[gmx-users] Energies in MM scanning using gmx

[fantasticqhl]

Dear all,

But I have questions about the energies calculated by GMX for bonds and
angles scanning.

For example, a series of conformations of one system should be generated for
a bond scanning, the only difference in geometry of these conformations is
the bond length A---B.
However, when I set the force constant as 0 for bond A---B, the bond
energies is not a flat line as the bond length changes, in principle, it
should be a flat line, but it is not.

 


This is an example I got for my system. Could some tell me how to explain
the energy differences? Thanks very much!

All the best,
qh 





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Re: [gmx-users] concatenating 2 xtc files

[Kavyashree M]

Dear Sir,

First trajectory - traj1.xtc (0 to 5... ns)
Second trajectory -  traj2.xtc (5... to 25ns)

But there is no gap in between.
for concatenating -
$ trjcat -f traj1.xtc traj2.xtc -o trajf.xtc

For nujump -
$ trjconv -f trajf.xtc -s md.tpr -pbc nojump -o trajf.xtc

I also have a case where I ran 10ns in 64 cores and later
continued in 8core machine. This also has the same problem.
While running in 64 cores by default it did not generate
the checkpoint file. So I has to use tpbconv to generate
a new tpr file for continuing from the same point  -

$ tpbconv -s old.tpr -f traj.trr -e ener.edr -o new.tpr

Thanks in advance.

Regards
Kavya




On Thu, Aug 1, 2013 at 12:20 PM, Tsjerk Wassenaar  wrote:

> Hi Kavya,
>
> That shouldn be a problem. Please post your sequence of commands for
> concatenating and further processing of the trajectory.
>
> Cheers,
>
> Tsjerk
>
>
> On Thu, Aug 1, 2013 at 8:12 AM, Kavyashree M  wrote:
>
> > Dear users,
> >
> > I ran a simulation for 25ns. First 5ns in 8 core machine
> > and late part in 64 cores. It ran without any problem. The
> > trajectories were concatenated, jumps are removed and
> > rmsd was calculated. But there was sudden jump in the
> > rmsd curve. Is it wrong to run simulations in different
> > cores like this?
> >
> > Thank you
> > Regards
> > Kavya
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>
>
> --
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[gmx-users] Re: fftw

[Andrish Reddy]

atila petrosian wrote
> Dear gromacs users
> 
> 
> Why should I install fftw before gromacs installation?
> 
> I want to know exact role of fftw in gromacs calculations.
> 
> Please guide me about that.
> 
> Best wishes
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FFTW = Fastest Fourier Transform in the West... hopefully you should see the
connection :)



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[gmx-users] QM/MM with gromacs 4.5.5-gaussian03

[azeif]

Hi all.I'm trying to run a test QM/MM calculation of Pd2+ in water using
gromacs-4.5.5+gaussian03 and it results in folowing error messages: 
225409.err   
(MDP file is here:  fep.mdp
  )I have compiled
gaussian as described here:
http://www.gromacs.org/Documentation/Installation_Instructions_4.5/compiling_QMMM
(however I have made several changes, e.g. there is no label 1042 in punout,
and several functions resides in osutil.f, but finally it compiled
well).Could you please advice me how to fix this problem (or how to find out
where mdrun crashes)?For me it looks like Gaussian works smoothly and
produces good input.log and then everything crashes when Gromacs tries to
access QM results (but I don't understand where).Currently the task was run
on 1 CPU using -nt 1 option. Is it possible to run gromacs+gaussian in
parallel? It is very important for me, and if it is impossible I'm afraid I
have to give up of using gromacs+gaussian...



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[gmx-users] Re: Energies in MM scanning using gmx

[fantasticqhl]

Thank you, all! I know the reason now!

All the best,
qh



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Re: [gmx-users] Re: Conserved energy ("Conserved En.") in NVT simulation

[Mark Abraham]

On Wed, Jul 31, 2013 at 9:42 PM, Janne Hirvi  wrote:
> Thanks for your comments Mark,
>
> If I understood correctly, you are saying, that maybe linear drift in 
> "Conserved En." could indicate conservation of
> that quantity, which we actually should be interested.
>
> However, I made meanwhile some additional calculations and noticed that drift 
> in "Conserved En." with v-rescale
> temperature coupling decreases if tau_t is increased.

What would you have expected from equation 15?

> So, in my opinion it would indicate that drift in "Conserved En."
> is more or less related to "disturbance" due to temperature coupling. If this 
> is true, there shouldn't be drift in perfect
> case - am I correct?

If you use any finite temperature coupling, then you are perturbing
the dynamics away from that of the NVE Hamiltonian. The Hamiltonian
"drift" is the time integral of the auxiliary dynamics. By
construction, this is drift non-zero for this thermostat.

Mark

> Btw. drifts in my previous mail were per ns.
>
> Regards,
>
> Janne
>
> 
>
>> Dear gmx-users,
>>
>> I have run some tests (especially) for pure water, being able to achieve 
>> pretty much perfect energy conservation in
>> NVE ensemble (with PME-switch and shifted VDW potential).
>
> Great.
>
>> Then, just for the test, I continued to NVT ensemble by using previous .tpr 
>> and .cpt files, but the result was a quite
>> surprise, because there seems to be constant drift in "Conserved En.".
>>
>> The drift (100kJ/mol = 0.3%) is not especially large, but it exists with 
>> v-rescale temperature coupling. On the other
>> hand, there is no drift at all, if I change to nose-hoover temperature 
>> coupling.
>>
>> The behavior is similar also my other systems (liquid mixtures), even though 
>> then neither of temperature coupling
>> methods will give exactly perfect conservation, but nose-hoover gives much 
>> better one (500 kJ/mol = 3% vs. 60
>> kJ/mol = 0.4%).
>>
>> Actually, I was expecting to see no drift at all, after all systems behaved 
>> fine in NVE ensemble with same parameters
>> with an exception of added temperature coupling (especially when I used 
>> double precision for test purpose).
>>
>> So, the main question is, if it is just normal that even such parameters, 
>> which give perfect energy conservation in NVE
>> ensemble may introduce drift in "Conserved En.", when NVT ensemble is used? 
>> Or is it just purely (only reason for drift)
>> indication that some temperature coupling methods"work better" than others 
>> in this sense?
>
> In the case of v-rescale, the description of "Conserved En." is an
> overbid. If you see the Bussi 2007 paper, there is a conserved
> quantity H-tilde, but computing it requires knowledge of the whole of
> history. IIRC their H is what mdrun reports as "Conserved En.". I
> don't know whether it can be shown that a linear trend in H is
> equivalent to conservation in H-tilde, but that would be a useful
> result!
>
> Mark
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Re: [gmx-users] Potential Energy Scan

[Mark Abraham]

http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy

On Thu, Aug 1, 2013 at 7:03 AM, tarak karmakar  wrote:
> Dear All,
>
> Can anyone guide me how to perform the 'potential energy scan' for a
> dihedral of a small molecule in gromacs?
>
> Regrads,
> Tarak
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Re: [gmx-users] concatenating 2 xtc files

[Justin Lemkul]

On 8/1/13 3:42 AM, Kavyashree M wrote:

