE constraints,
> would 'continuation=no' make a practical difference?
>

No difference in typical practice. Obviously you remove yourself even
further from the possibility of a binary reproducible trajectory.

The manual states "The relative constraint deviation [for LINCS after one
> iteration] will be less than 0.0001 for every constraint". Which suggests
> to me that the error in applying a second constraint step would be less
> than continuing from a .gro file.
>
> Is my understanding correct?
>

Seems good.

Mark


> Thanks,
> -Trayder
> --
> 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.
>
-- 
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.

[gmx-users] To calculate temperture in a specific region

[Krishna Mohan Gupta]

Dear Gromacs users,

I need to calculate temperature of molecules in a particular region after 
equilibration run (NVT or NPT) but during simulation molecules will exchange 
from one region to another.

Can anyone have any suggestion in this regards ?
Thanks.

Krishna




Important: This email is confidential and may be privileged. If you are not the 
intended recipient, please delete it and notify us immediately; you should not 
copy or use it for any purpose, nor disclose its contents to any other person. 
Thank you.
-- 
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.

Re: [gmx-users] addition of hydronium ion in simulation box

[Groenhof, Gerrit]

Hi,

> Hello justin,
>
> Thanks, actually I want to study movement of protons along the lenght of a
> water channel.
>

> What you need is constant-pH MD, which is not natively supported in GROMACS.

What Justin says. There is only a 3.3 version that currently supports this, 
which is available at:

http://www.mpibpc.mpg.de/grubmueller/constpH


In addition, if you're interested in proton transfer between waters only, HYDYN 
may be an option for you:

http://onlinelibrary.wiley.com/doi/10.1002/jcc.23536/suppinfo

However, from what you describe I assume that protein side chains may be 
involved as well in proton uptake/donation, but we have not yet extended HYDYN 
to include amino acids unfortunately.

Concerning the suggestion by Andre to use DFTB, there is a recent 
implementation in Gromacs by Tomas Kubar:

http://onlinelibrary.wiley.com/doi/10.1002/jcc.24029/abstract


Good luck,

Gerrit

-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

==


--

Message: 3
Date: Tue, 22 Sep 2015 14:22:41 +1200
From: James Lord 
To: "gmx-us...@gromacs.org" 
Subject: [gmx-users] force fields selection
Message-ID:

[gmx-users] What's the practical effect of 'continuation = yes/no'?

[Trayder Thomas]

What exactly does 'continuation = yes' do?

My understanding thus far is that it will move particles in the first step
(using the input velocities) before applying the constraints (LINCS bond
lengths etc.). When continuing a simulation with 'continuation=no' you
would apply constraints twice in a row.

So when using pull code, 'continuation=no' would give you a double-pull,
which would be bad.

But if you were dealing with, for example, only LINCS/SHAKE constraints,
would 'continuation=no' make a practical difference?
The manual states "The relative constraint deviation [for LINCS after one
iteration] will be less than 0.0001 for every constraint". Which suggests
to me that the error in applying a second constraint step would be less
than continuing from a .gro file.

Is my understanding correct?

Thanks,
-Trayder
-- 
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.

Re: [gmx-users] distance dependent energy

[Erik Marklund]

Dear Van,

Plot against the COM distance, which you can get as a function of time too.

Kind regards,
Erik

Erik Marklund, PhD
Postdoctoral Research Fellow
Fulford JRF, Somerville College

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ

> On 22 Sep 2015, at 16:47, Cuong Nguyen  wrote:
> 
> Dear Gromacs users,
> 
> I would like to work out the energy (total and kinetic) as a function of
> the distance from the center of mass of a droplet. However, using g_energy
> just gave me the values as a function of time. Could anyone tell me the way
> to get the distance dependent values?
> 
> Thank you very much in advance.
> 
> Kind regards,
> Van
> -- 
> 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.

-- 
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.

Re: [gmx-users] To calculate temperture in a specific region

[Krishna Mohan Gupta]

Thanks Mark,

Actually, at a particular time I am able to calculate temperature in a region. 
But on taking average of few picosecond trajectory to minimize the statistical 
error, molecules exchange their location with surrounding region. Therefore, it 
is difficult to take average.
Is there any way to handle to this type of situation ?


-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark 
Abraham
Sent: Wednesday, September 23, 2015 3:12 AM
To: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] To calculate temperture in a specific region

Hi,

If you're after such a group-wise temperature at a single point in time, then 
you can e.g. use gmx select to make your selection, and then gmx traj to get 
the velocities for those atoms (if you recorded them from mdrun with nstvout).

