date:20170601

Hi,

Indeed, the evidence of abrupt volume changes in your later posts are
rather more suggestive of a code problem. I suggest you open an issue at
https://redmine.gromacs.org, and attach a tarball of files associated e.g.
with
http://s1243.photobucket.com/user/ploetz/media/repeats_zpst3gbe9du.png.html.
grompp inputs, tpr, log and edr files would be of value in letting us
reason about and replicate any problem that exists.

Thanks very much,

Mark

On Thu, Jun 1, 2017 at 10:33 PM Elizabeth Ploetz  wrote:

> > Hi,
> >
> > Thanks for the report.
> >
> > On Wed, May 31, 2017 at 4:56 PM Elizabeth Ploetz  wrote:
> >
> >> Dear GMX-USERS,
> >>
> >> We are observing abrupt, discontinuous “jumps” in our simulation box
> >> volume for different chunks of trajectory when performing exact
> >> continuations of standard, explicit solvent, MD simulations in the NPT
> >> ensemble. Note that these volume jumps do not appear to occur after
> every
> >> single continuation (there seems to be some element of randomness);
> >> however, they occur at some point in almost all of our different
> >> simulations. There are no visually apparent problems with the
> trajectories
> >> upon viewing them in e.g., Pymol. We are not able to visualize anything
> >> unusual, such as “bubbles” for cases where the system volume jumps to
> >> larger values.
> >>
> >> Here is what we have tested:
> >>
> >>
> >>   *   Temperature/Pressure Coupling Methods:
> Nosé-Hoover/Parrinello-Rahman
> >> and Berendsen/Berendsen are both affected
> >>   *   Gromacs Versions: 4.6, 4.6.1, 5.0, and 2016 are all affected
> >>   *   Machines/Architectures: three different clusters (we don’t know
> of a
> >> machine where it does not occur) are all affected:
> >>  *   the lab’s cluster where we installed Gromacs ourselves
> >>  *   the university cluster where Gromacs was installed by the
> >> university IT staff
> >>  *   the Hansen cluster at Purdue, which we access only through a
> GUI
> >> at the DiaGrid portal
> >>   *   Systems: Pure water systems as well as solvated single solute
> >> systems where the solute is a single protein, LJ sphere, or
> >> buckminsterfullerene are all affected
> >>   *   Force fields: versions of AMBER, CHARMM, GROMOS, and OPLS force
> >> fields are all affected
> >>   *   Box shape: cubic boxes and rhombic dodecahedrons are both affected
> >>   *   Continuation method: Restarts of killed simulations (killed on
> >> purpose to increase the numbers of nodes as resources became available
> --
> >> we don't do this anymore, but this was how we first saw the problem) and
> >> exact continuations of completed simulations are both affected
> >>   *   Number of Nodes: We were almost convinced that it happened
> whenever
> >> we ran on >1 node (our usual situation), but not if we ran on 1 node
> only.
> >> We did some tests on one node on the lab’s cluster with and without
> MPI, to
> >> see whether or not it was MPI. System volume jumps were not (yet?)
> observed
> >> regardless of whether or not MPI was used. However, on the university
> >> cluster, we did tests of 24 processors using "-pe mpi-fill 24". Usually
> the
> >> 24 processors were spread across >1 node, but sometimes they completely
> >> filled one node. There was one instance where there was a system volume
> >> jump when the 24 processors changed from being distributed across >1
> node
> >> to being on 1 node only. However, MPI was used in all of those
> simulations.
> >> So, we still have not proved that it is not MPI that is a problem.
> >> Unfortunately, this test result is still murky. Perhaps we should not
> have
> >> even mentioned it.
> >>   *   Cut-off Scheme: We have done significantly fewer simulations with
> >> the Verlet cut-off scheme; however, so far the system volume jumps have
> not
> >> occurred with Verlet. We are continuing these tests.
> >>
> >
> > The simplest explanation is that your system has a phase transition that
> > happens eventually :-) We don't know what's in your system, so it's hard
> to
> > suggest what is going wrong.
>
> As noted in the original post, it happens for pure water simulations, as
> well as single solutes solvated in water. The solutes can be anything from
> a Lennard-Jones sphere to buckminsterfullerene to a protein. There are no
> phase transitions or anything weird  that we can observe, as noted above.
>
> >> Here is how we do exact continuations:
> >> gmx_mpi convert-tpr -s previous.tpr -extend 2 -o next.tpr
> >> mpiexec gmx_mpi mdrun -v -deffnm next -cpi previous.cpt -noappend >&
> myjob
> >>
>
> >Fine
>
> >> Here<
> >>
> https://docs.google.com/document/d/1NUi3H7agEFMeEq5qxTNXWopaFXqIjUbHpLUqifVRVys/edit?usp=sharing
> >
> >> is an example (CHARMM22*-based) MDP file (only used for the initial
> >> production run).
> >>
>
> > That is not a correct way to model with CHARMM (in particular those
> cutoffs
> > and cutoff treatments). This was tested extensively by CHARMM force

Re: [gmx-users] AMBER LIPID14 ff in GROMACS

2017-06-01 Thread Christopher Neale

Possibly build in amber and then convert to gromacs input format with parmed: 
https://github.com/ParmEd/ParmEd/issues/631

Looks like it might be a little tricky and of course you'd want to compare 
single-point energied in amber and then in the gromacs port, though that is 
complicated by code differences (e.g. as described in 
https://link.springer.com/article/10.1007/s10822-016-9977-1 
)

Not sure if Intermol would make that conversion task easier or harder, but it's 
here: https://github.com/shirtsgroup/InterMol

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Amit Singh 

Sent: 01 June 2017 12:50:14
To: Mark Abraham
Cc: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se; 
sudip.c...@gmail.com
Subject: Re: [gmx-users] AMBER LIPID14 ff in GROMACS

Hello Mark,
 Thank you very much for your prompt reply. Recently, Pluhackova K. *et
al have *reported a work
*(Ref: "A Critical Comparison of Biomembrane Force Fields: Structure and
Dynamics of Model DMPC, POPC, and POPE Bilayers" **DOI*

*: 10.1021/acs.jpcb.6b01870) related to the use of Amber Lipid14 force
field for Gromacs. Importantly, In their work, they have given a link for
*.itp file, which is not working now a days. In this regard, I am looking
your assistance.*
*Have a nice day,*

On Thu, Jun 1, 2017 at 7:05 PM, Mark Abraham 
wrote:

> Hi,
>
> I'm not aware of anybody who's done this. It's a lot of work to produce
> both the conversion and run a verification suite, which as far as I know
> the AMBER forcefield developers don't make available even for AMBER
> simulation package users.
>
> Mark
>
> On Wed, May 31, 2017 at 6:49 PM Amit Singh  wrote:
>
>> Is there any way to use Amber Lipid14 force field parameters for GROMACS
>> --
>> सस्नेह / with regards
>> अमित सिंह / Amit Singh
>> कम्प्यूटेशनल विज्ञान केंद्र / Centre for Computational Sciences
>> बुनियादी और अनुप्रयुक्त विज्ञान स्कूल / School of Basic and Applied
>> Sciences
>> पंजाब केन्द्रीय विश्वविद्यालय / Central University of Punjab
>> बठिंडा / Bathinda 151 001
>> भारत / INDIA
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/
[http://www.gromacs.org/@api/deki/files/187/=google_plus.jpg?size=webview]

Gromacs - Gromacs
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The development of Gromacs would not have been possible without generous 
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--
सस्नेह / with regards
अमित सिंह / Amit Singh
कम्प्यूटेशनल विज्ञान केंद्र / Centre for Computational Sciences
बुनियादी और अनुप्रयुक्त विज्ञान स्कूल / School of Basic and Applied Sciences
पंजाब केन्द्रीय विश्वविद्यालय / Central University of Punjab
बठिंडा / Bathinda 151 001
भारत / INDIA
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Re: [gmx-users] Umbrella sampling and PMF calculations

2017-06-01 Thread Alex

>
>
>>
> You have a membrane with water on either side, yes?  That's a layered
> system.
>
> But frankly, at this point I don't follow at all what you're trying to do.
>
> -

Let me try from the beginning. :)
A membrane in XY, water on both sides. At the center of the membrane, there
is a geometrically symmetric hole. A series of configurations exists,
starting with the ion at +Z_0 above the membrane (along Z) and ending at
-Z_0 below, only the Z coordinate is varying here. The center of the hole
and the XY-position of the ion are very close, i.e. things are aligned (the
series of configurations was generated in a pull simulation with the ion
restrained in XY and pulled along Z). The goal is to find the free energy
associated with ion's binding to the interior of the hole in membrane,
nothing else. I can share the trajectory (without -sep), but only
privately. Does this make sense?

Is there any reason you think I _cannot_ use your approach pretty much
directly?

Thanks,

Alex
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Re: [gmx-users] Doubt about gmx wham analysis

2017-06-01 Thread Varvdekar Bhagyesh Rajendra

Dear Justin,

Since I have the settings pull_coord1_dim = Y Y Y, I am not sure which axis the 
ligand is pulled. My initial simulation box size was 5 nm in each side. To care 
of the pulling of the ligand in any direction I made the box size 14 in each 
direction filled with water. The simulation runs perfectly and ending with the 
ligand almost 0.6 nm away from protein. But all this takes lot of computation 
power due to the need for rigorous sampling. Is there any way to cut the 
computation cost while maintaining the accuracy?

Best Regards,
Bhagyesh

- Original Message -
From: "Varvdekar Bhagyesh Rajendra" 
To: gmx-us...@gromacs.org
Sent: Thursday, June 1, 2017 7:35:16 PM
Subject: Re: [gmx-users] Doubt about gmx wham analysis

Dear Justin,

Gazillion thanks for the valuable insight!

Best Regards,
Bhagyesh

- Original Message -
From: "Justin Lemkul" 
To: gmx-us...@gromacs.org
Sent: Thursday, June 1, 2017 6:13:00 PM
Subject: Re: [gmx-users] Doubt about gmx wham analysis

On 5/31/17 10:49 AM, Varvdekar Bhagyesh Rajendra wrote:
> Dear Justin,
> 
> During the pulling part of the umbrella sampling for finding binding affinity 
> of the Protien-ligand system, the ligand(peptide) is deformed and its helices 
> straighten along with large conformational changes in Protein. This is when 
> the pull_coord1_dim = Y Y Y. But when I had used pull_coord1_dim = N N Y for 
> one of the systems the peptide helices didn't deform. Is it reasonable for 
> the ligand helices to deform when finding properties like Binding affinity?
> 
> Can it be avoided if the ligand orientation is not known and using 
> pull_coord1_dim = Y Y Y is necessary.
> 

Very simply, you should be using pull_coord1_dim = Y Y Y.  That is correct.  
The 
fact that you don't see a deformation with N N Y is irrelevant and perhaps 
coincidental.

Short peptides are largely unstructured in solution, and many only acquire a 
formed secondary structure upon binding to a larger protein.  This is a well 
known phenomenon.  Spurious instability of helices is a known issue with some 
parameter sets (e.g. GROMOS96 53A6 under-stabilizes helices) but with other 
force fields partial or full unfolding is not indicative of a problem.  You 
just 
need to be sure you're adequately sampling this conformational ensemble, which 
can be expensive.

-Justin

> Best Regards,
> Bhagyesh
> 
> - Original Message -
> From: "Varvdekar Bhagyesh Rajendra" 
> To: gmx-us...@gromacs.org
> Sent: Wednesday, May 31, 2017 6:42:41 PM
> Subject: Re: [gmx-users] Doubt about gmx wham analysis
> 
> Dear Justin,
> 
> Many Thanks for the swift reply and the help in answering my doubts.
> 
> Best Regards,
> Bhagyesh
> 
> - Original Message -
> From: "Justin Lemkul" 
> To: gmx-us...@gromacs.org
> Sent: Wednesday, May 31, 2017 6:06:59 PM
> Subject: Re: [gmx-users] Doubt about gmx wham analysis
> 
> On 5/31/17 8:34 AM, Varvdekar Bhagyesh Rajendra wrote:
>> Dear Justin,
>>
>> In my Protein-ligand system, I have used pull_coord1_dim = Y Y Y and the 
>> ligand is pulled along the COM of two groups protein-ligand in all 
>> directions to calculate binding affinity using umbrella sampling. On the 
>> other hand, the tutorials use pull_coord1_dim = N N Y. Hence, I concluded my 
>> reaction coordinate differs as mentioned in the help menu of gmx wham : "If 
>> you have some unusual  reaction coordinate you may also generate your own 
>> .pdo files and feed them with the -ip option into to gmx wham"
>>
> 
> The fact that your reaction coordinate is different from the tutorial is
> irrelevant.  You have an absolutely normal reaction coordinate and does not
> apply to what the gmx wham help text is talking about (which is probably a 
> very
> outdated note at this point, given the massive changes in the pull code in
> recent versions).
> 
>> Also, the following warning is thrown by gmx wham: " WARNING, no data point 
>> in bin 7 (z=0.403502) ! You may not get a reasonable profile. Check your 
>> histograms! "
>> I was not sure if the z corresponds to the coordinate axis or just the 
>> z-axis (which was not the only reaction coordinate in my system).
>>
> 
> It is the length along zeta, the reaction coordinate.  Don't confuse it with 
> the
> z-axis, it's just shorthand.
> 
>> All this made me conclude that the pullx files are not enough and the so 
>> called pdo files must be necessary, hence the doubt arised. I would 
>> appreciate if some more light is shed in this area.
>>
> 
> You need better sampling, not archaic file formats.
> 
> -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

[gmx-users] How to conserve total energy from a position-restrained step to a non-constrained step

2017-06-01 Thread Felix Y Yang

Hi all,

So I've noticed that the total energy of my system decreases every time I run 
an un-constrained production run immediately after a position-restrained 
heating step, most likely due to algorithms. I am attempting to string together 
multiple repeated steps of heating and running, and each period I am losing 
1500kJ/mol by the whole system, forming a "staircase" pattern in my total 
energy vs time graph, which makes the whole concatenated process hard to 
evaluate. If I remove the position-restraints on my heating steps, the system 
starts rotating out of control. Is there a way to circumvent this loss of 
energy due to algorithms, or another way to complete one whole process that has 
heating turned on and off throughout the process?

