date:20090924




nikhil damle wrote:

Hi all,

 I am facing the problem while calculating backbone RMSD over 30 ns. 
upto ~6-7 ns g_rms gives correct RMSDs and later all RMSD values are 
unexpectedly and unusually high (within 20 ps RMSD value shoots up by 
~8A). But when i calculate RMSD using g_confrms programme, it gives me 
expected and usual RMSD. I tried running g_rms separately for that 
particular time range which was giving me high values only to get same 
result once again. Is there problem with g_rms or i am calculating wrongly ?




Are you correcting the trajectory for periodicity?

-Justin


Regards,
Nikhil


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Re: [gmx-users] Re: Improper dihedrals, which way is correct?




Vitaly V. Chaban wrote:

Justin,

I think force field specific syntax is important for the utilities
like pdb2gmx or x2top but not for grompp which works with topol.top.
Here, I do not use any "standard" force field but define everything
myself from the very beginning. I believe this format (in topol.top)
should be FF-independent.

Am I not right?



You just have to be internally self-consistent.  You have to have some sort of 
[defaults] defined for whatever model you're making, so if your improper has 
type 2, then what you posted before should be fine.  If it is type 1 (like 
OPLS-AA), then impropers are defined like proper dihedrals, so the order will 
make a difference.


-Justin


Vitaly



I mention the syntax because the order of atoms is different between, e.g.,
Gromos and OPLS (as are the implementations of the forms of the dihedrals).

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


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[gmx-users] question about g_rdf

2009-09-24 Thread lammps lammps

Dear everyone,

I use the command (g_rdf -f traj.trr -s md.tpr -o rdf_12.xvg -sq sq_12.xvg
-b  1000 -bin 0.01 -cut 1.2 -grid 0.05 ) to calculate the RDF

There are two questions:

Question_1: Why should we do the three times selections[ the red line],

Reading file md.tpr, VERSION 4.0.4 (single precision)
Reading file md.tpr, VERSION 4.0.4 (single precision)

Select 1 group【the first time, what aim is this selection? 】
Opening library file /home/tianwd/soft/gromacs
4//share/gromacs/top/aminoacids.dat
Group 0 (  System) has  5240 elements
Group 1 ( SOL) has  5216 elements
Group 2 ( CL-) has12 elements
Group 3 ( NA+) has12 elements
Select a group: 3
Selected 3: 'NA+'
trn version: GMX_trn_file (single precision)

Reading frame1500 time 3000.000
Last frame   1500 time 3000.000
Reading file md.tpr, VERSION 4.0.4 (single precision)

Select a reference group and 1 group【the second time must select two groups
】
Opening library file
/home/tianwd/soft/gromacs4//share/gromacs/top/aminoacids.dat
Group 0 (  System) has  5240 elements
Group 1 ( SOL) has  5216 elements
Group 2 ( CL-) has12 elements
Group 3 ( NA+) has12 elements
Select a group: 1
Selected 1: 'SOL'
Select a group: 3
Selected 3: 'NA+'
Reading frame 600 time 1200.000


Q_2: What is the reasons for  the following error?


Select 1 group
Opening library file
/home/tianwd/soft/gromacs4//share/gromacs/top/aminoacids.dat
Group 0 (  System) has  5204 elements
Group 1 ( SOL) has  5168 elements
Group 2 ( CL-) has18 elements
Group 3 ( NA+) has18 elements
Select a group: 0
Selected 0: 'System'
Reading frame   0 time 1000.000
---
Program g_rdf, VERSION 4.0.4
Source code file: gmx_rdf.c, line: 639

Fatal error:

Error: atom (MW) not in list (5 types checked)!

---


Thanks in advance
-- 
wende
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[gmx-users] Trajectory files in vmd

2009-09-24 Thread Aditi Borkar

Dear All,

When I am loading the GROMACS trajectory in VMD, I cannot the
evolution of the protein structure with time.