Dear Sir,

First trajectory - traj1.xtc (0 to 5... ns)
Second trajectory -  traj2.xtc (5... to 25ns)

But there is no gap in between.
for concatenating -
$ trjcat -f traj1.xtc traj2.xtc -o trajf.xtc

For nujump -
$ trjconv -f trajf.xtc -s md.tpr -pbc nojump -o trajf.xtc

I also have a case where I ran 10ns in 64 cores and later
continued in 8core machine. This also has the same problem.
While running in 64 cores by default it did not generate
the checkpoint file. So I has to use tpbconv to generate
a new tpr file for continuing from the same point  -

$ tpbconv -s old.tpr -f traj.trr -e ener.edr -o new.tpr



I would suggest using gmxdump on new.tpr to verify that the coordinates it 
contains are the same as the last frame in traj.trr.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] fatal error with charmm/amber forcefield

[Mark Abraham]

On Wed, Jul 31, 2013 at 11:20 PM, Sanku M  wrote:
> Dear Gromacs users,
>   I am using gromacs 4.5.4 .
>  Is there any known issue/problem in running hamiltonian replica exchange 
> calculations or FEP  with charm27.ff or amber forcefield  in gromacs4.5.4 ?

Almost certainly. Do check out the release notes on the webpage.

> I tried running an hamiltonian replica exchange using charmm27.ff by 
> interpolating A state and B state but it gives error that dihedral terms with 
> multiple values can not be interpolated..One need to write all A and B states 
> in topol.top manually.
>  With opls.ff , it does not have any such problem. It works fine... Is it 
> resolved in gromacs 4.6

Answering that question would require a whole lot more detail from
you. You are better advised to install 4.6 and try it. :-)

Mark

> This is the series error I am getting when using charmm forcefield or amber 
> forcefield:
> WARNING 1197 [file topol_scale.top, line 2353]:
>   No default Proper Dih. types for perturbed atoms, using normal values
>
>
> ERROR 323 [file topol_scale.top, line 2354]:
>   Cannot automatically perturb a torsion with multiple terms to different
>   form.
>   Please specify perturbed parameters manually for this torsion in your
>   topology!
> Any idea?
> Thanks
> Sanku
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Re: [gmx-users] Box dimension size errors in MARTINI soft core simulation

[Scott Pendley]

Justin,

Much appreciation for the suggestions.  I found that the large time
constant (tau_p) on the pressure coupling was indeed a significant
contributor.  When I dropped that value down to 2.5, the box vectors scaled
down in a more reasonable manner maintaining the cubic simulation box.

With regard to your other questions:
Visualizing is possible but is more technical to do with MARTINI beads.  I
am still trying to figure out how to do this on vmd.

The prior npt run also used parrinello-rahman but with a tau-p of 2.0.
This may have contributed to some of the instability seen in this system so
I may switch it to berendsen per your suggestion.

I agree, isotropic coupling would be better for this system.

Some initial runs suggests that turning off the free energy portion does
allow the simulations to run to completion (for short simulations of 10 ns)
but I haven't analyzed them to determine if the sampling time is
insufficient to reveal developing instabilities.

Contrary to logic, at lambda = 0 this simulation instability also occurs.

The LJ changes are composed on contributions from both solvent-solvent
interactions and solvent-solute.  I am seeing a ~ 3000 kj/mol different
that grows but plateaus out before the system crashes.  I would be hesitant
about ascribing the instability to this term as the decrease in LJ and
total energy would be expected at lamba=0.4 and the energy reached its
maximum prior to the system instability.

Have an amazing day,

Scott


On Tue, Jul 30, 2013 at 10:44 AM, Justin Lemkul  wrote:

>
>
> On 7/30/13 10:17 AM, Scott Pendley wrote:
>
>> Justin,
>>
>> Thank you for the continued help.  I have copied the text of the mdp file
>> below.  It is a little long, so fair warning.  The system is a MARTINI
>>
>
> Perfect, thanks.
>
>
>  coarse grain representation of 1,2-dipalmitoyl-phosphatidyl-**glycerole
>> (LHG)
>> surrounded by 700 octanol molecules.  Being a neutral MARTINI
>> representation, all represented beads or atoms have a charge of 0.0.
>> Octanol parameters were taken from  MARTINI v 2.0 lipid parameters taken
>> from the official website.  1,2-dipalmitoyl-phosphatidyl-**glycerole
>> parameters were created in house (and seem to work well in aqueous
>> simulations). From your note yesterday, it sounded like it may have been a
>> rough day yesterday.  I hope today treats you better.
>>
>>
> I appreciate the sentiment, not sure what I've said to give the bad
> impression.  Yesterday was great.  Hopefully nothing I have said has come
> across as snarky :)
>
> Back to the issue at hand.  A couple of things I notice:
>
>  nstxtcout= 1000
>>
>
> Given the frequent .xtc output, you should have a pretty good
> visualization of the trajectory.  Does it provide any clues?
>
>  Pcoupl   = parrinello-rahman
>>
>
> You said you did prior NVT and NPT without free energy options.  What
> barostat did you use in the previous NPT?  Something forgiving like
> Berendsen?
>
>  Pcoupltype   = semiisotropic
>>
>
> I don't understand the use of semi-isotropic coupling here.  That's
> intended for layered systems like membranes.  Sounds to me like you've got
> a solute in a uniform solvent, and thus isotropic pressure coupling is
> appropriate.
>
>
>  tau_p= 12.0 12.0  ;parrinello-rahman is more stable
>> with larger tau-p, DdJ, 20130422
>>
>
> Very long tau_p, indeed.  Normally a value no larger than 5.0 should be
> necessary.  That's not necessarily the source of the problem here, but your
> pressure could be running away from you.
>
>
>  ; and set the free energy parameters
>> free-energy  = yes
>>
>
> Does turning the free energy code off result in a stable simulation?  Your
> first message seemed to indicate this would be the case, but I just want to
> clarify.
>
>
>  couple-moltype   = LHG
>> init-lambda  = 0.4
>> ; these 'soft-core' parameters make sure we never get overlapping
>> ; charges as lambda goes to 0
>> sc-power = 1
>> sc-sigma = 0.3
>> sc-alpha = 1.0
>> ; we still want the molecule to interact with itself at lambda=0
>> couple-intramol  = no
>> couple-lambda0   = vdw-q
>> couple-lambda1   = none
>>
>
> I don't think there's anything wrong with this approach, but I generally
> do not (de)couple vdW and charges simultaneously.  Might be worthwhile to
> try a simple vdw -> none transformation to test.
>
>
>  foreign-lambda   = 0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.65 0.7 0.75
>> 0.8
>> 0.85 0.9 0.95 1
>>
>>
> Nothing necessarily wrong here, though you'll get a lot of output that
> likely won't improve your result and will probably just slow the
> simulations down.
>
> What do results at lambda = 0 give you?  In theory, this should be a fully
> interacting system and would help track down any bugs in the free energy
> code itself.  If lambda = 0 works, then try a non-zero value.
>
> You mentioned before that

Re: [gmx-users] concatenating 2 xtc files

[Kavyashree M]

Sir,

Thank you for the suggestion.. I will make use of it in
future runs. but now the simulation is over.