Any feedback would be appreciated.

Thanks,
Felix Yang

Graduate Master's Student
Department of Chemistry & Biochemistry
University of California, San Diego
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Re: [gmx-users] Umbrella sampling and PMF calculations




On 6/1/17 6:16 PM, Alex wrote:






Your situation is completely different.  Look into the cylinder settings
for dealing with a layered system, but I have no experience with them.  To
be clear - you always need two groups to define the vector (reaction
coordinate) along which the bias is applied.  So you need to define a
second group; you can't just say "I'm biasing an ion and that's it."



Okay, I see. However, I have a pretty simple situation: an ion and the rest
of the system, i.e. a membrane with all the atoms it contains, water, and a
counterion to the ion of interest -- which could be the groups in question,
after I use make_ndx properly. The simulations that result in the
pullf/pullx data of interest are using "pseudo" pull, because your pulling
rate is set to zero, so in terms of moving things, nothing actually gets
pulled and this is merely a way of obtaining the pullf data in the
direction of the bias. It sounds like there is little difference between
our systems. My topology of the ion of interest has no restraint in the
Z-direction, i.e. indeed a cylinder type of constraint in-plane. So, when
you say that my situation is completely different, what do you mean? There
is really nothing "layered" about my system...



You have a membrane with water on either side, yes?  That's a layered system.

But frankly, at this point I don't follow at all what you're trying to do.

-Justin




2. It is my understanding that only pullx and pullf files are required for

WHAM, along with the tpr's for each of the MD runs, at least that's what
follows from the tutorial. Anything about trajectories or energy files?
May
I just clean those up in my script, or will they be needed at any point?








Might be useful for troubleshooting or inspecting the microscopic behavior
that gives rise to the free energy profile.  There's always useful stuff
there; rarely do you only care about just a single number coming out of
WHAM.



Sure. My HDD space is limited this time, hence the question on what's
necessary and what's a useful extra.

Thank you,

Alex






--
==

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] Umbrella sampling and PMF calculations

2017-06-01 Thread Alex

>
>
>>
> Your situation is completely different.  Look into the cylinder settings
> for dealing with a layered system, but I have no experience with them.  To
> be clear - you always need two groups to define the vector (reaction
> coordinate) along which the bias is applied.  So you need to define a
> second group; you can't just say "I'm biasing an ion and that's it."


Okay, I see. However, I have a pretty simple situation: an ion and the rest
of the system, i.e. a membrane with all the atoms it contains, water, and a
counterion to the ion of interest -- which could be the groups in question,
after I use make_ndx properly. The simulations that result in the
pullf/pullx data of interest are using "pseudo" pull, because your pulling
rate is set to zero, so in terms of moving things, nothing actually gets
pulled and this is merely a way of obtaining the pullf data in the
direction of the bias. It sounds like there is little difference between
our systems. My topology of the ion of interest has no restraint in the
Z-direction, i.e. indeed a cylinder type of constraint in-plane. So, when
you say that my situation is completely different, what do you mean? There
is really nothing "layered" about my system...


> 2. It is my understanding that only pullx and pullf files are required for
>> WHAM, along with the tpr's for each of the MD runs, at least that's what
>> follows from the tutorial. Anything about trajectories or energy files?
>> May
>> I just clean those up in my script, or will they be needed at any point?
>>
>>
>


> Might be useful for troubleshooting or inspecting the microscopic behavior
> that gives rise to the free energy profile.  There's always useful stuff
> there; rarely do you only care about just a single number coming out of
> WHAM.
>
>
Sure. My HDD space is limited this time, hence the question on what's
necessary and what's a useful extra.

Thank you,

Alex


>
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Re: [gmx-users] System volume "jumps" on exact continuations

On Thu, Jun 1, 2017 at 9:39 PM, Elizabeth Ploetz  wrote:

>>> However, if most runs are group scheme, a quick check could show whether
>>> jumps are present in runs that i) do PP-PME tuning ii) if logs go truncated
>>> during continuation at least whether they do use separate PME ranks
>>> (because otherwise CPU-only runs don't tune).
>>
>> i) If grepping "timed" from the LOG file does not give any output, does
>> that mean there was no PP-PME tuning? (Sorry for the stupid question. I'm
>> not sure which piece of information from the LOG file is going to answer
>> whether or not there was PP-PME tuning.)

> Do you run with -append? If so, the log file too gets truncated, but I do
> not recall exactly where and whether the PP-PME balancing messages are
> removed or not, but it's not hard to try -- just run with separate PME and
> too few of them (e.g. 1 out of 12) and that will trigger load balancing.

I run with -noappend, so I think the LOG files are intact. I get load balancing 
messages.

> On a second thought, instead of testing with Verlet, you might want to just
> do the above and try to directly observe the anomalies after the balancer.

>> If so, perhaps there is a correlation between having PP-PME tuning and
>> having a jump. Please see this link> com/albums/gg545/ploetz/volumeJumps_zps8hmlghtn.png>. *If* the volume for
>> 40-60ns of row 3 is the correct system volume, then all the data in this
>> figure is consistent with there being a jump when there is PP-PME tuning.
>> (Please note that while the data at 1 bar looks okay in this case, and
>> elevated pressures do not, this is not always true. We get jumps at 1 bar
>> as well sometimes.)
>> ii) These are all CPU-only runs. The simulations always use separate PME
>> ranks.
>> Please let me know if any particular data from the LOG file would be
>> helpful.
>>

> It would be easier if you provided logs that we can look through.

Please see three log files here: 
https://drive.google.com/open?id=0BznaVquT5XVyVkNjMHh2eXJ5amc . These 
correspond to the third row (6 kbar) data I just linked to in my previous post 
(directly above, the volumeJumps.png image). The 40-60ns log doesn't have the 
"PP-PME Load Balancing" section, but the other two do.

>>>
>>> If I understood correctly, it's only group scheme runs where this has been
>>> observed, so it could be some newer feature/change that interacts badly
>>> with the group scheme.
>>
>> You are correct, so far we have not seen any jumps with Verlet.
>>
>>> BTW, do you have any data with 4.5?
>>>
>> I have a few old simulations with version 4.5.3 (none with 4.5, sorry).
>> They were all ran with inexact continuations (i.e., I did not provide
>> checkpoint files when running multiple short runs to create one long
>> simulation) or single trajectories that I had killed at various points and
>> then continued using checkpoint files and -append. I don't have a huge data
>> set with 4.5.3, but none of them exhibited jumps!
>>
>>> I'd suggest that (especially if if investigation of current data does not
>>> reveal the reasons) pick a setup where you seemed to get the anomaly and
>>> run with the same settings using the Verlet scheme lots of short runs with
>>> restarts in a loop.
>>>
>> Thanks, we are doing this test.
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Re: [gmx-users] How to calculate number of cholesterol molecules




On 6/1/17 4:27 PM, Archana Sonawani-Jagtap wrote:

Hi,

I want to perform atomistic simulation in POPC bilayer with 30%
cholesterol. So I want to know how to calculate number of cholesterol
molecules for 30% concentration?



Depends on what the percentage means (and often the literature is unclear) - it 
can be mass % or mol % (though typically it's the former).  Either way, it's 
just the fraction of the total mass or total number of moles of lipids.


-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] charmm36 lipid forcefield error




On 6/1/17 4:43 PM, Archana Sonawani-Jagtap wrote:

Hi,

I want to perform GPCR simulation in POPC bilayer using Charmm36
forcefield. I have generated the bilayer using CHARMM-GUI. I am following
GPCR tutorial by Justin (modified to GPCR by Anirban).



CHARMM-GUI gives you the required force field files.  Use those and don't mess 
with them.



I want to remove periodicity of the generated bilayer using following
command:

grompp -f EM.mdp -c popc288.gro -p topol_popc.top -o EM.tpr
but I am getting below error:

Program gmx grompp, VERSION 5.1

Source code file:
/usr/local/gromacs-5.1/src/gromacs/gmxpreprocess/gmxcpp.c, line: 312

Fatal error:

Topology include file "charmm36_lipid.ff/forcefield.itp" not found

I have downloaded Charmm36 FF from gromacs user's section and placed it in



The force field files on gromacs.org are not authoritative CHARMM36 files and in 
fact contain a mixture of force field parameters (C36 for lipids, but C22+CMAP 
for protein, if I recall).  If you want correct C36 parameters, get them from 
our website:


http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs

But again, CHARMM-GUI gave you everything you need, from the parent force field 
files all the way through the topology of the system, so you shouldn't have to 
touch any of this.


-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] Umbrella sampling and PMF calculations




On 6/1/17 4:28 PM, Alex wrote:

Just a few quick questions for Justin.

I am looking at your tutorial, starting here:
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html

1. In your example, you have two pull groups. My understanding is that both
are pulled relative to each other. In my case, the only thing that's pulled
to create the series of configurations required for WHAM is a single ion,
which is pulled relative to the rest of the system (nothing but a hydrated
membrane with a particular type of hole inside of it). The ion starts above
the hole, enters the hole, then leaves it, the aim here is to find the free
energy associated with sitting in that hole.
I recall (maybe incorrectly) that pull code has some quirks, so will your
procedure work, or is there anything I should be aware of?



Your situation is completely different.  Look into the cylinder settings for 
dealing with a layered system, but I have no experience with them.  To be clear 
- you always need two groups to define the vector (reaction coordinate) along 
which the bias is applied.  So you need to define a second group; you can't just 
say "I'm biasing an ion and that's it."



2. It is my understanding that only pullx and pullf files are required for
WHAM, along with the tpr's for each of the MD runs, at least that's what
follows from the tutorial. Anything about trajectories or energy files? May
I just clean those up in my script, or will they be needed at any point?



Might be useful for troubleshooting or inspecting the microscopic behavior that 
gives rise to the free energy profile.  There's always useful stuff there; 
rarely do you only care about just a single number coming out of WHAM.


-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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[gmx-users] charmm36 lipid forcefield error

2017-06-01 Thread Archana Sonawani-Jagtap

Hi,

I want to perform GPCR simulation in POPC bilayer using Charmm36
forcefield. I have generated the bilayer using CHARMM-GUI. I am following
GPCR tutorial by Justin (modified to GPCR by Anirban).

I want to remove periodicity of the generated bilayer using following
command:

grompp -f EM.mdp -c popc288.gro -p topol_popc.top -o EM.tpr
but I am getting below error:

Program gmx grompp, VERSION 5.1

Source code file:
/usr/local/gromacs-5.1/src/gromacs/gmxpreprocess/gmxcpp.c, line: 312

Fatal error:

Topology include file "charmm36_lipid.ff/forcefield.itp" not found

I have downloaded Charmm36 FF from gromacs user's section and placed it in

/usr/local/gromacs/share/gromacs/top


Please help me to solve the error.

Thanks

Archana Jagtap
PhD student
9960791339
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Re: [gmx-users] System volume "jumps" on exact continuations

2017-06-01 Thread Szilárd Páll

On Thu, Jun 1, 2017 at 9:39 PM, Elizabeth Ploetz  wrote:

> However, if most runs are group scheme, a quick check could show whether
>
> jumps are present in runs that i) do PP-PME tuning ii) if logs go truncated
> during continuation at least whether they do use separate PME ranks
> (because otherwise CPU-only runs don't tune).
>
> i) If grepping "timed" from the LOG file does not give any output, does
> that mean there was no PP-PME tuning? (Sorry for the stupid question. I'm
> not sure which piece of information from the LOG file is going to answer
> whether or not there was PP-PME tuning.)


Do you run with -append? If so, the log file too gets truncated, but I do
not recall exactly where and whether the PP-PME balancing messages are
removed or not, but it's not hard to try -- just run with separate PME and
too few of them (e.g. 1 out of 12) and that will trigger load balancing.

On a second thought, instead of testing with Verlet, you might want to just
do the above and try to directly observe the anomalies after the balancer.