When I am creating pdb files from the trajectory at different time
steps using the dump option, I do see changes in the protein structure
with time. My final structure after the MD simulation is also a lot
different that my start. However, when loading the trajectory, I do
not see a gradual/drastic transition from the starting to the final
conformation in VMD.

Please suggest where am I going wrong.

Thank you
-- 
Aditi Borkar,
Tata Institute of Fundamental Research,
Mumbai.
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[gmx-users] Consecutive Simulations

If I run a simulation using mdrun and then run mdrun again, does it add
another interval of simulation or does it just re-run the last simulation.
I'll elaborate so it makes a little more sense, our project has this
progress bar that tells users the progress of the simulation. If I run mdrun
for 100ps they will think it is stuck in an endless loop. If we run
increments of mdrun, we can update the bar at each increment. Can we go
straight to mdrun or do we have to prep the next increment with grompp?

-- 
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org
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Re: [gmx-users] viscovity with a help of g_energy




Vitaly V. Chaban wrote:

Justin,

It looks especially strange for me that all these files contain only
the columns of data
but not the resulting shear viscosity value.



True, g_energy usually prints out an average, but that's for quantities it has 
stored.  However, if you have shear viscosity as a function of time, then 
g_analyze will make quick work of the data files.


-Justin


Vitaly

On Tue, Sep 22, 2009 at 8:26 PM, Justin A. Lemkul  wrote:


Vitaly V. Chaban wrote:

Hi,

I which file should one look for the value of shear viscosity as using
"g_energy -vis" to calculate it?

A variety of output files are generated with this command.  Either visco.xvg
or evisco.xvg should have what you're looking for, according to the headers
of the .xvg files printed.

-Justin





--


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


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Re: [gmx-users] Trajectory files in vmd

2009-09-24 Thread Omer Markovitch

How do you run vmd?
The first argument should be a GRO or PDB file, and the second argument is
the TRR or XTC trajectory.
Alternatively, you can open a new molecule in vmd and than load data into
that molecule.
--Omer.

On Thu, Sep 24, 2009 at 08:21, Aditi Borkar  wrote:

> Dear All,
>
> When I am loading the GROMACS trajectory in VMD, I cannot the
> evolution of the protein structure with time.
>
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RE: [gmx-users] all-bonds

2009-09-24 Thread Enemark Soeren

 Thank you so much for your input, Mark!

 For some reason I was so focused on turning the constraints off for a
group that I couldn't see that I can just imitate the way grompp works
and turn on the constraints for the rest of the system. Aiaaah!

-Soren

-Original Message-
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham
Sent: Wednesday, September 23, 2009 3:51 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] all-bonds

Enemark Soeren wrote:
> Dear GMX-users,
> 
> Is it possible to exclude a group of atoms or molecules from having 
> their bonds converted to constraints when using the all-bonds
mdp-option?

Not automatically, but you can edit the topology manually to specify [ 
constraints ] instead of [ bonds ] for those bonds you wish to be 
constraints. See chapter 5 for detail.

Mark
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[gmx-users] Re: gmx-users Digest, Vol 65, Issue 83 6. EVB and mapping potentials (rsf)

2009-09-24 Thread Gerrit Groenhof

Hi,

I think that you could use the free energy parts of gromacs for your
purposes.

V1 and V2 can be coupled via a parameter lambda, such that (assuming
you're not changing masses/atoms)
H(p,r,lambda) = (1-lambda)* V(A-B + C) + lambda*V(A + B-C).

IN the manual it is described how to inform gromacs what V(A-B + C)  and
V(A + B-C) are.

For new bonds, angles etc, define them all, but let the forceconstants
and equilibrium constants be 0 in one state, like:

A-B 1 r_e k 0 0
B-C 1 0 0 r_e k


For driving it, you can perform the MD at discrete lambda values along
the 0,1 interval.

Hope this helps.