Mark


On Tue, Sep 22, 2015 at 8:03 AM Krishna Mohan Gupta 
wrote:

> Dear Gromacs users,
>
> I need to calculate temperature of molecules in a particular region
> after equilibration run (NVT or NPT) but during simulation molecules
> will exchange from one region to another.
>
> Can anyone have any suggestion in this regards ?
> Thanks.
>
> Krishna
>
>
> 
>
> Important: This email is confidential and may be privileged. If you
> are not the intended recipient, please delete it and notify us
> immediately; you should not copy or use it for any purpose, nor
> disclose its contents to any other person. Thank you.
> --
> 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.
>
--
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.



Important: This email is confidential and may be privileged. If you are not the 
intended recipient, please delete it and notify us immediately; you should not 
copy or use it for any purpose, nor disclose its contents to any other person. 
Thank you.
-- 
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.

[gmx-users] Fwd: Diffusion of protein

[neha bharti]

Hello all

I am trying to performed molecular dynamics simulation of ligand-protein
complex in popc lipid with charmm36 force field. I am taking help from
Justin A. Lemkul tutorial.

I wanted to calculate the diffusion of the protein. Before performing the
study I removed the PBC of my system.
I am using msd command

*g_msd -f md_whole.xtc -s md.tpr  -b 0 -e 10 -o diffusion.xvg*

but the graph is not a straight line

[image: Inline image 1]

when I am using g_analyse after g_msd command i.e. *g_analyze -f
diffusion.xvg -msd diffusion_analyze.xvg *the graph is straight line  but
the graph is showing only for 50 ns (half of the simulation time)

Can anyone please tell me which graph should I refer. Or I am doing
something wrong??

Is there any other command to calculate the diffusion?

Please help

With Regards
Neha bharty
-- 
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.

Re: [gmx-users] force fields selection

[Justin Lemkul]

On 9/21/15 10:22 PM, James Lord wrote:

Dear gmx users,

I want to use either gromos 43a2 or 54a7 in Gromacs to simulate protein
partitioning at biphasic liquid-liquid interfaces (Similar Justin's
tutorial for biphasic system). Which one is recommended if anyone has
experience with such system and why? appreciate any comments? I know 54a7
is newer version but does it mean it is the best I mean in terms of
reproducing experimental data etc? or is there any well known problems with
43a2 for such a system?



54a7 corrected a well-known problem in 53a6 with helices being unstable. 
Previous version (45a3, 43a1, etc) did not have that problem.


-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.

Re: [gmx-users] SDF problem

[Justin Lemkul]

On 9/22/15 8:14 AM, Daniele Veclani wrote:

Dear gromacs user

My system consist of 1 molecule + 1000 of solvents (water) in cubic
box.  I did 5 ns NPT equilibration and currently I am doing analysis stuff
such as RDF, density, viscosity, etc. And now I want to try using g_spatial
but
I stuck on it. I would like to know if you can help me in this.

In Gromacs manual, they wrote like this:

1. Use make_ndx to create a group containing the atoms around which you
want
the SDF
2. trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none
3. trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans
4. run g_spatial on the .xtc output of step #3.
5. Load grid.cube into VMD and view as an isosurface

I have tried to follow those steps but I coud not get any pretty SDF
picture

This is what I have done following the above mentioned steps:
step 1: I have my index file
step 2: I choose my molecule ("solute") as group for centering
and I select "system" (1 molecule + 1000 solvents) as an output group
step 3: Again, I choose "solute" and choose "system" as an output
step 4: I run g_spatial and select "1000 solvents" for both calculation and
output. It gives me warning to increase nab values, so I increase the nab =
100. I got grid.cube but the size of the file is not that big (the manual
says
it is around 3 copies of *.xtc file).
step 5: I load grid.cube into VMD as an isosurface. I got only a sphere of
solvents there on the VMD display

How can I view the molecule?



By saving the solute coordinates (the output group in g_spatial) rather than the 
solvent molecules.  You will also need to adjust the isosurface value in VMD to 
get anything sensible.


-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.