> If so, perhaps there is a correlation between having PP-PME tuning and
> having a jump. Please see this link com/albums/gg545/ploetz/volumeJumps_zps8hmlghtn.png>. *If* the volume for
> 40-60ns of row 3 is the correct system volume, then all the data in this
> figure is consistent with there being a jump when there is PP-PME tuning.
> (Please note that while the data at 1 bar looks okay in this case, and
> elevated pressures do not, this is not always true. We get jumps at 1 bar
> as well sometimes.)
> ii) These are all CPU-only runs. The simulations always use separate PME
> ranks.
> Please let me know if any particular data from the LOG file would be
> helpful.
>

It would be easier if you provided logs that we can look through.


>
> If I understood correctly, it's only group scheme runs where this has been
> observed, so it could be some newer feature/change that interacts badly
> with the group scheme.
>
> You are correct, so far we have not seen any jumps with Verlet.
>
> BTW, do you have any data with 4.5?
>
> I have a few old simulations with version 4.5.3 (none with 4.5, sorry).
> They were all ran with inexact continuations (i.e., I did not provide
> checkpoint files when running multiple short runs to create one long
> simulation) or single trajectories that I had killed at various points and
> then continued using checkpoint files and -append. I don't have a huge data
> set with 4.5.3, but none of them exhibited jumps!
>
> I'd suggest that (especially if if investigation of current data does not
> reveal the reasons) pick a setup where you seemed to get the anomaly and
> run with the same settings using the Verlet scheme lots of short runs with
> restarts in a loop.
>
> Thanks, we are doing this test.
>
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Re: [gmx-users] System volume "jumps" on exact continuations

> Hi,
>
> Thanks for the report.
>
> On Wed, May 31, 2017 at 4:56 PM Elizabeth Ploetz  wrote:
>
>> Dear GMX-USERS,
>>
>> We are observing abrupt, discontinuous “jumps” in our simulation box
>> volume for different chunks of trajectory when performing exact
>> continuations of standard, explicit solvent, MD simulations in the NPT
>> ensemble. Note that these volume jumps do not appear to occur after every
>> single continuation (there seems to be some element of randomness);
>> however, they occur at some point in almost all of our different
>> simulations. There are no visually apparent problems with the trajectories
>> upon viewing them in e.g., Pymol. We are not able to visualize anything
>> unusual, such as “bubbles” for cases where the system volume jumps to
>> larger values.
>>
>> Here is what we have tested:
>>
>>
>>   *   Temperature/Pressure Coupling Methods: Nosé-Hoover/Parrinello-Rahman
>> and Berendsen/Berendsen are both affected
>>   *   Gromacs Versions: 4.6, 4.6.1, 5.0, and 2016 are all affected
>>   *   Machines/Architectures: three different clusters (we don’t know of a
>> machine where it does not occur) are all affected:
>>  *   the lab’s cluster where we installed Gromacs ourselves
>>  *   the university cluster where Gromacs was installed by the
>> university IT staff
>>  *   the Hansen cluster at Purdue, which we access only through a GUI
>> at the DiaGrid portal
>>   *   Systems: Pure water systems as well as solvated single solute
>> systems where the solute is a single protein, LJ sphere, or
>> buckminsterfullerene are all affected
>>   *   Force fields: versions of AMBER, CHARMM, GROMOS, and OPLS force
>> fields are all affected
>>   *   Box shape: cubic boxes and rhombic dodecahedrons are both affected
>>   *   Continuation method: Restarts of killed simulations (killed on
>> purpose to increase the numbers of nodes as resources became available --
>> we don't do this anymore, but this was how we first saw the problem) and
>> exact continuations of completed simulations are both affected
>>   *   Number of Nodes: We were almost convinced that it happened whenever
>> we ran on >1 node (our usual situation), but not if we ran on 1 node only.
>> We did some tests on one node on the lab’s cluster with and without MPI, to
>> see whether or not it was MPI. System volume jumps were not (yet?) observed
>> regardless of whether or not MPI was used. However, on the university
>> cluster, we did tests of 24 processors using "-pe mpi-fill 24". Usually the
>> 24 processors were spread across >1 node, but sometimes they completely
>> filled one node. There was one instance where there was a system volume
>> jump when the 24 processors changed from being distributed across >1 node
>> to being on 1 node only. However, MPI was used in all of those simulations.
>> So, we still have not proved that it is not MPI that is a problem.
>> Unfortunately, this test result is still murky. Perhaps we should not have
>> even mentioned it.
>>   *   Cut-off Scheme: We have done significantly fewer simulations with
>> the Verlet cut-off scheme; however, so far the system volume jumps have not
>> occurred with Verlet. We are continuing these tests.
>>
>
> The simplest explanation is that your system has a phase transition that
> happens eventually :-) We don't know what's in your system, so it's hard to
> suggest what is going wrong.

As noted in the original post, it happens for pure water simulations, as well 
as single solutes solvated in water. The solutes can be anything from a 
Lennard-Jones sphere to buckminsterfullerene to a protein. There are no phase 
transitions or anything weird  that we can observe, as noted above.

>> Here is how we do exact continuations:
>> gmx_mpi convert-tpr -s previous.tpr -extend 2 -o next.tpr
>> mpiexec gmx_mpi mdrun -v -deffnm next -cpi previous.cpt -noappend >& myjob
>>

>Fine

>> Here<
>>  
>> https://docs.google.com/document/d/1NUi3H7agEFMeEq5qxTNXWopaFXqIjUbHpLUqifVRVys/edit?usp=sharing>
>> is an example (CHARMM22*-based) MDP file (only used for the initial
>> production run).
>>

> That is not a correct way to model with CHARMM (in particular those cutoffs
> and cutoff treatments). This was tested extensively by CHARMM force field
> developers, and their recommendations are at
> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM.

These values were specifically chosen to match the DE Shaw CHARMM22* force 
field, according to  the following reference:
S. Piana, K. Lindorff-Larsen, D.E. Shaw
Atomic-level description of ubiquitin folding
Proc. Natl. Acad. Sci. U. S. A., 110 (15) (2013), pp. 5915–5920
Page 5916: "Nonbonded interactions were truncated to 10.5 Å..."
As noted in my original message, we have observed the same jumps with other 
force fields and we try to implement the force field as the force fields' 
authors did.

> You're also generating velocities at the start of your production run,
> which is not a great

[gmx-users] Umbrella sampling and PMF calculations

2017-06-01 Thread Alex

Just a few quick questions for Justin.

I am looking at your tutorial, starting here:
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html

1. In your example, you have two pull groups. My understanding is that both
are pulled relative to each other. In my case, the only thing that's pulled
to create the series of configurations required for WHAM is a single ion,
which is pulled relative to the rest of the system (nothing but a hydrated
membrane with a particular type of hole inside of it). The ion starts above
the hole, enters the hole, then leaves it, the aim here is to find the free
energy associated with sitting in that hole.
I recall (maybe incorrectly) that pull code has some quirks, so will your
procedure work, or is there anything I should be aware of?

2. It is my understanding that only pullx and pullf files are required for
WHAM, along with the tpr's for each of the MD runs, at least that's what
follows from the tutorial. Anything about trajectories or energy files? May
I just clean those up in my script, or will they be needed at any point?

Thank you,

Alex
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[gmx-users] How to calculate number of cholesterol molecules

2017-06-01 Thread Archana Sonawani-Jagtap

Hi,

I want to perform atomistic simulation in POPC bilayer with 30%
cholesterol. So I want to know how to calculate number of cholesterol
molecules for 30% concentration?

Thanks and Regards,

Archana Jagtap
PhD student
Mumbai, India.
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[gmx-users] gmx trjconv -center -boxcenter zero isn't amazing at putting the selection at (0, 0, 0), but I don't know why

2017-06-01 Thread Christopher Neale

Dear Users:

Using gmx 5.1.2, I find that centering a selection of the system at (0,0,0) 
works better via "editconf -c -center 0 0 0" than it does via "trjconv -center 
-boxcenter zero"

here's the comparison of the center of mass of the selection centered in these 
two different ways:
TRJCONV:
1000   -0.0356  -0.191707 -0.00163571
EDITCONF:
1000   0.00042  -1.42837e-05  0.000364283

And that was generated by this script:

#!/bin/bash
. ~/.gmx5.1.2

echo -e "r_2-26_r_40-56_r_69-166_AND_C-alpha\nSystem\n" | gmx trjconv  -f 
fittedx.gro -s fittedx.gro -n angindex.ndx -o fitted_t.gro "
echo -e "r_2-26_r_40-56_r_69-166_AND_C-alpha\nSystem\n" | gmx editconf -f 
fittedx.gro -n angindex.ndx -o fitted_e.gro -c -center 0 0 0

echo "r_2-26_r_40-56_r_69-166_AND_C-alpha" | gmx traj -f fitted_t.gro -s 
fitted_t.gro -n angindex.ndx -com -ox coord_t.xvg
echo "r_2-26_r_40-56_r_69-166_AND_C-alpha" | gmx traj -f fitted_e.gro -s 
fitted_e.gro -n angindex.ndx -com -ox coord_e.xvg

echo "TRJCONV:"
tail -n 1 coord_t.xvg
echo ""
echo "EDITCONF:"
tail -n 1 coord_e.xvg

#

I get exactly the same values with a double precision compilation of gmx used 
for all steps in the script.

All atoms in the selection are protein c-alpha (and I checked the selection to 
be sure there was no strange junk in there) so it should not be an issue with 
mass weighting.

If I change the box size of the input fittedx.gro to be huge, it doesn't affect 
either result.

I get the same result with gmx 4.6.7

If I take the editconf-centered output .gro file and run it through trjconv 
centering then it gives the same results as shown above for trjconv centering 
at zero (the ones that are not quite right).

If I make the box 100,100,100 (exactly) and then use trjconv -boxcenter rect it 
puts the center of mass at 49.964 49.808 49.904 -- so pretty much the same 
offsets from the intended value as I reported above for -boxcenter zero.

I can reproduce the issue of trjconv doing a worse job at centering than 
editconf as long as I have >2 atoms in the centered selection, and that's true 
even when I use "System" as the selection to be centered for a .gro file with 
only 3 atoms (all of type CA).

Can anyone see what I am missing?

Thank you,
Chris.
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[gmx-users] System volume "jumps" on exact continuations

However, if most runs are group scheme, a quick check could show whether

jumps are present in runs that i) do PP-PME tuning ii) if logs go truncated
during continuation at least whether they do use separate PME ranks
(because otherwise CPU-only runs don't tune).

i) If grepping "timed" from the LOG file does not give any output, does that 
mean there was no PP-PME tuning? (Sorry for the stupid question. I'm not sure 
which piece of information from the LOG file is going to answer whether or not 
there was PP-PME tuning.) If so, perhaps there is a correlation between having 
PP-PME tuning and having a jump. Please see this 
link.
 *If* the volume for 40-60ns of row 3 is the correct system volume, then all 
the data in this figure is consistent with there being a jump when there is 
PP-PME tuning. (Please note that while the data at 1 bar looks okay in this 
case, and elevated pressures do not, this is not always true. We get jumps at 1 
bar as well sometimes.)
ii) These are all CPU-only runs. The simulations always use separate PME ranks.
Please let me know if any particular data from the LOG file would be helpful.

If I understood correctly, it's only group scheme runs where this has been
observed, so it could be some newer feature/change that interacts badly
with the group scheme.

You are correct, so far we have not seen any jumps with Verlet.

BTW, do you have any data with 4.5?

I have a few old simulations with version 4.5.3 (none with 4.5, sorry). They 
were all ran with inexact continuations (i.e., I did not provide checkpoint 
files when running multiple short runs to create one long simulation) or single 
trajectories that I had killed at various points and then continued using 
checkpoint files and -append. I don't have a huge data set with 4.5.3, but none 
of them exhibited jumps!

I'd suggest that (especially if if investigation of current data does not
reveal the reasons) pick a setup where you seemed to get the anomaly and
run with the same settings using the Verlet scheme lots of short runs with
restarts in a loop.

Thanks, we are doing this test.

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[gmx-users] Disparity in total energy between consecutive steps

2017-06-01 Thread Felix Y Yang

Hi all,


So I've been trying a series of runs of heating-active-site-of-protein, then 
NVE, then heating again, and NVE again. And I've seemed to notice that the 
total energy of the system between the end of the heating process and the 
beginning of a NVE step right after it is significantly different, namely 
dropping a lot in total energy. The total energy seems to be retained a lot 
better between the end of an NVE step and the beginning of the next heating 
step.


Does anyone know what might be the cause of this? I have the protein 
position-restrained during the heating step, and released during the NVE step. 
The heating step is 3 ps, the NVE is 1 ns. For the heating step, I grouped the 
active site of the protein separately in an index file, and heated only that 
group, while the rest of the protein has the thermostat turned off. The other 
parameters in my mdp file are almost exactly the same for the heating and NVE 
processes.


Any feedback would be appreciated.


Thanks,


Felix Yang

Graduate Master's Student
Department of Chemistry & Biochemistry
University of California, San Diego

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Re: [gmx-users] System volume "jumps" on exact continuations

1. Once you identify a continuation (with associated run script) that gives the 
discontinuity, if you run many repeats of the original continuation then does 
the jump always occur or only sometimes?