Best,

Gerrit

> Hi
>
> Thanks for you answer, what I want to do is to study a reaction with MD
>
> A-B +C -> A+B-C
>
> , for that I am representing it by a two state system in an EVB
> representation, where I have my transferring group, B, attached to A in
> the first state(V1) and to C in the second(V2). I am describing the
> off-diagonal elements as a constant parameter fitted form experimental
> data to reproduce the experimental free energy profile.
>
> To sample the space I would like to drive the reaction using a mapping
> potential of the form
>
> Vmap= V1 + lamda*(V2-V1), with lambda ranging from [0.0,1.0].
>
> Therefore I would have to get gromacs to run on the potential surface
> generated by the mapping potential, which is a mixture of my two diagonal
> states. I have been trying to see if gromacs can deal with this situation
> with the present implementation, but I can't seem to find what I need. I
> can also program it in myself, but I would like to know if someone has an
> idea of how to do it properly within the existing framework of gromacs, or
> if someone is aware of some way of getting the current version of gromacs
> to do what I need.
>
> The difference between both states would be some topology parameters
> (charges, bonds, angles, dihedrals) as well as connectivities that
> describe the chemically active part of the system.
>
> Thanks so much for your comments.
>
> Romelia
>   
>>>6. EVB and mapping potentials (rsf)
>>>
>>>   
>> Hi,
>>
>> I do not understand your question, but what you try to do seems
>> interesting.
>>
>> This is how far I got:
>>
>> If you have only two states to interconnect, the diagonal elements would
>> be the energy H(lamda=0) and H(lamda=1). The off diagonals then have to be
>> parametrized as a function of lambda? Would diagonalization then give you
>> the forces on lambda?
>>
>> We have a version of gromacs which supports lambda dynamics, but I am not
>> sure if that's what you need?
>>
>> Best,
>>
>> Gerrit
>>
>>
>> 
>>> Hi
>>>
>>> I want to describe a reaction for what I have a system described by two
>>> different connectivities and need to run an MD calculation on a mapping
>>> potential of the type V1- C (V2-V1), where V1 and V2 are my diagonal
>>> elements of the evb matrix and C is a parameter. Does gromacs have
>>> support
>>> for running something like this?. Which would be the best way to run
>>> this
>>> calculation with the standard code, or should I modify it in order to do
>>> that. The states have some atoms with different connectivity between
>>> them,
>>> different forcefield parameters and different charges, the atom types
>>> are
>>> the same for both.
>>>
>>>
>>> Thanks for your comments.
>>>
>>>
>>> Romelia.
>>>
>>> --
>>> 
>>> Romelia Salomon
>>> Miller Group
>>> 132 Noyes
>>> Chemistry Department
>>> Caltech
>>>
>>>
>>>
>>>
>>> --
>>>
>>> ___
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>>> posting!
>>>
>>> End of gmx-users Digest, Vol 65, Issue 81
>>> *
>>>
>>>   
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>
>
>   

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Re: [gmx-users] Trajectory files in vmd

2009-09-24 Thread Aditi Borkar

Thanx Omer.

I have already tried both ways suggested by you here. But they do not
seem to work.

On Thu, Sep 24, 2009 at 1:23 PM, Omer Markovitch  wrote:
> How do you run vmd?
> The first argument should be a GRO or PDB file, and the second argument is
> the TRR or XTC trajectory.
> Alternatively, you can open a new molecule in vmd and than load data into
> that molecule.
> --Omer.
>
> On Thu, Sep 24, 2009 at 08:21, Aditi Borkar  wrote:
>>
>> Dear All,
>>
>> When I am loading the GROMACS trajectory in VMD, I cannot the
>> evolution of the protein structure with time.
>
>
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-- 
Aditi Borkar,
Tata Institute of Fundamental Research,
Mumbai.
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[gmx-users] Re:FATAL error in GROMACS: z-size of t he box‏()

2009-09-24 Thread wuxiao


Dear Gustavo,

  Firstly, I suggest you put the question into this maillist to benefit all 
other users. Your problem is practically the same to mine posted previously. 
Generally, this can be due to the bad initial configuration. When I use long 
NVT MD then NPT MD, all works very well. So I advice you that you perform 500 
ps -1 ns  NVT MD before running NPT MD. Wish you succeed.