There was some overlap of few ns in 8core machine.
so while checking the rmsd plot there was a significant
difference in rmsd between 8 core and 64 core overlapped
region of simulation.

1 more question is suppose I do not have checkpoint file
and if I need to continue from a stopped point (not extending)
does this command do the job?
$ tpbconv -s old.tpr -f traj.trr -e ener.edr -o new.tpr

Because when I tried with this there was a jump in the rmsd

Thank you
Regards
Kavya



On Thu, Aug 1, 2013 at 5:18 PM, Justin Lemkul  wrote:

>
>
> On 8/1/13 3:42 AM, Kavyashree M wrote:
>
>> Dear Sir,
>>
>> First trajectory - traj1.xtc (0 to 5... ns)
>> Second trajectory -  traj2.xtc (5... to 25ns)
>>
>> But there is no gap in between.
>> for concatenating -
>> $ trjcat -f traj1.xtc traj2.xtc -o trajf.xtc
>>
>> For nujump -
>> $ trjconv -f trajf.xtc -s md.tpr -pbc nojump -o trajf.xtc
>>
>> I also have a case where I ran 10ns in 64 cores and later
>> continued in 8core machine. This also has the same problem.
>> While running in 64 cores by default it did not generate
>> the checkpoint file. So I has to use tpbconv to generate
>> a new tpr file for continuing from the same point  -
>>
>> $ tpbconv -s old.tpr -f traj.trr -e ener.edr -o new.tpr
>>
>>
> I would suggest using gmxdump on new.tpr to verify that the coordinates it
> contains are the same as the last frame in traj.trr.
>
> -Justin
>
> --
> ==**
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul@outerbanks.umaryland.**edu  |
> (410) 706-7441
>
> ==**
>
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[gmx-users] Regarding g_order

[Venkat Reddy]

Dear Gmx-users,
In the GROMACS site, it has been mentioned that there is a bug (Instead of
numbering carbons from 2-17, the numbering starts from 1-16) in g_order
program up to, and including, v4.5.4. But when I am using v4.5.5, I am
getting the same sort of numbering. Is it normal or I should renumber from
2-17?

Thank you

-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
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Re: [gmx-users] Re: CUDA with QUADRO GPUs

[Szilárd Páll]

Dear Ramon,

Thanks for the kind words!

On Tue, Jun 18, 2013 at 10:22 AM, Ramon Crehuet Simon
 wrote:
> Dear Szilard,
> Thanks for your message. Your help is priceless and helps advance science 
> more than many publications. I extend that to many experts who kindly and 
> promptly answer questions in the mailing list. I wish that could be valued 
> when evaluating a CV. Sorry for the digression...
> The visualization I had in mind was the one most of us do: MD trajectories of 
> biomolecules. In particular I use VMD. From you message, I deduce that a GTX 
> card would work as good as a quadro for a much lower price. Right?

Molecular visualisation does not require Quadro cards, GTX works just
fine. In fact, when it comes to the redering itself even AMD GPUs
should be just fine (although vmd can use NVIDIA GPUs for accelerating
compute tasks).

> The problem is that most worksations come with quadro cards, not GTX. In 
> particular I was looking at Dell precision workstation. If you want a GTX 
> card you have to go to a gaming PC. Which is probably ok if the 
> administration understands it... :-)

I'm pretty sure you should be able to get a workstation with e.g. only
Intel integrated graphics and add another discrete GTX GPU to be used
for compute. In fact, it can be advantageous having separate display
and compute GPUs - especially if you plan to run Windows. The only
drawback of using a weak GPU for driving the display is that
visualisation of large/complex molecular systems also requires a fast
GPU. If that turns out to be the case, one can always disable the
integrated graphics and use the discrete GPU for both display and
compute.

> The GTX cards lack ECC. Is that an issue for running gromacs? or the memory 
> errors only result in adding a negligible stochastic term to the dynamics?

In our experience ECC is not really needed for MD - at least not to be
able to run simulations. Of course, error correction can always come
handy, but the question is at what cost. While data corruption e.g.
due to soft errors can (and does) happen, the chance of such an event
going unnoticed in the results of an MD simulation is IMHO quite low -
most of the time such an event will manifest as a crash, or corrupted
frame.

Cheers,
--
Szilárd

> Thanks again,
> Ramon
>
>
>
> Message: 5
> Date: Tue, 18 Jun 2013 00:20:00 +0200
> From: Szil?rd P?ll 
> Subject: Re: [gmx-users] CUDA with QUADRO GPUs?
> To: Discussion list for GROMACS users 
> Message-ID:
> 
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear Ramon,
>
> Compute capability does not reflect the performance of a card, but it
> is an indicator of what functionalities does the GPU provide - more
> like a generation number or feature set version.
>
> Quadro cards are typically quite close in performance/$ to Teslas with
> roughly 5-8x *lower* "GROMACS bang for the buck" compared to consumer
> (GTX) cards. You can find a bit more detailed and more general
> explanation here: http://goo.gl/80cQQ
>
> More concretely, the K4000 is roughly as fast as a GTX 650 Ti, a
> low-end consumer GPU (~120 Eur), for ~6x the price. For the price of
> the K4000 one can get a high-end card, e.g the GTX780 which is among
> the fastest NVIDIA GPUs to date (close to the Tesla K20 in single
> precision). Hence, unless you really *need* the capabilities of a
> Quadro card, that is if the visualization you are referring to means
> CAD or similar *professional* graphics work, I suggest getting
> consumer cards.
>
> If you want to compare cards, from the point of view of GROMACS 4.6,
> pretty much the only thing that matters is the number of cores (or
> multiprocessors) times the GPU clock frequency. Note that comparing
> cards between different generations (different "major" compute
> capability) is not as straightforward.
>
> Cheers,
> --
> Szil�rd
>
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Re: [gmx-users] Box dimension size errors in MARTINI soft core simulation

[Justin Lemkul]

On 8/1/13 11:35 AM, Scott Pendley wrote:

Justin,

Much appreciation for the suggestions.  I found that the large time
constant (tau_p) on the pressure coupling was indeed a significant
contributor.  When I dropped that value down to 2.5, the box vectors scaled
down in a more reasonable manner maintaining the cubic simulation box.

With regard to your other questions:
Visualizing is possible but is more technical to do with MARTINI beads.  I
am still trying to figure out how to do this on vmd.

The prior npt run also used parrinello-rahman but with a tau-p of 2.0.
This may have contributed to some of the instability seen in this system so
I may switch it to berendsen per your suggestion.

I agree, isotropic coupling would be better for this system.



Good plan.  An initial relaxation with the weak coupling method usually leads to 
fairly robust simulations.



Some initial runs suggests that turning off the free energy portion does
allow the simulations to run to completion (for short simulations of 10 ns)
but I haven't analyzed them to determine if the sampling time is
insufficient to reveal developing instabilities.

Contrary to logic, at lambda = 0 this simulation instability also occurs.



There have been numerous fixes to the free energy code since 4.5.5 was released. 
 I would suggest using version 4.6.3.  If it still has issues, then it will 
receive significant attention as it would probably be a bug needing fixing.  I 
think I recall a similar problem being reported that was already fixed.