The jumping does not always occur. See the linked 
figure.
 The data is the same for 0-10ns in all three rows. The top and middle rows 
show two 1-ns exact continuations after the 0-10ns run. This shows that the 
jumps don't always happen, and are not always the same. The bottom row shows 5 
exact continuations all starting from 10ns. It looks like only one of them 
jumped (yellow). The commands and input files were the same for all of the 
runs. We did NOT use -notunepme for these runs.

2. Did you do any of the MPI runs with -notunepme ? That would be my first 
suspect.

We have not used -notunepme in any of our past simulations. We are doing some 
tests of this now, based upon your suggestion. So far, we don't see jumps when 
using this flag.

3. Did you try explicitly setting a relatively large rlist and set 
verlet-buffer-tolerance = -1 (both in the .mdp file)? That would be my second 
suspect, though you say you've never seen the problem with verlet cutoff-scheme 
so I guess this suggestion is not related to the underlying issue.

So far we have not seen any jumps using Verlet. However, we have significantly 
fewer Verlet simulations. For many of our projects, we have not yet switched 
over to Verlet. It is much slower for us (we have tons of water in our systems).
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Re: [gmx-users] Simulated annealing

Hi,

Simulated annealing for system preparation is a waste of time in my
opinion. Recommended simulation preparation protocols are on the Gromacs
website, and are all you need unless your starting conformation has serious
problems, and then simulated annealing may or may not help

Mark

On Wed, 31 May 2017 14:04 Venkat Raman  wrote:

> Hi all,
>I am using Gromacs version 4.5.6 for peptide simulation. The
> structure of the peptide (16mer) was predicted from Pepfold3 server. I did
> Simulated annealing so that the side chains get properly oriented and the
> predicted structure will reach its global optimum so that the structure
> becomes more stable for production run. I have doubt in the mdp paramteres
> regarding position restraints and the annealing time and temperature. I
> tried with position restraints so that the backbone is restrained and the
> side chains are free to move. The annealing was pretty good. I did SA after
> NVT. I dont know to proceed further. How to finalize the mdp parameters
> like pressure couping and generate velocities for simulated annealing?
>
> Thanks in advance.
> K.L. Venkatraman
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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Re: [gmx-users] AMBER LIPID14 ff in GROMACS

On 6/1/17 12:50 PM, Amit Singh wrote:

Hello Mark,
Thank you very much for your prompt reply. Recently, Pluhackova K. *et
al have *reported a work
*(Ref: "A Critical Comparison of Biomembrane Force Fields: Structure and
Dynamics of Model DMPC, POPC, and POPE Bilayers" **DOI*

*: 10.1021/acs.jpcb.6b01870) related to the use of Amber Lipid14 force
field for Gromacs. Importantly, In their work, they have given a link for
*.itp file, which is not working now a days. In this regard, I am looking
your assistance.*
*Have a nice day,*

All published papers have corresponding authors and most journals have
data-sharing requirements. Contact the corresponding author, not this mailing list.

-Justin

On Thu, Jun 1, 2017 at 7:05 PM, Mark Abraham
wrote:

Hi,

I'm not aware of anybody who's done this. It's a lot of work to produce
both the conversion and run a verification suite, which as far as I know
the AMBER forcefield developers don't make available even for AMBER
simulation package users.

Mark

On Wed, May 31, 2017 at 6:49 PM Amit Singh wrote:

Is there any way to use Amber Lipid14 force field parameters for GROMACS
--
सस्नेह / with regards
अमित सिंह / Amit Singh
कम्प्यूटेशनल विज्ञान केंद्र / Centre for Computational Sciences
बुनियादी और अनुप्रयुक्त विज्ञान स्कूल / School of Basic and Applied
Sciences
पंजाब केन्द्रीय विश्वविद्यालय / Central University of Punjab
बठिंडा / Bathinda 151 001
भारत / INDIA
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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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Re: [gmx-users] AMBER LIPID14 ff in GROMACS

2017-06-01 Thread Amit Singh

Hello Mark,
 Thank you very much for your prompt reply. Recently, Pluhackova K. *et
al have *reported a work
*(Ref: "A Critical Comparison of Biomembrane Force Fields: Structure and
Dynamics of Model DMPC, POPC, and POPE Bilayers" **DOI*

*: 10.1021/acs.jpcb.6b01870) related to the use of Amber Lipid14 force
field for Gromacs. Importantly, In their work, they have given a link for
*.itp file, which is not working now a days. In this regard, I am looking
your assistance.*
*Have a nice day,*

On Thu, Jun 1, 2017 at 7:05 PM, Mark Abraham 
wrote:

> Hi,
>
> I'm not aware of anybody who's done this. It's a lot of work to produce
> both the conversion and run a verification suite, which as far as I know
> the AMBER forcefield developers don't make available even for AMBER
> simulation package users.
>
> Mark
>
> On Wed, May 31, 2017 at 6:49 PM Amit Singh  wrote:
>
>> Is there any way to use Amber Lipid14 force field parameters for GROMACS
>> --
>> सस्नेह / with regards
>> अमित सिंह / Amit Singh
>> कम्प्यूटेशनल विज्ञान केंद्र / Centre for Computational Sciences
>> बुनियादी और अनुप्रयुक्त विज्ञान स्कूल / School of Basic and Applied
>> Sciences
>> पंजाब केन्द्रीय विश्वविद्यालय / Central University of Punjab
>> बठिंडा / Bathinda 151 001
>> भारत / INDIA
>> --
>> 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.
>
>

-- 
सस्नेह / with regards
अमित सिंह / Amit Singh
कम्प्यूटेशनल विज्ञान केंद्र / Centre for Computational Sciences
बुनियादी और अनुप्रयुक्त विज्ञान स्कूल / School of Basic and Applied Sciences
पंजाब केन्द्रीय विश्वविद्यालय / Central University of Punjab
बठिंडा / Bathinda 151 001
भारत / INDIA
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Re: [gmx-users] please help clarifying units for potential energy and enthalpy from gmx energy

Hi,

I'm not sure, but I think David van der Spoel implemented these, so perhaps
we should invite his input specifically.

Mark

On Thu, Jun 1, 2017 at 5:44 PM Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:

> I am now presuming that the enthalpy is reported in kJ/mol where /mol
> means "per mole of simulation unit cells". That seems fine to me. I still
> think it's strange that the potential energy, but not the enthalpy, output
> by gmx energy is affected by the -nmol option, but perhaps that's for some
> reason the desired behaviour.
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of
> Christopher Neale 
> Sent: 30 May 2017 23:25:46
> To: Discussion list for GROMACS users
> Subject: [gmx-users] please help clarifying units for potential energy and
> enthalpy from gmx energy
>
> Dear Users:
>
>
> I am trying to figure out what “potential energy” and “enthalpy” really
> mean in the output from gmx energy. It took me a while to realize that even
> when the (more hidden than it should be) option -nmol is not used and
> therefore is set to its default value of 1, the .xvg output indicates units
> of kJ/mol for the potential energy, when in that default case it is likely
> reporting simply kJ, or perhaps kJ/unit cell.
>
>
> But then what about the “enthalpy”? It also is given units of kJ/mol in
> the .xvg output from gmx energy, but that numerical output is not affected
> at all by the value of -nmol.
>
>
> I show some output below to prove scaling of the output “potential energy”
> but no the “enthalpy” with the -nmol option to gmx energy, but that is just
> to show the change with different options to gmx energy on the same .edr
> file.
>
>
> Thank you for the help.
>
> Chris.
>
>
> ## without -nmol (default to 1)
>
>
> # Command line:
>
> #   gmx energy -f FEMSMNM.edr -o a.xvg
>
> # gmx energy is part of G R O M A C S:
>
> #
>
> # GRowing Old MAkes el Chrono Sweat
>
> #
>
> @title "GROMACS Energies"
>
> @xaxis  label "Time (ps)"
>
> @yaxis  label "(kJ/mol)"
>
> @TYPE xy
>
> @ view 0.15, 0.15, 0.75, 0.85
>
> @ legend on
>
> @ legend box on
>
> @ legend loctype view
>
> @ legend 0.78, 0.8
>
> @ legend length 2
>
> @ s0 legend "Potential"
>
> @ s1 legend "Enthalpy"
>
> 0.00  -555356.062500  -425480.937500
>
> 0.20 <020-00%2000>  -530695.812500  -415548.406250
>
> 0.40  -528639.75  -410765.75
>
> 0.60  -527722.50  -407132.125000
>
> 0.80  -526586.687500  -404519.687500
>
> 1.00  -526814.125000  -402872.875000
>
> 1.20  -525852.625000  -401044.656250
>
> 1.40  -525089.25  -399389.187500
>
> 1.60  -524979.625000  -398347.593750
>
> 1.80  -524312.50  -396957.187500
>
> 2.00  -524930.062500  -396691.562500
>
>
>
>
> # Command line:
>
> #   gmx energy -f FEMSMNM.edr -o b.xvg -nmol 100
>
> # gmx energy is part of G R O M A C S:
>
> #
>
> # GROwing Monsters And Cloning Shrimps
>
> #
>
> @title "GROMACS Energies"
>
> @xaxis  label "Time (ps)"
>
> @yaxis  label "(kJ/mol)"
>
> @TYPE xy
>
> @ view 0.15, 0.15, 0.75, 0.85
>
> @ legend on
>
> @ legend box on
>
> @ legend loctype view
>
> @ legend 0.78, 0.8
>
> @ legend length 2
>
> @ s0 legend "Potential"
>
> @ s1 legend "Enthalpy"
>
> 0.00  -5553.560547  -425480.937500
>
> 0.20 <020-00%2000>  -5306.958008  -415548.406250
>
> 0.40  -5286.397461  -410765.75
>
> 0.60  -5277.225098  -407132.125000
>
> 0.80  -5265.866699  -404519.687500
>
> 1.00  -5268.141113  -402872.875000
>
> 1.20  -5258.526367  -401044.656250
>
> 1.40  -5250.892578  -399389.187500
>
> 1.60  -5249.796387  -398347.593750
>
> 1.80  -5243.125000  -396957.187500
>
> 2.00  -5249.300781  -396691.562500
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
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Re: [gmx-users] please help clarifying units for potential energy and enthalpy from gmx energy

2017-06-01 Thread Christopher Neale

I am now presuming that the enthalpy is reported in kJ/mol where /mol means 
"per mole of simulation unit cells". That seems fine to me. I still think it's 
strange that the potential energy, but not the enthalpy, output by gmx energy 
is affected by the -nmol option, but perhaps that's for some reason the desired 
behaviour.


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Christopher 
Neale 
Sent: 30 May 2017 23:25:46
To: Discussion list for GROMACS users
Subject: [gmx-users] please help clarifying units for potential energy and 
enthalpy from gmx energy

Dear Users:


I am trying to figure out what “potential energy” and “enthalpy” really mean in 
the output from gmx energy. It took me a while to realize that even when the 
(more hidden than it should be) option -nmol is not used and therefore is set 
to its default value of 1, the .xvg output indicates units of kJ/mol for the 
potential energy, when in that default case it is likely reporting simply kJ, 
or perhaps kJ/unit cell.


But then what about the “enthalpy”? It also is given units of kJ/mol in the 
.xvg output from gmx energy, but that numerical output is not affected at all 
by the value of -nmol.


I show some output below to prove scaling of the output “potential energy” but 
no the “enthalpy” with the -nmol option to gmx energy, but that is just to show 
the change with different options to gmx energy on the same .edr file.


Thank you for the help.

Chris.


## without -nmol (default to 1)


# Command line:

#   gmx energy -f FEMSMNM.edr -o a.xvg

# gmx energy is part of G R O M A C S:

#

# GRowing Old MAkes el Chrono Sweat

#

@title "GROMACS Energies"

@xaxis  label "Time (ps)"

@yaxis  label "(kJ/mol)"

@TYPE xy

@ view 0.15, 0.15, 0.75, 0.85

@ legend on

@ legend box on

@ legend loctype view

@ legend 0.78, 0.8

@ legend length 2

@ s0 legend "Potential"

@ s1 legend "Enthalpy"

0.00  -555356.062500  -425480.937500

0.20  -530695.812500  -415548.406250

0.40  -528639.75  -410765.75

0.60  -527722.50  -407132.125000

0.80  -526586.687500  -404519.687500

1.00  -526814.125000  -402872.875000

1.20  -525852.625000  -401044.656250

1.40  -525089.25  -399389.187500

1.60  -524979.625000  -398347.593750

1.80  -524312.50  -396957.187500

2.00  -524930.062500  -396691.562500




# Command line:

#   gmx energy -f FEMSMNM.edr -o b.xvg -nmol 100

# gmx energy is part of G R O M A C S:

#

# GROwing Monsters And Cloning Shrimps

#

@title "GROMACS Energies"

@xaxis  label "Time (ps)"

@yaxis  label "(kJ/mol)"

@TYPE xy

@ view 0.15, 0.15, 0.75, 0.85

@ legend on

@ legend box on

@ legend loctype view

@ legend 0.78, 0.8

@ legend length 2

@ s0 legend "Potential"

@ s1 legend "Enthalpy"

0.00  -5553.560547  -425480.937500

0.20  -5306.958008  -415548.406250

0.40  -5286.397461  -410765.75

0.60  -5277.225098  -407132.125000

0.80  -5265.866699  -404519.687500

1.00  -5268.141113  -402872.875000

1.20  -5258.526367  -401044.656250

1.40  -5250.892578  -399389.187500

1.60  -5249.796387  -398347.593750

1.80  -5243.125000  -396957.187500

2.00  -5249.300781  -396691.562500
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Re: [gmx-users] "cmake" failed to install

2017-06-01 Thread ZHANG Cheng

Dear Mark and Mario,
Thank you very much. I delete the gromacs and redo the cmake and it works now.