Re: [gmx-users] PMF calculation_ Constraint

[Justin Lemkul]

On 9/22/15 3:46 PM, Sepideh Kavousi wrote:

Dear Gromacs users

I want to calculate the PMF of tocopherol in DMPC bilayer system. For this
means, I used Constraint method. the pull code in my .mdp file is :

pull = constraint
pull-geometry = distance;distance, direction, or cylinder
pull-dim = N N Y
pull-constr-tol = 1e-6
pull-start = yes;add current COM distance to pull_init?
pull-print-reference = no
pull-nstxout = 1
pull-nstfout = 5
pull-ngroups = 2
pull-ncoords = 1
pull-group1-name = DMPC
pull-group2-name = VIT
pull-coord1-groups = 1 2
pull-coord1-init = 0.0


In my output file which shows force over time, we have some sudden diverges
of force to a very high number.
I realized it is because of the boundary condition, one part of molecule
comes out of the box and enters from the other side of the box and it needs
a huge force to keep the molecule at the same position. Can you please help
me how to solve this problem



Use a bigger box, use a shorter reaction coordinate, or use an umbrella sampling 
method that supports PBC.  I suspect any output using the constraint method will 
be very poorly converged.


-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.

Re: [gmx-users] addition of hydronium ion in simulation box

[Catarina A. Carvalheda dos Santos]

Regarding CpHMD methods, I would just like to add that you have, in fact,
several options. In case you are interested, there is a good summary on
subject @
http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation.

Regards,

On 22 September 2015 at 06:59, Groenhof, Gerrit  wrote:

> Hi,
>
> > Hello justin,
> >
> > Thanks, actually I want to study movement of protons along the lenght of
> a
> > water channel.
> >
>
> > What you need is constant-pH MD, which is not natively supported in
> GROMACS.
>
> What Justin says. There is only a 3.3 version that currently supports
> this, which is available at:
>
> http://www.mpibpc.mpg.de/grubmueller/constpH
>
>
> In addition, if you're interested in proton transfer between waters only,
> HYDYN may be an option for you:
>
> http://onlinelibrary.wiley.com/doi/10.1002/jcc.23536/suppinfo
>
> However, from what you describe I assume that protein side chains may be
> involved as well in proton uptake/donation, but we have not yet extended
> HYDYN to include amino acids unfortunately.
>
> Concerning the suggestion by Andre to use DFTB, there is a recent
> implementation in Gromacs by Tomas Kubar:
>
> http://onlinelibrary.wiley.com/doi/10.1002/jcc.24029/abstract
>
>
> Good luck,
>
> Gerrit
>
> -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
>
> ==
>
>
> --
>
> Message: 3
> Date: Tue, 22 Sep 2015 14:22:41 +1200
> From: James Lord 
> To: "gmx-us...@gromacs.org" 
> Subject: [gmx-users] force fields selection
> Message-ID:
> 

Re: [gmx-users] Solvating in a solvent other than water

[Pallavi Banerjee]

Ah, yes! I hadn't made the molecules whole. It works just fine now.
Thank you guys, especially Justin for having pointed out the fault.

-Pallavi Banerjee
-- 
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.

Re: [gmx-users] Gibbs free energy landscape Vs. the stability of protein structure

[David van der Spoel]

On 22/09/15 07:42, Naba wrote:

Thank you Justin. I have to deduce some inference from this figure. Please
make me out about the following queries.

On Mon, Sep 21, 2015 at 5:48 PM, Justin Lemkul  wrote:




On 9/21/15 4:00 AM, Naba wrote:


Dear Gromacs users and Developers,

I have performed dihedral PCA for 4 extracellular loops of a transmembrane
protein after successfully finishing 100 ns of simulation at 300 and 310
K.
I obtained figures for each loops for two different temperatures as in
this
link: http://s28.postimg.org/dlva5i42l/d_PCA.jpg .

As we can see in that figure that, the loop L1 has got only one minimum at
both temperatures, whereas, L2 and L3 have got 4 minima at 300 K. I have
also calculated the amount of frames in percentages at their respective
minima. It seems that L2 and L3 have got more number of frames at their
minima when combined in comparison to L1. Now my question is:

Can we say that L2 and L3 are tend to be more stable at 300K than that of
L1 at the both temperatures?



I wouldn't make any argument about "stability" here.



Then what can be concluded from this figure? Please hint some possible
explanations.
Dihedral PCA is tricky business. For instance the "volume" of phase 
space sampled in each grid point varies making it difficult to compare 
the probability per volume (which is related to the free energy).


The fact that the difference between 300K and 310K is so large proves 
your sampling is far from complete as well, so basically your results 
are inconclusive (e.g. you sample areas at 300K that you don't at 310K).




Conformational sampling, maybe, but the question is whether or not these
PCs are the same between the different simulations. If you're not
projecting one trajectory onto the other's eigenvectors, you're quite
possibly comparing apples and oranges.