 

Sincerely,

Chaofu Wu, Dr.

 

>>Dear Chaofu Wu, I'm surfing in the GROMACS mail list and I've found you've 
>>got a similar error than me.I'm using GROMACS 4 and in my umbrella sampling 
>>calculations I get the following error:

Fatal error:
The Z-size of the box (7.373262) times the triclinic skew factor (1.00) is 
smaller than the number of DD cells (8) times the smallest allowed cell size 
(0.921775)

If you have any suggestions, please let me know.

Thank you in advance,

Gustavo
  
_
打工，挣钱，买房子，快来MClub一起”金屋藏娇”！
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Re: [gmx-users] nvt.gro

2009-09-24 Thread ram bio

Dear Justin,

As suggested in the tutorial by you i applied the lipid position restraints,
while running the NVT  equillibration, but after the job is finished, when i
observed the nvt.gro file in VMD, still there is a gap between the lipid
bilayers but this time the gap is not so large as it was in the earlier run
(as discussed earlier in previous email).

As I was already running the NPT equillibration(which I obtained after the
earlier NVT job, which ended in large gap between layers), i just wanted to
observe it and here there is no gap in between the layers i.e. in npt.gro.

Please suggest me what to do to lower the gap after NVT equillibration even
after applying the lipid restraints and is it ok for my NPT equillibration
as there are no gaps between the layers after this NPT equillibration.

Thanks

Ram

On Tue, Sep 22, 2009 at 8:25 PM, ram bio  wrote:

> Dear Justin,
>
> Thanks for the suggestion, will try to apply position restraints on lipid
> as mentioned in the advanced trouble shooting section.
>
> Ram
>
>
> On Tue, Sep 22, 2009 at 8:08 PM, Justin A. Lemkul  wrote:
>
>>
>>
>> ram bio wrote:
>>
>>> Dear Gromacs Users,
>>>
>>> I am following the justin tutorial on KALP-15 in lipid bilayer, I have a
>>> query regarding the nvt.gro that is after the NVT equillibration phase. The
>>> mdrun was proper without any warnings or errors, but when i visuallized the
>>> nvt.gro in VMD, i found that the peptide is intact in between the bilayers,
>>> but the the two layers got separated or else it is like the peptide bridging
>>> the the two halves of the lipid bilayer with gap in between the layers and
>>> also found few water molecules to the sides of the peptide or in the gap
>>> mentioned betwwn the layers.
>>>
>>> Please let me know is the simulation going on normally or there is an
>>> defect or wrong going on, as the nvt equillibration was proper as i think i
>>> continued for the next equillibration that is npt for 1ns.
>>>
>>>
>> You shouldn't continue blindly if you get weird results.  Please see the
>> "Advanced Troubleshooting" page (part of the tutorial!), because I
>> specifically address the issue of a bilayer separating:
>>
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/advanced_troubleshooting.html
>>
>> -Justin
>>
>>  Ram
>>>
>>>
>>> 
>>>
>>> ___
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>>
>> --
>> 
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> 
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>
>
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RE: [gmx-users] editconf and g_rmsdist

2009-09-24 Thread Enemark Soeren

Dear Tsjerk,
Thanks for your suggestion. I tried changing the box values, and it still give 
a deviation, so I have filed a bug report.

Best regards,
Soren





-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Tsjerk Wassenaar
Sent: Friday, September 18, 2009 7:21 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] editconf and g_rmsdist

Hi Soren,

>  Why I am seeing this difference? Is it due to round-off's after the
> transformation to center the molecule in the box? Or am I using g_rmsdist
> wrongly?

It's a bit weird indeed. You might be right that it's due to round-off
errors. You can try to copy the original gro file and replace the last
line with "   4.0   4.0   4.0" to set the box manually.
That should rule out whether it's the box, which I can hardly imagine.
The other test is to add a shift, but you'd want to make sure that
rounding could get an issue then...