Yours sincerely
Cheng




-- Original --
From:  "mario";;
Date:  Thu, Jun 1, 2017 04:07 PM
To:  "ZHANG Cheng"<272699...@qq.com>; 
Cc:  "mario"; "gmx-users"; 
"gromacs.org_gmx-users"; 
Subject:  Re: Re:  [gmx-users] "cmake" failed to install



Seems to be an old problem. You should read this

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-May/097312.html

> After following Mario's link, I still could not solve it. The same problem
> happens.
>
>
> My command line is:
>
>
> lee@ubuntu:~/Jef/gromacs/gromacs-5.1.4/build$ cmake ..
> -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> -- The CXX compiler identification is GNU 4.8.4
> -- Check for working CXX compiler: /usr/bin/c++
> -- Check for working CXX compiler: /usr/bin/c++ -- works
> -- Detecting CXX compiler ABI info
> -- Detecting CXX compiler ABI info - done
> -- No compatible CUDA toolkit found (v4.0+), disabling native GPU
> acceleration
> -- Performing Test CXXFLAGS_PRAGMA
> -- Performing Test CXXFLAGS_PRAGMA - Success
> -- Performing Test CXXFLAGS_WARN
> -- Performing Test CXXFLAGS_WARN - Success
> -- Performing Test CXXFLAGS_WARN_EXTRA
> -- Performing Test CXXFLAGS_WARN_EXTRA - Success
> -- Performing Test CXXFLAGS_WARN_UNDEF
> -- Performing Test CXXFLAGS_WARN_UNDEF - Success
> -- Performing Test CXXFLAGS_WARN_REL
> -- Performing Test CXXFLAGS_WARN_REL - Success
> -- Performing Test CXXFLAGS_EXCESS_PREC
> -- Performing Test CXXFLAGS_EXCESS_PREC - Success
> -- Performing Test CXXFLAGS_COPT
> -- Performing Test CXXFLAGS_COPT - Success
> -- Performing Test CXXFLAGS_NOINLINE
> -- Performing Test CXXFLAGS_NOINLINE - Success
> CMake Warning at cmake/gmxTestCompilerProblems.cmake:44 (message):
>   The versions of the C and C++ compilers do not match (4.8.2 and 4.8.4,
>   respectively).  Mixing different C/C++ compilers can cause problems.
> Call Stack (most recent call first):
>   CMakeLists.txt:310 (gmx_test_compiler_problems)
>
>
>
>
> CMake Error at cmake/gmxManageSimd.cmake:67 (message):
>   Cannot find AVX compiler flag.  Use a newer compiler, or choose SSE4.1
> SIMD
>   (slower).
> Call Stack (most recent call first):
>   cmake/gmxManageSimd.cmake:261
> (gmx_give_fatal_error_when_simd_support_not_found)
>   CMakeLists.txt:648 (gmx_manage_simd)
>
>
>
>
> -- Configuring incomplete, errors occurred!
> See also
> "/home/lee/Jef/gromacs/gromacs-5.1.4/build/CMakeFiles/CMakeOutput.log".
> See also
> "/home/lee/Jef/gromacs/gromacs-5.1.4/build/CMakeFiles/CMakeError.log".
>
>
>
>
>
> -- Original --
> From:  "mario";;
> Date:  Thu, Jun 1, 2017 02:44 PM
> To:  "gmx-users";
> Cc:  "gromacs.org_gmx-users";
> "ZHANG Cheng"<272699...@qq.com>;
> Subject:  Re: [gmx-users] "cmake" failed to install
>
>
>
> Dear Cheng:
> I solved that problem by following step by step instructions of the next
> page:
>
> https://bioinformaticsreview.com/20151126/how-to-install-gromacs-5-x-x-on-linux-ubuntu-14-04-lts/
>
> Best Regards
> Mario Campo
> Dpto Física - UNLPam
> La Pampa Argentina
>
>> Dear Gromacs,
>> I did the below on Ubuntu 14.04:
>>
>>
>> tar xfz gromacs-5.1.4.tar.gz
>> cd gromacs-5.1.4
>> mkdir build
>> cd build
>>
>>
>>
>> Then, I got error message when running:
>> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
>>
>>
>> The error log files can be found here:
>> https://1drv.ms/f/s!AjIs-W_id1LzobZfGThismE4so_SRQ
>>
>>
>> Can I ask how to solve this?
>>
>>
>> Thank you.
>>
>>
>> Yours sincerely
>> Cheng
>> --
>> 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] Third column of the " hbnum.xvg " file?...What is it meant for ?

On 6/1/17 11:02 AM, Erik Marklund wrote:

Hi Mark,

Exactly. But we want to phrase it such that it is legible in the legend if the 
file is plotted.

I think we should adjust the help description in a manner like I suggested 
before (or more verbose if needed) and perhaps change the legend to "Non 
H-bonding atom pairs within 0.35 nm" to clearly indicate that the two columns 
are different quantities.

-Justin

Erik

On 1 Jun 2017, at 16:51, Mark Abraham 
> wrote:

Hi,

"Pairs within 0.35" has misled David, Justin and I, and doubtless others...
without clarification, it is normal to assume that if a hydrogen bond is
"pairs within 0.35 nm and a suitable angle," then "pairs within 0.35" would
be a superset of the former. But the field is actually "pairs within 0.35
that do not satisfy the angle requirement."

Mark

On Thu, Jun 1, 2017 at 3:47 PM Erik Marklund 
>
wrote:

Yes. The sets have no overlap. But for some reason putting that in a short
description seems difficult :-)

On 1 Jun 2017, at 15:31, Mark Abraham 
> wrote:

Hi,

I still don't understand your description. Is the third column
*additional*
pairs within 0.35 that do not satisfy the angle criterion?

Mark

On Sat, May 27, 2017 at 4:36 PM Erik Marklund 
>
wrote:

On 26 May 2017, at 22:12, David van der Spoel 

> wrote:

On 26/05/17 22:05, Erik Marklund wrote:
“Pairs within 0.35 nm”. They also don’t fulfil the angle criterion,
which
is why they are sometimes fewer than the hbonds.

Therefore I would assume they are more instead.

They sometimes are, but not necessarily. I pointed it out because
sometimes people ask if g_hbond is buggy when they see that there are
occasionally lower numbers in the third column, assuming that it
contains
all pairs within 3.5 Å regardless of angle which should more numeorus
than
the pairs that also fullfil the angle criterion. That’s not the meaning
of
the third column however.

Kind regards,
Erik

On 26 May 2017, at 19:38, Adarsh V. K. 

> wrote:

Dear all,

The 'gmx hbond' command returns a *.xvg file... viz. " hbnum.xvg "

I would like to edit the file before viewing in 'Xmgrace'

I opened the hbnum.xvg using 'gedit'. It shows following details (see
below)

Can you please tell me what is there in the third column of the file?

-
# gmx hbond is part of G R O M A C S:
#
# GROtesk MACabre and Sinister
#
@title "Hydrogen Bonds"
@xaxis  label "Time (ps)"
@yaxis  label "Number"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Hydrogen bonds"
@ s1 legend "Pairs within 0.35 nm"
  02   7
 10   2   5
 20   4   3
 30   3   2
 40   3   3
 50   5   1
 60   3   6
 70   3   6
 80   2   3
 90   5   1
100  3   3
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Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

2017-06-01 Thread Erik Marklund

Hi Mark,

Exactly. But we want to phrase it such that it is legible in the legend if the 
file is plotted.

Erik

On 1 Jun 2017, at 16:51, Mark Abraham 
> wrote:

Hi,

"Pairs within 0.35" has misled David, Justin and I, and doubtless others...
without clarification, it is normal to assume that if a hydrogen bond is
"pairs within 0.35 nm and a suitable angle," then "pairs within 0.35" would
be a superset of the former. But the field is actually "pairs within 0.35
that do not satisfy the angle requirement."

Mark

On Thu, Jun 1, 2017 at 3:47 PM Erik Marklund 
>
wrote:

Yes. The sets have no overlap. But for some reason putting that in a short
description seems difficult :-)

On 1 Jun 2017, at 15:31, Mark Abraham 
> wrote:

Hi,

I still don't understand your description. Is the third column
*additional*
pairs within 0.35 that do not satisfy the angle criterion?

Mark

On Sat, May 27, 2017 at 4:36 PM Erik Marklund 
>
wrote:

On 26 May 2017, at 22:12, David van der Spoel 

> wrote:

On 26/05/17 22:05, Erik Marklund wrote:
“Pairs within 0.35 nm”. They also don’t fulfil the angle criterion,
which
is why they are sometimes fewer than the hbonds.

Therefore I would assume they are more instead.

They sometimes are, but not necessarily. I pointed it out because
sometimes people ask if g_hbond is buggy when they see that there are
occasionally lower numbers in the third column, assuming that it
contains
all pairs within 3.5 Å regardless of angle which should more numeorus
than
the pairs that also fullfil the angle criterion. That’s not the meaning
of
the third column however.

Kind regards,
Erik

On 26 May 2017, at 19:38, Adarsh V. K. 

> wrote:

Dear all,

The 'gmx hbond' command returns a *.xvg file... viz. " hbnum.xvg "

I would like to edit the file before viewing in 'Xmgrace'

I opened the hbnum.xvg using 'gedit'. It shows following details (see
below)

Can you please tell me what is there in the third column of the file?

-
# gmx hbond is part of G R O M A C S:
#
# GROtesk MACabre and Sinister
#
@title "Hydrogen Bonds"
@xaxis  label "Time (ps)"
@yaxis  label "Number"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Hydrogen bonds"
@ s1 legend "Pairs within 0.35 nm"
 02   7
10   2   5
20   4   3
30   3   2
40   3   3
50   5   1
60   3   6
70   3   6
80   2   3
90   5   1
   100  3   3
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--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205
<018-471%2042%2005> <018-471%2042%2005>
.
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Re: [gmx-users] REMD analysis of trajectories

2017-06-01 Thread Smith, Micholas D.

Ouyang,

Each Replica corresponds to 1 temperature in Gromacs (unlike other software 
packages). If you want to have continuous trajectories (i.e. follow the motion 
of one replica through temperature exchanges) then you have to demux. But the 
demux is really only useful (in my experience) with use of the retired 
g_kinetics tool.

===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Mark Abraham 

Sent: Thursday, June 01, 2017 10:53 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] REMD analysis of trajectories

Hi,

What did you learn from the first sentence of the link I gave you?

Mark

On Thu, Jun 1, 2017 at 3:20 PM YanhuaOuyang <15901283...@163.com> wrote:

> Do you mean  that the original trajectories REMD generated are belong to
> "one trajectory per temperature" (i.e. the md2.xtc is a trajectory at 298K)?
>
>
>
> Ouyang
>
>
>
>
> At 2017-06-01 21:00:52, "Mark Abraham"  wrote:
> >Hi,
> >
> >That's what you already have. See
> >http://www.gromacs.org/Documentation/How-tos/REMD#Post-Processing
> >
> >Mark
> >
> >On Thu, Jun 1, 2017 at 5:37 AM YanhuaOuyang <15901283...@163.com> wrote:
> >
> >> Hi,
> >>I have run a 100ns-REMD of protein, which has 20 replicas (i.e.
> >> remd1.xtc, remd2.xtc, ..., remd20.xtc).  I want to analyze a trajectory
> at
> >> specific temperature  such as a trajectory at experiment temperature
> 298K
> >> rather than analyzing the continuous trajectory. I have known GROMACS
> >> exchange coordinate when REMD running. Do I just analyze remd2.xtc of
> >> replica 2(T=298K) if I want to analyze a trajectory at 298K? Do I need
> to
> >> do something else on the trajectories to get a trajectory at specific
> >> temperature(i.e. 298K)?
> >>
> >> Best regards,
> >> Ouyang
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
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> >> posting!
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> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
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Re: [gmx-users] REMD analysis of trajectories

Hi,

What did you learn from the first sentence of the link I gave you?