The PCs are same for both simulations. I followed dPCA procedure as you
have explained in http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA
. To obtained the 2D projections as in the link of the figure I issued the
following command for each and every loops:

g_anaeig -v eigenvec_L*.trr -f dangle_L*.trr -s resized_loop*.gro
-first 1 -last 2 -2d 2dproj_1_2.xvg

I think, I am comparing the same projections for both the simulations.




-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.








--
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
--
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.

[gmx-users] Free energy perturbation with hamiltonian replica exchange (FEP - HEX)

[Julian]

Dear Gromacs Users,

I am running relative binding free energy calculations with free energy
perturbations (FEP) but the lambda points do not converge within 10ns of
simulation time so I am thinking of using hamiltonian replica exchange
(HEX, HREX or H-REMD) with FEP as described in this paper
 on FEP/H-REMD using
CHARMM.

As I understand, Gromacs offers termperature replica exchange (T-REMD),
which does not work for me as my system is too big and furthermore contains
a membrane, and λ-dynamics in the "free-energy expanded"  module.

On alchemistry.org

it
states that Expanded Ensemble or λ-dynamics are NOT recommended for
beginners - does any body have any experience with this?
If so, could anybody recommend me any of the parameters, ... as I cannot
find any example, tutorial, and the manual is very short on it.

An alternative would be the HREX-Plumed plugin by Giovanni Bussi. However
it seems to work only for Gromacs 4.6 (not sure about this) and I would
prefer to use Gromacs 5.0 as Gromacs 4.6 does not allow the LINCS algorithm
on free energy calculations. Furthermore Giovanni Bussi states that he is
not sure whether his HREX plugin works properly with FEP calculations.

This makes me think that maybe I should give it a try with λ-dynamics?
Any suggestions? Should I try something completely different?

Best regards,
Julian
-- 
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.

Re: [gmx-users] backward.py script

[Tsjerk Wassenaar]

Hi Juan,

Unfortunately... not yet. But if you're interested, contact me off-list and
let's see what we can do :)

Cheers,

Tsjerk

On Tue, Sep 22, 2015 at 2:41 PM, Juan Munoz-Garcia <
juan.munoz-gar...@bioch.ox.ac.uk> wrote:

> Dear all,
>
> I’m using the backward.py script to convert CG to atomistic
> representation. However, to my knowledge (and testing) it only works for 1
> frame .gro or .pdb files. Is there any way to make it working for a
> trajectory in either .gro or .pdb format?
>
> Regards.
> Juan C. Munoz-Garcia
>
>
> --
> 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.




-- 
Tsjerk A. Wassenaar, Ph.D.
-- 
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.

[gmx-users] SDF problem

[Daniele Veclani]

Dear gromacs user

My system consist of 1 molecule + 1000 of solvents (water) in cubic
box.  I did 5 ns NPT equilibration and currently I am doing analysis stuff
such as RDF, density, viscosity, etc. And now I want to try using g_spatial
but
I stuck on it. I would like to know if you can help me in this.

In Gromacs manual, they wrote like this:

1. Use make_ndx to create a group containing the atoms around which you
want
the SDF
2. trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none
3. trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans
4. run g_spatial on the .xtc output of step #3.
5. Load grid.cube into VMD and view as an isosurface

I have tried to follow those steps but I coud not get any pretty SDF
picture

This is what I have done following the above mentioned steps:
step 1: I have my index file
step 2: I choose my molecule ("solute") as group for centering
and I select "system" (1 molecule + 1000 solvents) as an output group
step 3: Again, I choose "solute" and choose "system" as an output
step 4: I run g_spatial and select "1000 solvents" for both calculation and
output. It gives me warning to increase nab values, so I increase the nab =
100. I got grid.cube but the size of the file is not that big (the manual
says
it is around 3 copies of *.xtc file).
step 5: I load grid.cube into VMD as an isosurface. I got only a sphere of
solvents there on the VMD display

How can I view the molecule?

I use Gromacs 5.0.4.

Regards.
D.V.
-- 
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.

[gmx-users] backward.py script

[Juan Munoz-Garcia]

Dear all,

I’m using the backward.py script to convert CG to atomistic representation. 
However, to my knowledge (and testing) it only works for 1 frame .gro or .pdb 
files. Is there any way to make it working for a trajectory in either .gro or 
.pdb format?

Regards.
Juan C. Munoz-Garcia


-- 
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.

[gmx-users] distance dependent energy

[Cuong Nguyen]

Dear Gromacs users,

I would like to work out the energy (total and kinetic) as a function of
the distance from the center of mass of a droplet. However, using g_energy
just gave me the values as a function of time. Could anyone tell me the way
to get the distance dependent values?

Thank you very much in advance.

Kind regards,
Van
-- 
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.