The LJ changes are composed on contributions from both solvent-solvent
interactions and solvent-solute.  I am seeing a ~ 3000 kj/mol different
that grows but plateaus out before the system crashes.  I would be hesitant
about ascribing the instability to this term as the decrease in LJ and
total energy would be expected at lamba=0.4 and the energy reached its
maximum prior to the system instability.



OK, if the same issue shows up in 4.6.3, let's explore it further.  That seems 
to be the most immediate solution.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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Re: [gmx-users] concatenating 2 xtc files

[Justin Lemkul]

On 8/1/13 11:44 AM, Kavyashree M wrote:

Sir,

Thank you for the suggestion.. I will make use of it in
future runs. but now the simulation is over.



But if something went wrong, then "over" is rather irrelevant, isn't it?


There was some overlap of few ns in 8core machine.
so while checking the rmsd plot there was a significant
difference in rmsd between 8 core and 64 core overlapped
region of simulation.



So your simulation started from some previous point and re-ran?  I don't see how 
this would be possible given what you have been posting.



1 more question is suppose I do not have checkpoint file
and if I need to continue from a stopped point (not extending)
does this command do the job?
$ tpbconv -s old.tpr -f traj.trr -e ener.edr -o new.tpr

Because when I tried with this there was a jump in the rmsd



That's why I asked before about checking the contents of the .tpr file.  You 
need to verify what it is exactly that you're doing and identify sources of 
potential problems.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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Re: [gmx-users] Intel vs gcc compilers

[Szilárd Páll]

Hi,

The Intel compilers are only recommended for pre-Bulldozer AMD
processors (K10: Magny-Cours, Intanbul, Barcelona, etc.). On these,
PME non-bonded kernels (not the RF or plain cut-off!) are 10-30%
slower with gcc than with icc. The icc-gcc difference is the smallest
with gcc 4.7, typically around 10-15% with Verlet scheme, AFAIR a bit
larger with the group scheme.

This is a performance issue in gcc specific to our non-bonded kernels
on AMD K10. On all other Intel and AMD architectures we tried, gcc
4.7/4.8 always matched or slightly outperformed icc 12 (13 is
typically slightly slower).
Note that other parts of the code (where gcc will do some AMD-specific
optimizations (while Intel won't) can/will be faster with gcc, e.g.
PME is typically faster. Therefore, the icc-gcc difference on AMD K10
will depend on factors like cut-off (PP/PME ratio) and cut-off scheme,
but typically icc will result in overall slightly (1-10%) faster
binaries.

Your processors are K10/Istanbul, so icc should be faster in your
case. To see the details of where the performance difference is, I
suggest you compare the performance stats table at the end of the log
file; tip: for easier comparison run a fixed number of steps and
compare the cycles columns (e.g. in a diff tool).

Cheers,
--
Szilárd


On Wed, Jun 26, 2013 at 9:30 AM, Djurre de Jong-Bruinink
 wrote:
>>You're using a real-MPI process per core, and you have six cores per
>
>
> I was using the current setup, which is indeed not fully optimized, just to 
> see how much the speed-up is between intel and gcc compiled.
>
>
>>processor. The recommended procedure is to map cores to OpenMP
>>threads, and choose the number of MPI processes per processor (and
>>thus the number of OpenMP threads per MPI process) to maximize
>>performance. See
>>http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Multi-level_parallelization.3a_MPI.2fthread-MPI_.2b_OpenMP
>
> I have optimized this before. In my experience one only gets a speedup from 
> using openMP at high parrellization (+/-200 particles per PP core) and if I 
> use #mpi = total number of cores AND 2 openMP threads per mpi process. The 
> total number of processes is then double the number of cores, so you are 
> effectively overloading/hyperthreading the cores (and thus the number of 
> particles per PP process is +/- 100). I have a similar experience on a newer, 
> intel based system, although there the advantage already starts at lower 
> parrallelization. I was wondering if openMP is always used in combination 
> with hyperthreading?

No, not necessarily/not only. While multi-threading should *in theory*
nearly always help, there are two caveats:
- There are parts of the code, mostly data/cache intensive like
integration or domain-decomposition which (unlike e.g. the PP force
calculation which is flop-intensive) don't scale that very well with
threads. Parallelization inefficiencies get amplified with many
threads both on AMD (due to its weaker cache performance wrt Intel) as
well as on Intel with HT (2x threads banding the same cache).
- OpenMP has an additional overhead which should be negligible in most
cases, but not always (e.g not .

At the same time, multi-threading has numerous advantages among them:

Therefore, when running without DD (a single process), using OpenMP
only is typically fastest on Intel with up to 12-24 threads (even
across sockets and with HT), and with 4-6 threads on AMD. However,
with DD using HT

>
> On the machine from my previous email, using openMP gives the warning:
>
> "Can not set thread affinities on the current platform. On NUMA systems this
> can cause performance degradation. If you think your platform should support
> setting affinities, contact the GROMACS developers."
>
>
> With the gcc compiled version the, using 72 cores\700 particles/PP core this 
> indeed leads a slightly lower performance. However using the intel compiled 
> version the simulations get orders of magnitude slower.
>
>
> Groetnis,
> Djurre
>
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Re: [gmx-users] Regarding g_order

[Justin Lemkul]

On 8/1/13 12:07 PM, Venkat Reddy wrote:

Dear Gmx-users,
In the GROMACS site, it has been mentioned that there is a bug (Instead of
numbering carbons from 2-17, the numbering starts from 1-16) in g_order
program up to, and including, v4.5.4. But when I am using v4.5.5, I am
getting the same sort of numbering. Is it normal or I should renumber from
2-17?



If you're getting a number starting with 1, it's probably wrong.  You can't 
calculated Scd for the first carbon in a chain because there is no n-1 carbon 
from which to determine the necessary vectors.  Someone (probably me) updated 
the wiki when version 4.5.4 was current, so probably any 4.5.x version is really 
affected, and 4.6.x may be as well, since this really is just a trivial bug that 
requires simple reinterpretation.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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Re: Re: Re: [gmx-users] GPU-based workstation

[Szilárd Páll]

I may be late with the reply, but here are my 2 cents.

If you need a single very fast machine (i.e. maximum single simulation
performance), you should get
- either a very fast desktop CPU: i7 3930 or for 2x more the 3970 -
which, BTW, I think is not worth it ($600-1000)
- or 1-2 fast Xeon E5-s - depending on how many and which these will
be $1k-2k each.

For a single CPU setup two Titans may be an overkill and (at least
with the current code) you may get very little extra performance from
using two iso one GPU. With a dual-socket machine (and decently fast
CPUs), if you have a large enough input system, two GPUs will work
nicely.

However, if you care about total simulation throughput and you have
multiple simulations to run, I'd suggest that you buy 2-3 machines
with the components that give the best ns/day/$: something like
i7-4670 or 4770 with GTX 680/770 (or 780).