Mark

On Thu, Jun 1, 2017 at 3:20 PM YanhuaOuyang <15901283...@163.com> wrote:

> Do you mean  that the original trajectories REMD generated are belong to
> "one trajectory per temperature" (i.e. the md2.xtc is a trajectory at 298K)?
>
>
>
> Ouyang
>
>
>
>
> At 2017-06-01 21:00:52, "Mark Abraham"  wrote:
> >Hi,
> >
> >That's what you already have. See
> >http://www.gromacs.org/Documentation/How-tos/REMD#Post-Processing
> >
> >Mark
> >
> >On Thu, Jun 1, 2017 at 5:37 AM YanhuaOuyang <15901283...@163.com> wrote:
> >
> >> Hi,
> >>I have run a 100ns-REMD of protein, which has 20 replicas (i.e.
> >> remd1.xtc, remd2.xtc, ..., remd20.xtc).  I want to analyze a trajectory
> at
> >> specific temperature  such as a trajectory at experiment temperature
> 298K
> >> rather than analyzing the continuous trajectory. I have known GROMACS
> >> exchange coordinate when REMD running. Do I just analyze remd2.xtc of
> >> replica 2(T=298K) if I want to analyze a trajectory at 298K? Do I need
> to
> >> do something else on the trajectories to get a trajectory at specific
> >> temperature(i.e. 298K)?
> >>
> >> Best regards,
> >> Ouyang
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
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> >>
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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] "cmake" failed to install

On Thu, Jun 1, 2017 at 2:39 PM  wrote:

> Dear Cheng:
> I solved that problem by following step by step instructions of the next
> page:
>
>
> https://bioinformaticsreview.com/20151126/how-to-install-gromacs-5-x-x-on-linux-ubuntu-14-04-lts/


That's a bit of a strange guide. It describes the process as tedious,
provides some useful tips about how to prepare that Ubuntu system, adds
some manual (possibly tedious) stages that deliberately circumvent existing
convenience automation, and then gives an unnecessarily complex call to
cmake that explicitly disable those convenience features that are off by
default.

Do follow the advice about using apt for this OS, but having prepared the
system, then follow the standard installation advice at
http://manual.gromacs.org/documentation/5.1.1/install-guide/index.html#quick-and-dirty-installation
and be happy :-)

Mark


>
> Best Regards
> Mario Campo
> Dpto Física - UNLPam
> La Pampa Argentina
>
> > Dear Gromacs,
> > I did the below on Ubuntu 14.04:
> >
> >
> > tar xfz gromacs-5.1.4.tar.gz
> > cd gromacs-5.1.4
> > mkdir build
> > cd build
> >
> >
> >
> > Then, I got error message when running:
> > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> >
> >
> > The error log files can be found here:
> > https://1drv.ms/f/s!AjIs-W_id1LzobZfGThismE4so_SRQ
> >
> >
> > Can I ask how to solve this?
> >
> >
> > Thank you.
> >
> >
> > Yours sincerely
> > Cheng
> > --
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> > posting!
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>
>
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Re: [gmx-users] Doubt about gmx wham analysis

2017-06-01 Thread Varvdekar Bhagyesh Rajendra

Dear Justin,

Gazillion thanks for the valuable insight!

Best Regards,
Bhagyesh

- Original Message -
From: "Justin Lemkul" 
To: gmx-us...@gromacs.org
Sent: Thursday, June 1, 2017 6:13:00 PM
Subject: Re: [gmx-users] Doubt about gmx wham analysis

On 5/31/17 10:49 AM, Varvdekar Bhagyesh Rajendra wrote:
> Dear Justin,
> 
> During the pulling part of the umbrella sampling for finding binding affinity 
> of the Protien-ligand system, the ligand(peptide) is deformed and its helices 
> straighten along with large conformational changes in Protein. This is when 
> the pull_coord1_dim = Y Y Y. But when I had used pull_coord1_dim = N N Y for 
> one of the systems the peptide helices didn't deform. Is it reasonable for 
> the ligand helices to deform when finding properties like Binding affinity?
> 
> Can it be avoided if the ligand orientation is not known and using 
> pull_coord1_dim = Y Y Y is necessary.
> 

Very simply, you should be using pull_coord1_dim = Y Y Y.  That is correct.  
The 
fact that you don't see a deformation with N N Y is irrelevant and perhaps 
coincidental.

Short peptides are largely unstructured in solution, and many only acquire a 
formed secondary structure upon binding to a larger protein.  This is a well 
known phenomenon.  Spurious instability of helices is a known issue with some 
parameter sets (e.g. GROMOS96 53A6 under-stabilizes helices) but with other 
force fields partial or full unfolding is not indicative of a problem.  You 
just 
need to be sure you're adequately sampling this conformational ensemble, which 
can be expensive.

-Justin

> Best Regards,
> Bhagyesh
> 
> - Original Message -
> From: "Varvdekar Bhagyesh Rajendra" 
> To: gmx-us...@gromacs.org
> Sent: Wednesday, May 31, 2017 6:42:41 PM
> Subject: Re: [gmx-users] Doubt about gmx wham analysis
> 
> Dear Justin,
> 
> Many Thanks for the swift reply and the help in answering my doubts.
> 
> Best Regards,
> Bhagyesh
> 
> - Original Message -
> From: "Justin Lemkul" 
> To: gmx-us...@gromacs.org
> Sent: Wednesday, May 31, 2017 6:06:59 PM
> Subject: Re: [gmx-users] Doubt about gmx wham analysis
> 
> On 5/31/17 8:34 AM, Varvdekar Bhagyesh Rajendra wrote:
>> Dear Justin,
>>
>> In my Protein-ligand system, I have used pull_coord1_dim = Y Y Y and the 
>> ligand is pulled along the COM of two groups protein-ligand in all 
>> directions to calculate binding affinity using umbrella sampling. On the 
>> other hand, the tutorials use pull_coord1_dim = N N Y. Hence, I concluded my 
>> reaction coordinate differs as mentioned in the help menu of gmx wham : "If 
>> you have some unusual  reaction coordinate you may also generate your own 
>> .pdo files and feed them with the -ip option into to gmx wham"
>>
> 
> The fact that your reaction coordinate is different from the tutorial is
> irrelevant.  You have an absolutely normal reaction coordinate and does not
> apply to what the gmx wham help text is talking about (which is probably a 
> very
> outdated note at this point, given the massive changes in the pull code in
> recent versions).
> 
>> Also, the following warning is thrown by gmx wham: " WARNING, no data point 
>> in bin 7 (z=0.403502) ! You may not get a reasonable profile. Check your 
>> histograms! "
>> I was not sure if the z corresponds to the coordinate axis or just the 
>> z-axis (which was not the only reaction coordinate in my system).
>>
> 
> It is the length along zeta, the reaction coordinate.  Don't confuse it with 
> the
> z-axis, it's just shorthand.
> 
>> All this made me conclude that the pullx files are not enough and the so 
>> called pdo files must be necessary, hence the doubt arised. I would 
>> appreciate if some more light is shed in this area.
>>
> 
> You need better sampling, not archaic file formats.
> 
> -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] "cmake" failed to install

2017-06-01 Thread mario

Seems to be an old problem. You should read this

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-May/097312.html

> After following Mario's link, I still could not solve it. The same problem
> happens.
>
>
> My command line is:
>
>
> lee@ubuntu:~/Jef/gromacs/gromacs-5.1.4/build$ cmake ..
> -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> -- The CXX compiler identification is GNU 4.8.4
> -- Check for working CXX compiler: /usr/bin/c++
> -- Check for working CXX compiler: /usr/bin/c++ -- works
> -- Detecting CXX compiler ABI info
> -- Detecting CXX compiler ABI info - done
> -- No compatible CUDA toolkit found (v4.0+), disabling native GPU
> acceleration
> -- Performing Test CXXFLAGS_PRAGMA
> -- Performing Test CXXFLAGS_PRAGMA - Success
> -- Performing Test CXXFLAGS_WARN
> -- Performing Test CXXFLAGS_WARN - Success
> -- Performing Test CXXFLAGS_WARN_EXTRA
> -- Performing Test CXXFLAGS_WARN_EXTRA - Success
> -- Performing Test CXXFLAGS_WARN_UNDEF
> -- Performing Test CXXFLAGS_WARN_UNDEF - Success
> -- Performing Test CXXFLAGS_WARN_REL
> -- Performing Test CXXFLAGS_WARN_REL - Success
> -- Performing Test CXXFLAGS_EXCESS_PREC
> -- Performing Test CXXFLAGS_EXCESS_PREC - Success
> -- Performing Test CXXFLAGS_COPT
> -- Performing Test CXXFLAGS_COPT - Success
> -- Performing Test CXXFLAGS_NOINLINE
> -- Performing Test CXXFLAGS_NOINLINE - Success
> CMake Warning at cmake/gmxTestCompilerProblems.cmake:44 (message):
>   The versions of the C and C++ compilers do not match (4.8.2 and 4.8.4,
>   respectively).  Mixing different C/C++ compilers can cause problems.
> Call Stack (most recent call first):
>   CMakeLists.txt:310 (gmx_test_compiler_problems)
>
>
>
>
> CMake Error at cmake/gmxManageSimd.cmake:67 (message):
>   Cannot find AVX compiler flag.  Use a newer compiler, or choose SSE4.1
> SIMD
>   (slower).
> Call Stack (most recent call first):
>   cmake/gmxManageSimd.cmake:261
> (gmx_give_fatal_error_when_simd_support_not_found)
>   CMakeLists.txt:648 (gmx_manage_simd)
>
>
>
>
> -- Configuring incomplete, errors occurred!
> See also
> "/home/lee/Jef/gromacs/gromacs-5.1.4/build/CMakeFiles/CMakeOutput.log".
> See also
> "/home/lee/Jef/gromacs/gromacs-5.1.4/build/CMakeFiles/CMakeError.log".
>
>
>
>
>
> -- Original --
> From:  "mario";;
> Date:  Thu, Jun 1, 2017 02:44 PM
> To:  "gmx-users";
> Cc:  "gromacs.org_gmx-users";
> "ZHANG Cheng"<272699...@qq.com>;
> Subject:  Re: [gmx-users] "cmake" failed to install
>
>
>
> Dear Cheng:
> I solved that problem by following step by step instructions of the next
> page:
>
> https://bioinformaticsreview.com/20151126/how-to-install-gromacs-5-x-x-on-linux-ubuntu-14-04-lts/
>
> Best Regards
> Mario Campo
> Dpto Física - UNLPam
> La Pampa Argentina
>
>> Dear Gromacs,
>> I did the below on Ubuntu 14.04:
>>
>>
>> tar xfz gromacs-5.1.4.tar.gz
>> cd gromacs-5.1.4
>> mkdir build
>> cd build
>>
>>
>>
>> Then, I got error message when running:
>> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
>>
>>
>> The error log files can be found here:
>> https://1drv.ms/f/s!AjIs-W_id1LzobZfGThismE4so_SRQ
>>
>>
>> Can I ask how to solve this?
>>
>>
>> Thank you.
>>
>>
>> Yours sincerely
>> Cheng
>> --
>> 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.
>>


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Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

2017-06-01 Thread Erik Marklund

Yes. The sets have no overlap. But for some reason putting that in a short 
description seems difficult :-)

> On 1 Jun 2017, at 15:31, Mark Abraham  wrote:
> 
> Hi,
> 
> I still don't understand your description. Is the third column *additional*
> pairs within 0.35 that do not satisfy the angle criterion?
> 
> Mark
> 
> On Sat, May 27, 2017 at 4:36 PM Erik Marklund 
> wrote:
> 
>> 
>> 
>> On 26 May 2017, at 22:12, David van der Spoel > > wrote:
>> 
>> On 26/05/17 22:05, Erik Marklund wrote:
>> “Pairs within 0.35 nm”. They also don’t fulfil the angle criterion, which
>> is why they are sometimes fewer than the hbonds.
>> 
>> Therefore I would assume they are more instead.
>> 
>> 
>> They sometimes are, but not necessarily. I pointed it out because
>> sometimes people ask if g_hbond is buggy when they see that there are
>> occasionally lower numbers in the third column, assuming that it contains
>> all pairs within 3.5 Å regardless of angle which should more numeorus  than
>> the pairs that also fullfil the angle criterion. That’s not the meaning of
>> the third column however.
>> 
>> Kind regards,
>> Erik
>> 
>> On 26 May 2017, at 19:38, Adarsh V. K. > > wrote:
>> 
>> Dear all,
>> 
>> The 'gmx hbond' command returns a *.xvg file... viz. " hbnum.xvg "
>> 
>> I would like to edit the file before viewing in 'Xmgrace'
>> 
>> I opened the hbnum.xvg using 'gedit'. It shows following details (see
>> below)
>> 
>> Can you please tell me what is there in the third column of the file?
>> 
>> -
>> # gmx hbond is part of G R O M A C S:
>> #
>> # GROtesk MACabre and Sinister
>> #
>> @title "Hydrogen Bonds"
>> @xaxis  label "Time (ps)"
>> @yaxis  label "Number"
>> @TYPE xy
>> @ view 0.15, 0.15, 0.75, 0.85
>> @ legend on
>> @ legend box on
>> @ legend loctype view
>> @ legend 0.78, 0.8
>> @ legend length 2
>> @ s0 legend "Hydrogen bonds"
>> @ s1 legend "Pairs within 0.35 nm"
>>   02   7
>>  10   2   5
>>  20   4   3
>>  30   3   2
>>  40   3   3
>>  50   5   1
>>  60   3   6
>>  70   3   6
>>  80   2   3
>>  90   5   1
>> 100  3   3
>> --
>> 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-requ...@gromacs.org>.
>> 
>> 
>> 
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Head of Department, Cell & Molecular Biology, Uppsala University.
>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205 <018-471%2042%2005>
>> .
>> http://www.icm.uu.se
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>> 
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>> 
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>> send a mail to gmx-users-requ...@gromacs.org> gmx-users-requ...@gromacs.org>.
>> 
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at
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>> posting!
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>> send a mail to gmx-users-requ...@gromacs.org.
> -- 
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Re: [gmx-users] "cmake" failed to install

Hi,

I don't think that cmake command can produce that result. Please remove
everything from the build directory and run that cmake command again.