Hope it helps,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] Consecutive Simulations




Jack Shultz wrote:
If I run a simulation using mdrun and then run mdrun again, does it add 
another interval of simulation or does it just re-run the last 
simulation. I'll elaborate so it makes a little more sense, our project 
has this progress bar that tells users the progress of the simulation. 
If I run mdrun for 100ps they will think it is stuck in an endless loop. 
If we run increments of mdrun, we can update the bar at each increment. 
Can we go straight to mdrun or do we have to prep the next increment 
with grompp?




You have to make use of checkpointing.  This page might be useful:

http://www.gromacs.org/Documentation/How-tos/Extending_Simulations

-Justin


--
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http://drugdiscoveryathome.com
http://hydrogenathome.org




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Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Tabulated potential - Problem

2009-09-24 Thread albita...@virgilio.it

Hi,

I'm trying to carry out a CG simulation and I'm using
a tabulated potential for a bond stretching term.
My MD simulations stops immediately with the error message:

---
Program mdrun_mpi, VERSION 4.0.5
Source code file: bondfree.c, line: 1772

Fatal error:
A tabulated bond interaction table number 0 is out of the table range: r 
23.678833, between table indices 12069 and 12070, table length 1020
---

This should mean that some distances are beyond table length (as reported in 
the manual) but this is
nonsense considering my input files and topology.

Do you have any suggestion?
Thanks!

AM

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Re: [gmx-users] nvt.gro

ram bio wrote:

Dear Justin,

As suggested in the tutorial by you i applied the lipid position
restraints, while running the NVT equillibration, but after the job is
finished, when i observed the nvt.gro file in VMD, still there is a gap
between the lipid bilayers but this time the gap is not so large as it
was in the earlier run (as discussed earlier in previous email).

As I was already running the NPT equillibration(which I obtained after
the earlier NVT job, which ended in large gap between layers), i just
wanted to observe it and here there is no gap in between the layers i.e.
in npt.gro.

Please suggest me what to do to lower the gap after NVT equillibration
even after applying the lipid restraints and is it ok for my NPT
equillibration as there are no gaps between the layers after this NPT
equillibration.

The gap arises because the lipids (when free to move) are attracted to the water
above and below the bilayer. If the protein is restrained, it doesn't move.
The box size in NVT is fixed, so the system is trying to fill it. It could be
that your box was inappropriately assigned (too large), but maybe not.

I am surprised that, even when using position restraints, the lipids still
separated at all. Did you use the lipid_posre.itp file that I provide on the
tutorial site? It has always worked well for me in such cases. You could also
try increasing the force constant in the z-dimension.

The other option is to do NPT simulated annealing, as I also suggest in the
troubleshooting page. Using NPT allows the box to deform in response to the
system, so you will probably get less weird behavior. I have found that both
NVT with PR and simulated annealing can get the job done.

-Justin

Thanks

Ram

On Tue, Sep 22, 2009 at 8:25 PM, ram bio > wrote:

Dear Justin,

Thanks for the suggestion, will try to apply position restraints on
lipid as mentioned in the advanced trouble shooting section.

Ram

On Tue, Sep 22, 2009 at 8:08 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote:

ram bio wrote:

Dear Gromacs Users,

I am following the justin tutorial on KALP-15 in lipid
bilayer, I have a query regarding the nvt.gro that is after
the NVT equillibration phase. The mdrun was proper without
any warnings or errors, but when i visuallized the nvt.gro
in VMD, i found that the peptide is intact in between the
bilayers, but the the two layers got separated or else it is
like the peptide bridging the the two halves of the lipid
bilayer with gap in between the layers and also found few
water molecules to the sides of the peptide or in the gap
mentioned betwwn the layers.

Please let me know is the simulation going on normally or
there is an defect or wrong going on, as the nvt
equillibration was proper as i think i continued for the
next equillibration that is npt for 1ns.