--
Szilárd


On Thu, Jun 27, 2013 at 1:01 PM, James Starlight  wrote:
> Back to my question
> I want to build gpu-based workstation based onto 2 titans geforces.
>
> My current budget allow me only hight-end  6nodes core i 7-3930  and MB
> with 5 PCI-E (like Asus rampage IV series). Would this system be balanced
> with two GPUs ? Should I use two 6-8 nodes XEONS instead of i7?
>
> James
>
> 2013/5/29 James Starlight 
>
>> Dear Dr. Pall!
>>
>> Thank you for your suggestions!
>>
>> Asumming that I have budget of 5000 $ and I want to build gpu-based
>> desktop on this money.
>>
>> Previously I've used single 4 core i5 with GTX 670 and obtain average 10
>> ns\day performance for the 70k atoms systems (1.0 cutoffs, no virtual sites
>> , sd integrator).
>>
>> Now I'd like to build system based on 2 hight-end GeForces (e.g like
>> TITAN).
>> Should that system include 2 cpu's for good balancing? (e.g two 6 nodes
>> XEONS with faster clocks for instance could be better for simulations than
>> i7, couldnt it?)
>>
>> What addition properties to the MB should I consider for such system ?
>>
>> James
>>
>>
>> 2013/5/28 lloyd riggs 
>>
>>> Dear Dr. Pali,
>>>
>>> Thank you,
>>>
>>> Stephan Watkins
>>>
>>> *Gesendet:* Dienstag, 28. Mai 2013 um 19:50 Uhr
>>> *Von:* "Szilárd Páll" 
>>>
>>> *An:* "Discussion list for GROMACS users" 
>>> *Betreff:* Re: Re: [gmx-users] GPU-based workstation
>>> Dear all,
>>>
>>> As far as I understand, the OP is interested in hardware for *running*
>>> GROMACS 4.6 rather than developing code. or running LINPACK.
>>>
>>>
>>> To get best performance it is important to use a machine with hardware
>>> balanced for GROMACS' workloads. Too little GPU resources will result
>>> in CPU idling; too much GPU resources will lead to the runs being CPU
>>> or multi-GPU scaling bound and above a certain level GROMACS won't be
>>> able to make use of additional GPUs.
>>>
>>> Of course, the balance will depend both on hardware and simulation
>>> settings (mostly the LJ cut-off used).
>>>
>>> An additional factor to consider is typical system size. To reach near
>>> peak pair-force throughput on GPUs you typically need >20k-40k
>>> particles/GPU (depends on the architecture) and throughput drops below
>>> these values. Hence, in most cases it is preferred to use fewer and
>>> faster GPUs rather than more.
>>>
>>> Without knowing the budgdet and indented use of the machine it is hard
>>> to make suggestions, but I would say for a budget desktop box a
>>> quad-core Intel Ivy Bridge or the top-end AMD Piledriver CPU with a
>>> fast Kepler GTX card (e.g. GTX 680 or GTX 770/780) should work well.
>>> If you're considering dual-socket workstations, I suggest you go with
>>> the higher core-count and higher frequency Intel CPUs (6+ cores >2.2
>>> GHz), otherwise you may not see as much benefit as you would expect
>>> based on the insane price tag (especially if you compare to an i7
>>> 3939K or its IVB successor).
>>>
>>> Cheers,
>>> --
>>> Szilárd
>>>
>>>
>>> On Sat, May 25, 2013 at 1:02 PM, lloyd riggs  wrote:
>>> > More RAM the better, and the best I have seen is 4 GPU work station. I
>>> can
>>> > use/have used 4. The GPU takes 2 slots though, so a 7-8 PCIe board is
>>> > really 3-4 GPU, except the tyan mentioned (there designed as blades so
>>> an 8
>>> > or 10 slot board really holds 8 or 10 GPU's). There's cooling problems
>>> > though with GPU's, as on a board there packed, so extra cooling things
>>> may
>>> > help not blow a GPU, but I would look for good ones (ask around), as
>>> its a
>>> > video game market and they go for looks even though its in casing? The
>>> > external RAM (not onboard GPU RAM) helps if you do a larger sim, but I
>>> dont
>>> > know performance wise, the onboard GPU, the more RAM the marrier...so
>>> yes,
>>> > normal work stations you can get 4 GPU's for a 300 US$ board, but then
>>> the
>>> > price goes way up (3-4000 US$ for an 8-10 gpu board). RAM ordered
>>> abroad is
>>> > also cheep, 8 or 16 MB Vs. Shop...I have used 4 GPU's but only on tests
>>> > software, not Gromacs, so would be nice to see performance..

[gmx-users] Using Charmm 36 forcefield on Gromacs 4.6 or higher

[akk5r]

Hi All,

I am trying to run a membrane protein simulation on Gromacs 4.6 using the
Charmm 36 force field parameters. 

I found the following parameters on the gromacs mailing list for Charmm 36:
*; nblist cut-off 
rlist= 1.2 
; long-range cut-off for switched potentials 
rlistlong= 1.4 

; OPTIONS FOR ELECTROSTATICS AND VDW 
; Method for doing electrostatics 
coulombtype  = PME 
rcoulomb-switch  = 0 
rcoulomb = 1.2 
; Relative dielectric constant for the medium and the reaction field 
epsilon_r= 1 
epsilon_rf   = 1 
; Method for doing Van der Waals 
vdw-type = switch 
; cut-off lengths 
rvdw-switch  = 0.8 
rvdw = 1.2 
; Apply long range dispersion corrections for Energy and Pressure 
DispCorr = No *




Putting these setting into my .mdp file, I then get this error on grompp:

*ERROR 1 [file nvt.mdp]:
  With Verlet lists only cut-off LJ interactions are supported*

I then turned off the Verlet cut-off scheme and was able to create a .tpr
file. 

Then I ran my .tpr on mdrun and got the following error:

*Program mdrun, VERSION 4.6.1
Source code file: /home/akk5r/Downloads/gromacs-4.6.1/src/kernel/runner.c,
line: 824

Fatal error:
OpenMP threads have been requested with cut-off scheme Group, but these are
only supported with cut-off scheme Verlet
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors*

At this point, I don't know what to do. I have to run this job on a cluster
system due to the size of the system. Does any one know how to run Charmm 36
simulations on Gromacs 4.6 or higher using Verlet cut-off scheme?