I would also investigate why your compiler versions are mismatched. If you
are using the compilers provided by Ubuntu, then this is wildly unlikely to
happen. If you're using compilers you got somehow else, then I suggest you
stop doing that until you have things working with the standard compilers.

Mark

On Thu, Jun 1, 2017 at 3:21 PM ZHANG Cheng <272699...@qq.com> wrote:

> After following Mario's link, I still could not solve it. The same problem
> happens.
>
>
> My command line is:
>
>
> lee@ubuntu:~/Jef/gromacs/gromacs-5.1.4/build$ cmake ..
> -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> -- The CXX compiler identification is GNU 4.8.4
> -- Check for working CXX compiler: /usr/bin/c++
> -- Check for working CXX compiler: /usr/bin/c++ -- works
> -- Detecting CXX compiler ABI info
> -- Detecting CXX compiler ABI info - done
> -- No compatible CUDA toolkit found (v4.0+), disabling native GPU
> acceleration
> -- Performing Test CXXFLAGS_PRAGMA
> -- Performing Test CXXFLAGS_PRAGMA - Success
> -- Performing Test CXXFLAGS_WARN
> -- Performing Test CXXFLAGS_WARN - Success
> -- Performing Test CXXFLAGS_WARN_EXTRA
> -- Performing Test CXXFLAGS_WARN_EXTRA - Success
> -- Performing Test CXXFLAGS_WARN_UNDEF
> -- Performing Test CXXFLAGS_WARN_UNDEF - Success
> -- Performing Test CXXFLAGS_WARN_REL
> -- Performing Test CXXFLAGS_WARN_REL - Success
> -- Performing Test CXXFLAGS_EXCESS_PREC
> -- Performing Test CXXFLAGS_EXCESS_PREC - Success
> -- Performing Test CXXFLAGS_COPT
> -- Performing Test CXXFLAGS_COPT - Success
> -- Performing Test CXXFLAGS_NOINLINE
> -- Performing Test CXXFLAGS_NOINLINE - Success
> CMake Warning at cmake/gmxTestCompilerProblems.cmake:44 (message):
>   The versions of the C and C++ compilers do not match (4.8.2 and 4.8.4,
>   respectively).  Mixing different C/C++ compilers can cause problems.
> Call Stack (most recent call first):
>   CMakeLists.txt:310 (gmx_test_compiler_problems)
>
>
>
>
> CMake Error at cmake/gmxManageSimd.cmake:67 (message):
>   Cannot find AVX compiler flag.  Use a newer compiler, or choose SSE4.1
> SIMD
>   (slower).
> Call Stack (most recent call first):
>   cmake/gmxManageSimd.cmake:261
> (gmx_give_fatal_error_when_simd_support_not_found)
>   CMakeLists.txt:648 (gmx_manage_simd)
>
>
>
>
> -- Configuring incomplete, errors occurred!
> See also
> "/home/lee/Jef/gromacs/gromacs-5.1.4/build/CMakeFiles/CMakeOutput.log".
> See also
> "/home/lee/Jef/gromacs/gromacs-5.1.4/build/CMakeFiles/CMakeError.log".
>
>
>
>
>
> -- Original --
> From:  "mario";;
> Date:  Thu, Jun 1, 2017 02:44 PM
> To:  "gmx-users";
> Cc:  "gromacs.org_gmx-users";
> "ZHANG Cheng"<272699...@qq.com>;
> Subject:  Re: [gmx-users] "cmake" failed to install
>
>
>
> Dear Cheng:
> I solved that problem by following step by step instructions of the next
> page:
>
>
> https://bioinformaticsreview.com/20151126/how-to-install-gromacs-5-x-x-on-linux-ubuntu-14-04-lts/
>
> Best Regards
> Mario Campo
> Dpto Física - UNLPam
> La Pampa Argentina
>
> > Dear Gromacs,
> > I did the below on Ubuntu 14.04:
> >
> >
> > tar xfz gromacs-5.1.4.tar.gz
> > cd gromacs-5.1.4
> > mkdir build
> > cd build
> >
> >
> >
> > Then, I got error message when running:
> > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> >
> >
> > The error log files can be found here:
> > https://1drv.ms/f/s!AjIs-W_id1LzobZfGThismE4so_SRQ
> >
> >
> > Can I ask how to solve this?
> >
> >
> > Thank you.
> >
> >
> > Yours sincerely
> > Cheng
> > --
> > 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!
>
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>
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Re: [gmx-users] AMBER LIPID14 ff in GROMACS

Hi,

I'm not aware of anybody who's done this. It's a lot of work to produce
both the conversion and run a verification suite, which as far as I know
the AMBER forcefield developers don't make available even for AMBER
simulation package users.

Mark

On Wed, May 31, 2017 at 6:49 PM Amit Singh  wrote:

> Is there any way to use Amber Lipid14 force field parameters for GROMACS
> --
> सस्नेह / with regards
> अमित सिंह / Amit Singh
> कम्प्यूटेशनल विज्ञान केंद्र / Centre for Computational Sciences
> बुनियादी और अनुप्रयुक्त विज्ञान स्कूल / School of Basic and Applied
> Sciences
> पंजाब केन्द्रीय विश्वविद्यालय / Central University of Punjab
> बठिंडा / Bathinda 151 001
> भारत / INDIA
> --
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>
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> posting!
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[gmx-users] Analysis

2017-06-01 Thread RAHUL SURESH

I have few doubts in MD analysis.

*How to calculate the deviation angle between two helix of a protein? (for
every ns) or in other words how can I know whether the two helices
(consecutive)
 have moved apart during simulation?

*In saltbridge analysis how can I eliminate CL and NA ions? (Before the
analysis)

PS:- Its Protein-Ligand complex simulated for  100ns.

-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

Hi,

I still don't understand your description. Is the third column *additional*
pairs within 0.35 that do not satisfy the angle criterion?

Mark

On Sat, May 27, 2017 at 4:36 PM Erik Marklund 
wrote:

>
>
> On 26 May 2017, at 22:12, David van der Spoel  > wrote:
>
> On 26/05/17 22:05, Erik Marklund wrote:
> “Pairs within 0.35 nm”. They also don’t fulfil the angle criterion, which
> is why they are sometimes fewer than the hbonds.
>
> Therefore I would assume they are more instead.
>
>
> They sometimes are, but not necessarily. I pointed it out because
> sometimes people ask if g_hbond is buggy when they see that there are
> occasionally lower numbers in the third column, assuming that it contains
> all pairs within 3.5 Å regardless of angle which should more numeorus  than
> the pairs that also fullfil the angle criterion. That’s not the meaning of
> the third column however.
>
> Kind regards,
> Erik
>
> On 26 May 2017, at 19:38, Adarsh V. K.  > wrote:
>
> Dear all,
>
> The 'gmx hbond' command returns a *.xvg file... viz. " hbnum.xvg "
>
> I would like to edit the file before viewing in 'Xmgrace'
>
> I opened the hbnum.xvg using 'gedit'. It shows following details (see
> below)
>
> Can you please tell me what is there in the third column of the file?
>
> -
> # gmx hbond is part of G R O M A C S:
> #
> # GROtesk MACabre and Sinister
> #
> @title "Hydrogen Bonds"
> @xaxis  label "Time (ps)"
> @yaxis  label "Number"
> @TYPE xy
> @ view 0.15, 0.15, 0.75, 0.85
> @ legend on
> @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "Hydrogen bonds"
> @ s1 legend "Pairs within 0.35 nm"
>02   7
>   10   2   5
>   20   4   3
>   30   3   2
>   40   3   3
>   50   5   1
>   60   3   6
>   70   3   6
>   80   2   3
>   90   5   1
>  100  3   3
> --
> 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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> send a mail to gmx-users-requ...@gromacs.org gmx-users-requ...@gromacs.org>.
>
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205 <018-471%2042%2005>
> .
> http://www.icm.uu.se
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
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> send a mail to gmx-users-requ...@gromacs.org gmx-users-requ...@gromacs.org>.
>
> --
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>
> * Please search the archive at
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Re: [gmx-users] gmx freevolume

Hi,

I have no idea, but David van der Spoel implemented this tool, so perhaps
forward your gmx-users query to him personally?

Mark

On Mon, May 29, 2017 at 3:43 PM Federico Gallino <
federico_gall...@saes-group.com> wrote:

> Dear All,
>
> I would like to put your attention on the output of gmx freevolume.
> I cannot understand how the "Molecular van der Waals volume" is computed.
> I made some crosschecks from the FFV but I never got the value written by
> gmx.
>
> E.g:
>
> Free volume 35.97 +/- 0.00 %
> Total volume 68.07 +/- 0.00 nm^3
> Number of molecules 64 total mass 51773.89 Dalton
> Average molar mass: 808.97 Dalton
> Density rho: 1263.06 +/- 0.00 nm^3
> Molecular volume Vm assuming homogeneity: 1.0635 +/- 0. nm^3
> Molecular van der Waals volume assuming homogeneity:  0.6810 +/- 0.
> nm^3
> Fractional free volume 0.168 +/- 0.000
>
> If I use the empirical correlation formula:
>
> FFV=1-density*Vw/MW
>
> I got:
>
> FFV=-0.06326   vs   FFv=0.168   (gmx
> freevolume, see above)
>
>
> Vice versa if I compute Vw I got:
>
> Vw= 0.748086   vs   Vw=0.6810 (gmx freevolume, see above)
>
> In the manual, it is written that the algorithm come from the paper from
> Bondi, that is similar to the ones from Van Krevelen.
>
> I applied the Van Krevelen group contribution approach and I got:
>
> Vw=0.728  in good agreement with the formula above but in disagreement
> with the output from gmx freevolume
>
>
> Thank you in advance for any clarifications.
>
> Best regards,
>
> Federico
>
>
> Federico Gallino, Ph.D.
> Computational Science & Engineering
>
> mail: federico_gall...@saes-group.com
> T: +39 02 93178316 <+39%2002%209317%208316>
> Fax: +39 02 93178460 <+39%2002%209317%208460>
>
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>
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Re: [gmx-users] How to perform final MD simulation after extending a NPT simulation

Hi

On Wed, May 31, 2017 at 2:50 AM Adarsh V. K. 
wrote:

> Dear all,
>
> *I used following command to extend a NPT simulation*
>
> gmx convert-tpr -s npt.tpr -extend 500 -o tpxout.tpr
> gmx mdrun -deffnm tpxout -cpi npt_prev.cpt -v
>

If the npt run was long enough, you'll have both npt.cpt and npt_prev.cpt
(as a backup). Use the one that was written later.

> *Now to do final MD simulation what command I should use?*
>
> gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
> md_0_1.tpr
> gmx mdrun -deffnm md_0_1 -v
>
> or
>
> gmx grompp -f md.mdp -c npt.gro -t tpxout.cpt -p topol.top -n index.ndx -o
> md_0_1.tpr
> gmx mdrun -deffnm md_0_1 -v
>

Give to grompp -t the cpt file from the end of the run you're intending to
continue.

Using npt.cpt would be particularly strange if you used npt_prev.cpt to
extend the npt run and write tpxout, because now you've thrown away the
extended component.

Mark

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Re: [gmx-users] System volume "jumps" on exact continuations

Hi,

Thanks for the report.