You shouldn't continue blindly if you get weird results. Please
see the "Advanced Troubleshooting" page (part of the tutorial!),
because I specifically address the issue of a bilayer separating:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/advanced_troubleshooting.html

-Justin

Ram

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

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Re: [gmx-users] nvt.gro

2009-09-24 Thread Pramod Akula

Dear Justin,

Thanks, will try the options described.

Ram

On Thu, Sep 24, 2009 at 4:16 PM, Justin A. Lemkul  wrote:

>
>
> ram bio wrote:
>
>> Dear Justin,
>>
>> As suggested in the tutorial by you i applied the lipid position
>> restraints, while running the NVT  equillibration, but after the job is
>> finished, when i observed the nvt.gro file in VMD, still there is a gap
>> between the lipid bilayers but this time the gap is not so large as it was
>> in the earlier run (as discussed earlier in previous email).
>>
>> As I was already running the NPT equillibration(which I obtained after the
>> earlier NVT job, which ended in large gap between layers), i just wanted to
>> observe it and here there is no gap in between the layers i.e. in npt.gro.
>>
>> Please suggest me what to do to lower the gap after NVT equillibration
>> even after applying the lipid restraints and is it ok for my NPT
>> equillibration as there are no gaps between the layers after this NPT
>> equillibration.
>>
>>
> The gap arises because the lipids (when free to move) are attracted to the
> water above and below the bilayer.  If the protein is restrained, it doesn't
> move. The box size in NVT is fixed, so the system is trying to fill it.  It
> could be that your box was inappropriately assigned (too large), but maybe
> not.
>
> I am surprised that, even when using position restraints, the lipids still
> separated at all.  Did you use the lipid_posre.itp file that I provide on
> the tutorial site?  It has always worked well for me in such cases.  You
> could also try increasing the force constant in the z-dimension.
>
> The other option is to do NPT simulated annealing, as I also suggest in the
> troubleshooting page.  Using NPT allows the box to deform in response to the
> system, so you will probably get less weird behavior.  I have found that
> both NVT with PR and simulated annealing can get the job done.
>
> -Justin
>
>  Thanks
>>
>> Ram
>>
>> On Tue, Sep 22, 2009 at 8:25 PM, ram bio > rmbio...@gmail.com>> wrote:
>>
>>Dear Justin,
>>
>>Thanks for the suggestion, will try to apply position restraints on
>>lipid as mentioned in the advanced trouble shooting section.
>>
>>Ram
>>
>>
>>On Tue, Sep 22, 2009 at 8:08 PM, Justin A. Lemkul >> wrote:
>>
>>
>>
>>ram bio wrote:
>>
>>Dear Gromacs Users,
>>
>>I am following the justin tutorial on KALP-15 in lipid
>>bilayer, I have a query regarding the nvt.gro that is after
>>the NVT equillibration phase. The mdrun was proper without
>>any warnings or errors, but when i visuallized the nvt.gro
>>in VMD, i found that the peptide is intact in between the
>>bilayers, but the the two layers got separated or else it is
>>like the peptide bridging the the two halves of the lipid
>>bilayer with gap in between the layers and also found few
>>water molecules to the sides of the peptide or in the gap
>>mentioned betwwn the layers.
>>
>>Please let me know is the simulation going on normally or
>>there is an defect or wrong going on, as the nvt
>>equillibration was proper as i think i continued for the
>>next equillibration that is npt for 1ns.
>>
>>
>>You shouldn't continue blindly if you get weird results.  Please
>>see the "Advanced Troubleshooting" page (part of the tutorial!),
>>because I specifically address the issue of a bilayer separating:
>>
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/advanced_troubleshooting.html
>>
>>-Justin
>>
>>Ram
>>
>>
>>
>>  
>>
>>___
>>gmx-users mailing listgmx-users@gromacs.org
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search
>>before posting!
>>Please don't post (un)subscribe requests to the list. Use
>>the www interface or send it to
>>gmx-users-requ...@gromacs.org
>>.
>>Can't post? Read
>> http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>--
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu  | (540) 231-9080
>>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>
>>___
>>gmx-users mailing listgmx-users@gromac

RE: [gmx-users] Tabulated potential - Problem

2009-09-24 Thread Berk Hess


This is not nonsense, it is exactly what is says.
The distance between two atoms is more than 10 times as large as your table 
length.