Best Wishes,
Ali



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Re: [gmx-users] Using Charmm 36 forcefield on Gromacs 4.6 or higher

[francesco oteri]

Hi,
just try to disable OpenMP threads, unsetting OMP_NUM_THREADS environment
variable

Francesco


2013/8/1 akk5r 

> Hi All,
>
> I am trying to run a membrane protein simulation on Gromacs 4.6 using the
> Charmm 36 force field parameters.
>
> I found the following parameters on the gromacs mailing list for Charmm 36:
> *; nblist cut-off
> rlist= 1.2
> ; long-range cut-off for switched potentials
> rlistlong= 1.4
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype  = PME
> rcoulomb-switch  = 0
> rcoulomb = 1.2
> ; Relative dielectric constant for the medium and the reaction field
> epsilon_r= 1
> epsilon_rf   = 1
> ; Method for doing Van der Waals
> vdw-type = switch
> ; cut-off lengths
> rvdw-switch  = 0.8
> rvdw = 1.2
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr = No *
>
>
>
>
> Putting these setting into my .mdp file, I then get this error on grompp:
>
> *ERROR 1 [file nvt.mdp]:
>   With Verlet lists only cut-off LJ interactions are supported*
>
> I then turned off the Verlet cut-off scheme and was able to create a .tpr
> file.
>
> Then I ran my .tpr on mdrun and got the following error:
>
> *Program mdrun, VERSION 4.6.1
> Source code file: /home/akk5r/Downloads/gromacs-4.6.1/src/kernel/runner.c,
> line: 824
>
> Fatal error:
> OpenMP threads have been requested with cut-off scheme Group, but these are
> only supported with cut-off scheme Verlet
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors*
>
> At this point, I don't know what to do. I have to run this job on a cluster
> system due to the size of the system. Does any one know how to run Charmm
> 36
> simulations on Gromacs 4.6 or higher using Verlet cut-off scheme?
>
> Best Wishes,
> Ali
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/Using-Charmm-36-forcefield-on-Gromacs-4-6-or-higher-tp5010290.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Re: [gmx-users] Using Charmm 36 forcefield on Gromacs 4.6 or higher

[Justin Lemkul]

On 8/1/13 4:10 PM, akk5r wrote:

Hi All,

I am trying to run a membrane protein simulation on Gromacs 4.6 using the
Charmm 36 force field parameters.

I found the following parameters on the gromacs mailing list for Charmm 36:
*; nblist cut-off
rlist= 1.2
; long-range cut-off for switched potentials
rlistlong= 1.4

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = PME
rcoulomb-switch  = 0
rcoulomb = 1.2
; Relative dielectric constant for the medium and the reaction field
epsilon_r= 1
epsilon_rf   = 1
; Method for doing Van der Waals
vdw-type = switch
; cut-off lengths
rvdw-switch  = 0.8
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = No *




Putting these setting into my .mdp file, I then get this error on grompp:

*ERROR 1 [file nvt.mdp]:
   With Verlet lists only cut-off LJ interactions are supported*

I then turned off the Verlet cut-off scheme and was able to create a .tpr
file.

Then I ran my .tpr on mdrun and got the following error:

*Program mdrun, VERSION 4.6.1
Source code file: /home/akk5r/Downloads/gromacs-4.6.1/src/kernel/runner.c,
line: 824

Fatal error:
OpenMP threads have been requested with cut-off scheme Group, but these are
only supported with cut-off scheme Verlet
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors*

At this point, I don't know what to do. I have to run this job on a cluster
system due to the size of the system. Does any one know how to run Charmm 36
simulations on Gromacs 4.6 or higher using Verlet cut-off scheme?



The error messages are inconsistent.  Can you please post a full .mdp file and 
your exact mdrun command?


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] 1. Re: Interaction energy between specific residue in a set of residues (Justin Lemkul)

[Collins Nganou]

Dear Justin,

Thanks

I am simulating a DNA with different residues. I am looking the way to
extract only the energy of adjacent DT. I intend print out this energy
group via the energygrps = DT
I would like to have only DT in the index file. But it doesn't work.


This is the error encounter:

Fatal error:
Group DNA referenced in the .mdp file was not found in the index file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the '-n' option
of grompp.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


Best regards

 Collins
On Thu, Aug 1, 2013 at 1:16 AM,  wrote:

> Send gmx-users mailing list submissions to
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>
> Today's Topics:
>
>1. Re: Interaction energy between specific residue in a  set of
>   residues (Justin Lemkul)
>2. Re: inconsistent energy drops (Brad Van Oosten)
>3. Re: Expanded ensemble simulation died with fatal error:
>   Something wrong in choosing new lambda state with a Gibbs move
>   (Michael Shirts)
>4. fatal error with charmm/amber forcefield (Sanku M)
>5. Re: Re: inconsistent energy drops (Justin Lemkul)
>
>
> --
>
> Message: 1
> Date: Wed, 31 Jul 2013 16:27:52 -0400
> From: Justin Lemkul 
> Subject: Re: [gmx-users] Interaction energy between specific residue
> in aset of residues
> To: Discussion list for GROMACS users 
> Message-ID: <51f97348.1010...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 7/31/13 4:20 PM, Collins Nganou wrote:
> > Dear all,
> >
> > I am looking how  I can extract the interaction energy between  specific
> > residue in a set of  residues.
> >
>
> Nonbonded energy terms are decomposed using energygrps in the .mdp file
> along
> with suitable index groups.
>
> > example:
> >
> > I have DT and DA residues, I would like to plot only the energy of the
> DT.
> > I can extract the DT with the index file, But I am missing information on
> > how to plot the energy base on my index file where I can select only DT.
> >
>
> You can create index groups for any base or bases you want individually.
>  You
> haven't shown us what you've done, so it's hard to critique beyond that.
>
> > I was only looking the way to extract the c5-c6 distance of adjacent DT
> > without include DA.
> >
>
> Distances are calculated with g_dist and suitable index groups.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>
> ==
>
>
> --
>
> Message: 2
> Date: Wed, 31 Jul 2013 13:45:02 -0700 (PDT)
> From: Brad Van Oosten 
> Subject: [gmx-users] Re: inconsistent energy drops
> To: gmx-users@gromacs.org
> Message-ID: <1375303502523-5010267.p...@n6.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
> looking at the first 2 peaks, they are created from single outlying points
> in
> the trajectory. Visually, I can see no discernible difference between it
> and
> the frame before/after with the higher energy.
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/inconsistent-energy-drops-tp5010260p5010267.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>
>
> --
>
> Message: 3
> Date: Wed, 31 Jul 2013 17:17:04 -0400
> From: Michael Shirts 
> Subject: Re: [gmx-users] Expanded ensemble simulation died with fatal
> error:  Something wrong in choosing new lambda state with a Gibbs
> move
> To: Discussion list for GROMACS users 
> Message-ID:
>  g...@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Dejun-
>
> The basic problem is that for this particular configuration, the
> current state is the only state with nonzero weight. Note that the
> state with the second highest weight has weight 10^-7.  When it tries
> to compare weights in single precision, it has a numerical overflow
> and fails.
>
> A few things:
>
> 1. This really should be more robust, so that it will realize it's
> supposed to stay in the most likely state, since that's the only state

[gmx-users] Re: inconsistent energy drops

[Brad Van Oosten]

I used the mdrun -rerun option to recalculate the energies of the system and
it gave me nearly the same energy plot but without the random drops(see plot
below).  I am still unsure what is causing the jumps but i do not believe it
is from my system.  Since the energy is used in the calculation for the next
step, is there reason to worry about the validity of this run?

potential energy (black being the original potential and red being the
-rerun)
 
Zoomed in on first peaks:
 

Thanks, 
Brad



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Re: [gmx-users] 1. Re: Interaction energy between specific residue in a set of residues (Justin Lemkul)

[Justin Lemkul]

On 8/1/13 4:55 PM, Collins Nganou wrote:

Dear Justin,

Thanks

I am simulating a DNA with different residues. I am looking the way to
extract only the energy of adjacent DT. I intend print out this energy
group via the energygrps = DT
I would like to have only DT in the index file. But it doesn't work.