On Wed, May 31, 2017 at 4:56 PM Elizabeth Ploetz  wrote:

> Dear GMX-USERS,
>
> We are observing abrupt, discontinuous “jumps” in our simulation box
> volume for different chunks of trajectory when performing exact
> continuations of standard, explicit solvent, MD simulations in the NPT
> ensemble. Note that these volume jumps do not appear to occur after every
> single continuation (there seems to be some element of randomness);
> however, they occur at some point in almost all of our different
> simulations. There are no visually apparent problems with the trajectories
> upon viewing them in e.g., Pymol. We are not able to visualize anything
> unusual, such as “bubbles” for cases where the system volume jumps to
> larger values.
>
> Here is what we have tested:
>
>
>   *   Temperature/Pressure Coupling Methods: Nosé-Hoover/Parrinello-Rahman
> and Berendsen/Berendsen are both affected
>   *   Gromacs Versions: 4.6, 4.6.1, 5.0, and 2016 are all affected
>   *   Machines/Architectures: three different clusters (we don’t know of a
> machine where it does not occur) are all affected:
>  *   the lab’s cluster where we installed Gromacs ourselves
>  *   the university cluster where Gromacs was installed by the
> university IT staff
>  *   the Hansen cluster at Purdue, which we access only through a GUI
> at the DiaGrid portal
>   *   Systems: Pure water systems as well as solvated single solute
> systems where the solute is a single protein, LJ sphere, or
> buckminsterfullerene are all affected
>   *   Force fields: versions of AMBER, CHARMM, GROMOS, and OPLS force
> fields are all affected
>   *   Box shape: cubic boxes and rhombic dodecahedrons are both affected
>   *   Continuation method: Restarts of killed simulations (killed on
> purpose to increase the numbers of nodes as resources became available --
> we don't do this anymore, but this was how we first saw the problem) and
> exact continuations of completed simulations are both affected
>   *   Number of Nodes: We were almost convinced that it happened whenever
> we ran on >1 node (our usual situation), but not if we ran on 1 node only.
> We did some tests on one node on the lab’s cluster with and without MPI, to
> see whether or not it was MPI. System volume jumps were not (yet?) observed
> regardless of whether or not MPI was used. However, on the university
> cluster, we did tests of 24 processors using "-pe mpi-fill 24". Usually the
> 24 processors were spread across >1 node, but sometimes they completely
> filled one node. There was one instance where there was a system volume
> jump when the 24 processors changed from being distributed across >1 node
> to being on 1 node only. However, MPI was used in all of those simulations.
> So, we still have not proved that it is not MPI that is a problem.
> Unfortunately, this test result is still murky. Perhaps we should not have
> even mentioned it.
>   *   Cut-off Scheme: We have done significantly fewer simulations with
> the Verlet cut-off scheme; however, so far the system volume jumps have not
> occurred with Verlet. We are continuing these tests.
>

The simplest explanation is that your system has a phase transition that
happens eventually :-) We don't know what's in your system, so it's hard to
suggest what is going wrong.


> Here is how we do exact continuations:
> gmx_mpi convert-tpr -s previous.tpr -extend 2 -o next.tpr
> mpiexec gmx_mpi mdrun -v -deffnm next -cpi previous.cpt -noappend >& myjob
>

Fine


> Here<
> https://docs.google.com/document/d/1NUi3H7agEFMeEq5qxTNXWopaFXqIjUbHpLUqifVRVys/edit?usp=sharing>
> is an example (CHARMM22*-based) MDP file (only used for the initial
> production run).
>

That is not a correct way to model with CHARMM (in particular those cutoffs
and cutoff treatments). This was tested extensively by CHARMM force field
developers, and their recommendations are at
http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM.
You're also generating velocities at the start of your production run,
which is not a great idea (but I don't think it is related to your
problem). Do an exact restart from the end of your equlibration, e.g. gmx
grompp ... -t equil_state.cpt -o production. Your LINCS settings are
unnecessarily strict - use the recommendations in the mdp documentation.


> We have performed the Gromacs regression tests (with one processor, >1
> processor but only 1 node, and with more processors than will fit on one
> node) on the two machines that we have command line access to (lab and
> university clusters). Some of the regression tests reset the number of
> processors to 8 and thus are running on only one node. But, for what it is
> worth, all tests passed.
>
> A linked Photobucket image<
> http://i1243.photobucket.com/albums/gg545/ploetz/box-volume_zps0foiwzs9.png>
> shows the same system ran for five 1-ns chunks with exact continuations on
> 2 machines: the university's or the lab's

Re: [gmx-users] "cmake" failed to install

2017-06-01 Thread ZHANG Cheng

After following Mario's link, I still could not solve it. The same problem 
happens.


My command line is:


lee@ubuntu:~/Jef/gromacs/gromacs-5.1.4/build$ cmake .. -DGMX_BUILD_OWN_FFTW=ON 
-DREGRESSIONTEST_DOWNLOAD=ON
-- The CXX compiler identification is GNU 4.8.4
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- No compatible CUDA toolkit found (v4.0+), disabling native GPU acceleration
-- Performing Test CXXFLAGS_PRAGMA
-- Performing Test CXXFLAGS_PRAGMA - Success
-- Performing Test CXXFLAGS_WARN
-- Performing Test CXXFLAGS_WARN - Success
-- Performing Test CXXFLAGS_WARN_EXTRA
-- Performing Test CXXFLAGS_WARN_EXTRA - Success
-- Performing Test CXXFLAGS_WARN_UNDEF
-- Performing Test CXXFLAGS_WARN_UNDEF - Success
-- Performing Test CXXFLAGS_WARN_REL
-- Performing Test CXXFLAGS_WARN_REL - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
CMake Warning at cmake/gmxTestCompilerProblems.cmake:44 (message):
  The versions of the C and C++ compilers do not match (4.8.2 and 4.8.4,
  respectively).  Mixing different C/C++ compilers can cause problems.
Call Stack (most recent call first):
  CMakeLists.txt:310 (gmx_test_compiler_problems)




CMake Error at cmake/gmxManageSimd.cmake:67 (message):
  Cannot find AVX compiler flag.  Use a newer compiler, or choose SSE4.1 SIMD
  (slower).
Call Stack (most recent call first):
  cmake/gmxManageSimd.cmake:261 
(gmx_give_fatal_error_when_simd_support_not_found)
  CMakeLists.txt:648 (gmx_manage_simd)




-- Configuring incomplete, errors occurred!
See also "/home/lee/Jef/gromacs/gromacs-5.1.4/build/CMakeFiles/CMakeOutput.log".
See also "/home/lee/Jef/gromacs/gromacs-5.1.4/build/CMakeFiles/CMakeError.log".





-- Original --
From:  "mario";;
Date:  Thu, Jun 1, 2017 02:44 PM
To:  "gmx-users"; 
Cc:  "gromacs.org_gmx-users"; "ZHANG 
Cheng"<272699...@qq.com>; 
Subject:  Re: [gmx-users] "cmake" failed to install



Dear Cheng:
I solved that problem by following step by step instructions of the next
page:

https://bioinformaticsreview.com/20151126/how-to-install-gromacs-5-x-x-on-linux-ubuntu-14-04-lts/

Best Regards
Mario Campo
Dpto Física - UNLPam
La Pampa Argentina

> Dear Gromacs,
> I did the below on Ubuntu 14.04:
>
>
> tar xfz gromacs-5.1.4.tar.gz
> cd gromacs-5.1.4
> mkdir build
> cd build
>
>
>
> Then, I got error message when running:
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
>
>
> The error log files can be found here:
> https://1drv.ms/f/s!AjIs-W_id1LzobZfGThismE4so_SRQ
>
>
> Can I ask how to solve this?
>
>
> Thank you.
>
>
> Yours sincerely
> Cheng
> --
> Gromacs Users mailing list
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> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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Re: [gmx-users] REMD analysis of trajectories

2017-06-01 Thread YanhuaOuyang

Do you mean  that the original trajectories REMD generated are belong to "one 
trajectory per temperature" (i.e. the md2.xtc is a trajectory at 298K)?



Ouyang




At 2017-06-01 21:00:52, "Mark Abraham"  wrote:
>Hi,
>
>That's what you already have. See
>http://www.gromacs.org/Documentation/How-tos/REMD#Post-Processing
>
>Mark
>
>On Thu, Jun 1, 2017 at 5:37 AM YanhuaOuyang <15901283...@163.com> wrote:
>
>> Hi,
>>I have run a 100ns-REMD of protein, which has 20 replicas (i.e.
>> remd1.xtc, remd2.xtc, ..., remd20.xtc).  I want to analyze a trajectory at
>> specific temperature  such as a trajectory at experiment temperature 298K
>> rather than analyzing the continuous trajectory. I have known GROMACS
>> exchange coordinate when REMD running. Do I just analyze remd2.xtc of
>> replica 2(T=298K) if I want to analyze a trajectory at 298K? Do I need to
>> do something else on the trajectories to get a trajectory at specific
>> temperature(i.e. 298K)?
>>
>> Best regards,
>> Ouyang
>> --
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>>
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Re: [gmx-users] REMD analysis of trajectories

Hi,

That's what you already have. See
http://www.gromacs.org/Documentation/How-tos/REMD#Post-Processing

Mark

On Thu, Jun 1, 2017 at 5:37 AM YanhuaOuyang <15901283...@163.com> wrote:

> Hi,
>I have run a 100ns-REMD of protein, which has 20 replicas (i.e.
> remd1.xtc, remd2.xtc, ..., remd20.xtc).  I want to analyze a trajectory at
> specific temperature  such as a trajectory at experiment temperature 298K
> rather than analyzing the continuous trajectory. I have known GROMACS
> exchange coordinate when REMD running. Do I just analyze remd2.xtc of
> replica 2(T=298K) if I want to analyze a trajectory at 298K? Do I need to
> do something else on the trajectories to get a trajectory at specific
> temperature(i.e. 298K)?
>
> Best regards,
> Ouyang
> --
> Gromacs Users mailing list
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Re: [gmx-users] "cmake" failed to install

Hi,

We can't see the error message you got on the terminal, so we don't know
what the problem is.

Mark

On Thu, Jun 1, 2017 at 12:50 PM ZHANG Cheng <272699...@qq.com> wrote:

> Dear Gromacs,
> I did the below on Ubuntu 14.04:
>
>
> tar xfz gromacs-5.1.4.tar.gz
> cd gromacs-5.1.4
> mkdir build
> cd build
>
>
>
> Then, I got error message when running:
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
>
>
> The error log files can be found here:
> https://1drv.ms/f/s!AjIs-W_id1LzobZfGThismE4so_SRQ
>
>
> Can I ask how to solve this?
>
>
> Thank you.
>
>
> Yours sincerely
> Cheng
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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Re: [gmx-users] DrudeFF topology transfer from CHARMM to GROMACS

2017-06-01 Thread Tomasz Piskorz

Thank you, Justin. That solves my problem.

Best,
Tomasz K. Piskorz



On 31 May 2017 at 13:51, Justin Lemkul  wrote:

>
>
> On 5/31/17 7:06 AM, Tomasz Piskorz wrote:
>
>> Dear all,
>>
>> I would like to simulate cyclohexane using Drude FF in GROMACS. I've seen
>> that the topology is already available in CHARMM-DrudeFF and I would like
>> to transfer it to GROMACS. However, I don't know how to calculate the
>> charge of Drude particle, which is required by topology in GROMACS. Does
>> anyone know how to do it?
>>
>> Atomic polarizability can be described by equation:
>> alpha = (q_D)^2/k,
>> where k = 418400 kJ/(mol*nm^2) and alpha is given in CHARMM topology (i.g.
>> for O in glycine alpha=0.000651 nm^3). However, when I try to calculate
>> the
>> charge I always get a wrong result. Is this question which I should use or
>> there is something more which I don't take under consideration?
>>
>>
> Yes, there is an implicit conversion factor of Coulomb's constant.
>
> qD = sqrt((alpha/kD)/CCELEC)
>
> In CHARMM units, this is
>
> qD = sqrt((0.651/1000)/332.0716)
>
> I'll add the model compounds to the next release of the GROMACS-formatted
> Drude force field.  I have other issues to sort out before doing that,
> though.
>
> -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] Reg: creation of separate chains in .pdb file

On 6/1/17 4:30 AM, Syed Azeem wrote:

On 5/31/17 8:26 AM, Syed Azeem wrote:

On 5/29/17 8:00 AM, Syed Azeem wrote:

Hey all,

I simulated a protein-peptide docked complex. Post simulation, I
created an index file selecting only the Protein Group
(protein-peptide complex). Then using editconf, I created a .pdb file
for the same.

When I view the prtn.pdb file, only the protein is available but not
the peptide. Still the prtn.pdb file has coordinates for peptide as
well. The pdb file also lacks a chain identifier, which was present in

If you're having trouble viewing the coordinates, that's a problem with
the

viewer itself. You say that the coordinates are there (as they should
be)
so
there's no reason they can't be visualized if rendered properly.

the initial structure.

How to overcome this?

Add suitable chain identifiers back into the coordinate file.

Hey Justin,

I tried adding chain identifiers naming A & B to the file. It creates
another linear peptide chain away from main complex, when I view it in
Pymol.

Sounds like a periodicity issue. PyMOL is only telling you what's there;
it's
not "creating" anything :)

Hey Justin,

How do I overcome this periodicity issue?

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow

If I had a nickel for every time I've posted that link...

-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] Deuterium Order Parameter Calculations




On 5/31/17 11:35 AM, Sanim Rahman wrote:

Thank you Justin,

That makes much more sense. I was able to fix the error. I have one more
question that is out of topic from the original question. Is there a guide
that informs the user on what index groups should be made for each type of
analysis? I am also trying to use gmx_potential to do electrostatic
potential on a membrane solvated in KCl. If I want to do this, what index
group would I use?



The group(s) you supply to any analysis tool depend on what you want to do. 
Sorry, no one-size-fits all guide exists, nor should it.  Scientific inquiry 
rarely fits into a neat little box.


-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] tetrahedral order parameter




On 6/1/17 3:42 AM, ISHRAT JAHAN wrote:

Dear all,
I want to calculate tetrahedral order parameter of water molecule.can
anyone tell me how to calculate it.


Use gmx hydorder

-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] Doubt about gmx wham analysis