Maybe you are somehow having issues with periodic boundary conditions.
Is you box size close to 23?

Berk


Date: Thu, 24 Sep 2009 12:32:36 +0200
From: albita...@virgilio.it
To: gmx-users@gromacs.org
Subject: [gmx-users] Tabulated potential - Problem

Hi,

I'm trying to carry out a CG simulation and I'm using
a tabulated potential for a bond stretching term.
My MD simulations stops immediately with the error message:

---
Program mdrun_mpi, VERSION 4.0.5
Source code file: bondfree.c, line: 1772

Fatal error:
A tabulated bond interaction table number 0 is out of the table range: r 
23.678833, between table indices 12069 and 12070, table length 1020
---

This should mean that some distances are beyond table length (as reported in 
the manual) but this is
nonsense considering my input files and topology.

Do you have any suggestion?
Thanks!

AM

  
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[gmx-users] overlapping trajectories in multiple MD runs

2009-09-24 Thread Lizhe Zhu


Dear all,

I have run multiple runs of a system using the following command:

mdrun_mpi -deffnm md -multi 8 >& main.log

in which the md.tpr is obtained from grompp with md.mdp file containting 
the following parameters to get different initial velocities for each run:


###
gen_vel  = yes
gen_temp   = 300.0
gen_seed= 173529
###

But still out of these 8 parallel runs, there are always certain number 
of trajectories overlapping each other.


Anyone has a clue?

Many thanks in advance.

Lizhe

--
Lizhe Zhu

Van 't Hoff Institute for Molecular Sciences
University of Amsterdam
Nieuwe Achtergracht 166
1018 WV Amsterdam

room: B6.38
phone: (+31) 20 525 6541
l@uva.nl

http://molsim.chem.uva.nl/users/zhu/index.html

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Re: [gmx-users] overlapping trajectories in multiple MD runs




Lizhe Zhu wrote:

Dear all,

I have run multiple runs of a system using the following command:

mdrun_mpi -deffnm md -multi 8 >& main.log

in which the md.tpr is obtained from grompp with md.mdp file containting 
the following parameters to get different initial velocities for each run:


###
gen_vel  = yes
gen_temp   = 300.0
gen_seed= 173529
###

But still out of these 8 parallel runs, there are always certain number 
of trajectories overlapping each other.


Anyone has a clue?



If you are using the same .mdp file (the same gen_seed), then theoretically the 
trajectories should actually be identical.  Given the inherent chaos in MD and 
other optimization factors (like dynamic load balancing), you will probably see 
some divergence.


But if you want different initial velocities, use a different seed for each.

-Justin


Many thanks in advance.

Lizhe



--


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


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Re: [gmx-users] Trajectory files in vmd

2009-09-24 Thread J. Rui Rodrigues

Dear Aditi,

What do you mean with "evolution of the protein structure"? Are you referring to
*secondary structure*? By default, VMD only calculates it for the first 
trajectory frame.

--Rui


On Thu, 24 Sep 2009 10:51:04 +0530, Aditi Borkar wrote
> Dear All,
> 
> When I am loading the GROMACS trajectory in VMD, I cannot the
> evolution of the protein structure with time.
> 
> When I am creating pdb files from the trajectory at different time
> steps using the dump option, I do see changes in the protein structure
> with time. My final structure after the MD simulation is also a lot
> different that my start. However, when loading the trajectory, I do
> not see a gradual/drastic transition from the starting to the final
> conformation in VMD.
> 
> Please suggest where am I going wrong.
> 
> Thank you
> -- 
> Aditi Borkar,
> Tata Institute of Fundamental Research,
> Mumbai.
> ___
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--
Webmail ESTG de Leiria (http://webmail.estg.ipleiria.pt)

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[gmx-users] Adsorption and nucleation of proteins on surfaces

2009-09-24 Thread Agnese Zicari




Dear all I am mainly a scientist and I would like to complete my experimental 
data with some software simulation.
Can Gromacs or model the adsorption and the nucleation of proteins on surfaces 
or there is no technical feasibility for this Software on such a modeling?
 