This is the error encounter:

Fatal error:
Group DNA referenced in the .mdp file was not found in the index file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the '-n' option
of grompp.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors



There are other groups required for proper functioning of your .mdp file.  As 
such, you cannot use an index file with only DT defined.  Just add the DT group 
as a new group into an index file that includes all other necessary groups.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] Re: inconsistent energy drops

[Justin Lemkul]

On 8/1/13 4:58 PM, Brad Van Oosten wrote:

I used the mdrun -rerun option to recalculate the energies of the system and
it gave me nearly the same energy plot but without the random drops(see plot
below).  I am still unsure what is causing the jumps but i do not believe it
is from my system.  Since the energy is used in the calculation for the next
step, is there reason to worry about the validity of this run?



Forces dictate the dynamics, not the energies.  This could be either a dynamics 
bug or an output bug.



potential energy (black being the original potential and red being the
-rerun)

Zoomed in on first peaks:




OK, that does look weird.  What Gromacs version is this?  What is in your .mdp 
file?

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] Re: inconsistent energy drops

[Brad Van Oosten]

This was done on v 4.6.1 

md50.mdp:


title= MD simulation
integrator   = md   ; MD integrator
tinit= 0
dt   = 0.002; 2 fs timestep
nsteps   = 5000 ; Number of steps
pbc  = xyz  ; Periodic boundary conditions 
in xyz
comm-mode= linear   
nstcomm  = 1
comm-grps= SOL_CL DMPC_CCCHX

; OUTPUT CONTROL OPTIONS
nstxout  = 0; Do not want .trr-files
nstxtcout= 1000 ; But do want .xtc-files
nstvout  = 0; No velocities in output
nstfout  = 0; No forces in output
nstlist  = 20   ; Update neighbor list between 
cut-offs
ns_type  = grid ; Fastest option
nstenergy= 1000 ; .edr-file output
energygrps   = DMPC_CCCHX SOL_CL; Energy groups

; OPTIONS FOR ELECTROSTATICS AND VDW
cutoff-scheme = Verlet
coulombtype  = pme  ; Particle mesh Ewald, do not 
change
rcoulomb = 1.4  ; Real-space cut-off

rlist= 1.0  ; Short-range neighbor list
rlistlong= 1.6  ; Long-range neighbor list 
rvdw = 1.4  
DispCorr = EnerPres ; Dispersion corrections to 
both the
potential and pressure
table-extension  = 1
fourierspacing   = 0.12 ; PME grid

; OPTIONS FOR WEAK COUPLING ALGORITHMS 
tcoupl   = nose-hoover  ; Thermostat, v-rescale is also 
fine
tc-grps  = DMPC_CCCHX SOL_CL; Couple lipids and SOL
seperatly
tau-t= 1.0 1.0  ; Time constant for temperature 
coupling
ref-t= 323 323  ; Desired temperature (K)
Pcoupl   = parrinello-rahman; Barostat
Pcoupltype   = semiisotropic; Pressure in xy and z couple
separately
ref-p= 1.013 1.013  ; Desired pressure (bar)
tau-p= 10.0 10.0; Time constant for pressure 
coupling
compressibility  = 4.5e-5 4.5e-5; Same as for water

; CONSTRAINTS
constraints  = all-bonds; Constrain all bonds
constraint-algorithm = Lincs; With Lincs



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Re: [gmx-users] Re: inconsistent energy drops

[Justin Lemkul]

On 8/1/13 5:08 PM, Brad Van Oosten wrote:

This was done on v 4.6.1



Does the same problem persist in 4.6.3?

-Justin


md50.mdp:


title= MD simulation
integrator   = md   ; MD integrator
tinit= 0
dt   = 0.002; 2 fs timestep
nsteps   = 5000 ; Number of steps
pbc  = xyz  ; Periodic boundary conditions 
in xyz
comm-mode= linear   
nstcomm  = 1
comm-grps= SOL_CL DMPC_CCCHX

; OUTPUT CONTROL OPTIONS
nstxout  = 0; Do not want .trr-files
nstxtcout= 1000 ; But do want .xtc-files
nstvout  = 0; No velocities in output
nstfout  = 0; No forces in output
nstlist  = 20   ; Update neighbor list between 
cut-offs
ns_type  = grid ; Fastest option
nstenergy= 1000 ; .edr-file output
energygrps   = DMPC_CCCHX SOL_CL; Energy groups

; OPTIONS FOR ELECTROSTATICS AND VDW
cutoff-scheme = Verlet
coulombtype  = pme  ; Particle mesh Ewald, do not 
change
rcoulomb = 1.4  ; Real-space cut-off

rlist= 1.0  ; Short-range neighbor list
rlistlong= 1.6  ; Long-range neighbor list
rvdw = 1.4  
DispCorr = EnerPres ; Dispersion corrections to 
both the
potential and pressure
table-extension  = 1
fourierspacing   = 0.12 ; PME grid

; OPTIONS FOR WEAK COUPLING ALGORITHMS
tcoupl   = nose-hoover  ; Thermostat, v-rescale is also 
fine
tc-grps  = DMPC_CCCHX SOL_CL; Couple lipids and SOL
seperatly
tau-t= 1.0 1.0  ; Time constant for temperature 
coupling
ref-t= 323 323  ; Desired temperature (K)
Pcoupl   = parrinello-rahman; Barostat
Pcoupltype   = semiisotropic; Pressure in xy and z couple
separately
ref-p= 1.013 1.013  ; Desired pressure (bar)
tau-p= 10.0 10.0; Time constant for pressure 
coupling
compressibility  = 4.5e-5 4.5e-5; Same as for water

; CONSTRAINTS
constraints  = all-bonds; Constrain all bonds
constraint-algorithm = Lincs; With Lincs



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--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] Re: inconsistent energy drops

[Brad Van Oosten]

To be honest, i have not updated that box to the newest version.  If it
appears to be a serious bug i could do it and rerun these sims to see if it
does persist.



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Re: [gmx-users] Re: inconsistent energy drops

[Justin Lemkul]

On 8/1/13 5:18 PM, Brad Van Oosten wrote:

To be honest, i have not updated that box to the newest version.  If it
appears to be a serious bug i could do it and rerun these sims to see if it
does persist.



I think it is worth doing.  If -rerun calculates sensible energies but the 
original simulation does not, there is something potentially wrong there, but 
troubleshooting an old version is not very productive.  Working with 4.6.3 is 
more worthwhile.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] g_potential and trjconv: problems with bilayer simulation analysis

[wood irene]

Hi all
I'm trying to calculate the electrostatic potential of POPC membrane
systems from a trajectory.
When I use g_potential, the calculation is well done but the results are
plotted from 0 to 7 nm of Z coordinates, with the bilayer center near to
3.5nm. Is possible, modifying the trajectory in order to obtain the results
centered in Z=0nm for my membrane simulation? Wich are the steps that I
need to follow?
I have tried using trjconv but I can not achieve any good solution, with
the system centered in bilayer core at z=0. I think that may be using a
combination of boxcenter/center, pbc and trans I could resolve it, but I'm
not familiar with the correct steps.
I will be very grateful with any advice,
Thanks in advance
*

Irene*
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Re: [gmx-users] g_potential and trjconv: problems with bilayer simulation analysis

[Justin Lemkul]

On 8/1/13 6:55 PM, wood irene wrote:

Hi all
I'm trying to calculate the electrostatic potential of POPC membrane
systems from a trajectory.
When I use g_potential, the calculation is well done but the results are
plotted from 0 to 7 nm of Z coordinates, with the bilayer center near to
3.5nm. Is possible, modifying the trajectory in order to obtain the results
centered in Z=0nm for my membrane simulation? Wich are the steps that I
need to follow?
I have tried using trjconv but I can not achieve any good solution, with
the system centered in bilayer core at z=0. I think that may be using a
combination of boxcenter/center, pbc and trans I could resolve it, but I'm
not familiar with the correct steps.


trjconv -center (centering on POPC) followed by trjconv -trans 0 0 -3.5 -pbc mol 
should get you pretty close, though if you're using pressure coupling, that 7-nm 
z-dimension is not fixed so you may need to tweak the translation distance.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] COM of a molecule

[Sikandar Mashayak]

Hi

I want to determine center of mass position of a molecule given an index of
any of the atoms of the molecule. One may be able to do this if given an
atom index one can access indices and hence the position of all other atoms
belonging to the same molecule. Is there a way to do this in a program
using gmx library?

Thanks
Sikandar
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[gmx-users] Trying to explain differences in behaviour between 2fs and 5fs timesteps

[Trayder]

Hi all,
I've been running an analysis of the same system (protein/ligand/water/ions)
using multiple timesteps (1-5fs) to identify differences in behaviour
between the settings. To do this I've compared the energy outputs of the 5
simulations, specifically the averages from g_energy and binning the
energies at each step from the log files.

What I've found is that 1/2/3fs simulations behave nigh identically, as do
4/5fs. However there is a notable difference between the two groups (graph
linked below). I've additionally matched timestep dependent variables
between simulations to rule out causes such as different coupling
frequencies, the difference was unaffected. 
The difference in the Total Energy seems to arise from the Coulomb (SR) and
LJ-SR terms. While the differences are in the order of 0.1% (~170kJ/mol) I
would rest easier being able to explain the sudden change in behaviour from
3-4fs.
Anyone have any ideas?

Thanks,
-Trayder

Binned total energies:
https://docs.google.com/file/d/0By3TeVcanmk8U0EwXzhNYk5JZUk/edit?usp=sharing

2fs mdp file:
integrator  =  md  ; simulation algorithm
tinit= 0
dt   = 0.002
nsteps  =  1000; # steps
;
;   Output Control
nstxout =  50; write coordinates to .trr
nstvout =  50; write velocities to .trr
nstlog  =  500 ; write energies to .log
nstenergy   =  500  ; write energies to .edr
nstxtcout   =  8000  ; write coordinates to .xtc
energygrps  =  Protein OLAT Water_and_Ions  ;
;
;   Neighbour Searching
nstlist =  10   ; update neighbour list
ns_type =  grid ; neighbour list method
pbc =  xyz  ; periodic boundary
conditions
rlist   =  0.9  ; cut-off for short-range
neighbour (nm)
cutoff-scheme   =  verlet
;
;   Electrostatics and VdW
coulombtype =  PME  ; type of coulomb
interaction
rcoulomb=  0.9  ; cut-off distance for
coulomb
epsilon_r   =  1; dielectric constant
rvdw=  0.9  ; cut-off for vdw
fourierspacing  =  0.12 ; maximum grid spacing for
FFT
pme_order   =  4; interpolation order for
PME
ewald_rtol  =  1e-5 ; relative strength of
Ewald-shifted
DispCorr=  EnerPres ; long range dispersion
corrections
;
;   Temperature Coupling
Tcoupl  =  v-rescale; type of temperature
coupling
tc-grps =  Protein non-Protein   ; coupled
groups
tau_t   =  .1 .1; T-coupling time constant
(ps)
ref_t   =  310 310  ; reference temperature (K)
;
;   Pressure Coupling
Pcoupl  =  parrinello-rahman; type of pressure
coupling
Pcoupltype  =  isotropic; pressure coupling geometry
tau_p   =  2.0 ; p-coupling time constant
(ps)
compressibility =  4.5e-5   ; compressibiity
ref_p   =  1.0  ; reference pressure (bar)
;
;   Velocity Generation
gen_vel =  no   ; generate initial
velocities
;
;   Bonds
constraints =  all-bonds; which bonds to contrain
constraint_algorithm= lincs ; algorithm to use
lincs_order =  4
lincs_iter =  2




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Re: [gmx-users] Potential Energy Scan

[tarak karmakar]

Thank you Mark.

So, if I got it properly, for my system (dihedral scanning), I need to
generate configurations, manually, and then perform this 'single point
energy calculations' for each of the configurations. If so, then better I
would opt for a script to do my job.

Regards,
Tarak


On Thu, Aug 1, 2013 at 5:07 PM, Mark Abraham wrote:

> http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
>
> On Thu, Aug 1, 2013 at 7:03 AM, tarak karmakar 
> wrote:
> > Dear All,
> >
> > Can anyone guide me how to perform the 'potential energy scan' for a
> > dihedral of a small molecule in gromacs?
> >
> > Regrads,
> > Tarak
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Re: [gmx-users] Regarding g_order

[Venkat Reddy]

Thanks Justin for the quick reply. I am simulating a protein with bound
lipids. I am in a dilemma to choose the direction of the normal to
calculate order parameter. In your *Membrane-protein *simulation tutorial,
you have chosen normal to the bilayer along the z-axis. But in my case,
there is no bilayer, infact, only few bound lipids are there. In which
direction I should choose the normal (*-d option*)?


On Thu, Aug 1, 2013 at 10:54 PM, Justin Lemkul  wrote:

>
>
> On 8/1/13 12:07 PM, Venkat Reddy wrote:
>
>> Dear Gmx-users,
>> In the GROMACS site, it has been mentioned that there is a bug (Instead of
>> numbering carbons from 2-17, the numbering starts from 1-16) in g_order
>> program up to, and including, v4.5.4. But when I am using v4.5.5, I am
>> getting the same sort of numbering. Is it normal or I should renumber from
>> 2-17?
>>
>>
> If you're getting a number starting with 1, it's probably wrong.  You
> can't calculated Scd for the first carbon in a chain because there is no
> n-1 carbon from which to determine the necessary vectors.  Someone
> (probably me) updated the wiki when version 4.5.4 was current, so probably
> any 4.5.x version is really affected, and 4.6.x may be as well, since this
> really is just a trivial bug that requires simple reinterpretation.
>
> -Justin
>
> --
> ==**
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul@outerbanks.umaryland.**edu  | 
> (410)
> 706-7441
>
> ==**
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
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[gmx-users] remd

[Shine A]

Sir,

 I did an 80 ns Remd simulation, after completion of the simulation
extended it up to 480 ns using tpbconv. Now the extended trajectories also
write on old trajectory files(traj.trr)?
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