 



  
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Re: [gmx-users] Adsorption and nucleation of proteins on surfaces




Agnese Zicari wrote:


Dear all I am mainly a scientist and I would like to complete my 
experimental data with some software simulation.
Can Gromacs or model the adsorption and the nucleation of proteins on 
surfaces or there is no technical feasibility for this Software on 
such a modeling?




Theoretically, anything *could* be done with a simulation.  However, it may be 
very difficult to derive appropriate parameters that are self-consistent with 
protein force fields.  This is not a trivial task for anyone, especially someone 
starting out in simulations.


Gromacs is well-suited to the task, but you have to consider whether or not it 
would be worth the time (it could take months) it would take to develop the 
appropriate force field parameters for your surfaces.


-Justin

 
 






Chiama da PC a PC e. taglia i costi delle chiamate! 






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--


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


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[gmx-users] Re: Re: help with gmx C source code

2009-09-24 Thread Inon Sharony



Hi Alex! (and everyone else)

I 

RE: HELP WITH GMX C SOURCE CODE

set the CFLAGS environment variable with

CFLAGS="-O0 -g3" 

and then installed, using 

./configure
make
make install

but it seems that I'm still doing something wrong, because when I do 

gdb mdrun 

there appear to still be no debugging symbols in the program:

(gdb) file mdrun
Reading symbols from /usr/bin/mdrun...(no debugging symbols found)...done.
(gdb) file mdrun_d
Reading symbols from /usr/bin/mdrun_d...(no debugging symbols found)...done. 

Do you have any idea what I might be doing wrong? 

Thanks for all the help,

-- 
Inon   Sharony
ינון שרוני
+972(3)6407634
atto.TAU.ac.IL/~inonshar
Please consider your environmental responsibility before printing this e-mail.___
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[gmx-users] trying to get better performance in a Rocks cluster running GROMACS 4.0.4

2009-09-24 Thread FLOR MARTINI

hi,

   We are about to start running GROMACS 4.0.4 with OpenMPI, in 8
nodes, quad core Rocks cluster. We made some tests, without PME and
found two notable things:

* We are getting the best speedup (6) with 2 nodes ( == 8 cores ). I read
the "Speeding Up Parallel GROMACS in High Latency networks" paper, and
thought that the culprit was the switch, but ifconfig shows no retransmits
(neither does ethtool -s or netstat -s). Does version 4 includes the
alltoall patch? Is the paper irrelevant with GROMACS 4?

* When running with the whole cluster ( 8 nodes, 32 cores ), top reports
in any node a 50% system CPU usage. Is that normal? Can it be accounted to
the use of the network? The sys usage gets a bit up when we configured the
Intel NICs with Interrupt Coalescense Off, so I'm tempted to think it is
just OpenMPI hammering the tcp stack, polling for packages.

Thanks in advance,

Dra.M.Florencia Martini

Laboratorio de Fisicoquímica de Membranas Lipídicas y Liposomas

Cátedra de Química General e Inorgánica

Facultad de Farmacia y Bioquímica

Universidad de Buenos Aires

Junín 956 2º (1113)

TE: 54 011 4964-8249 int 24


  Yahoo! Cocina

Encontra las mejores recetas con Yahoo! Cocina.


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RE: [gmx-users] Re: Re: help with gmx C source code

2009-09-24 Thread Berk Hess

You should put the cflags on the configure command line, I use:
configure --enable-debug CFLAGS="-O0 -msse2 -g"

Berk

Date: Thu, 24 Sep 2009 16:51:45 +0300
From: inons...@tau.ac.il
To: gmx-users@gromacs.org
Subject: [gmx-users] Re: Re: help with gmx C source code

Hi Alex! (and everyone else)

I

Re: help with gmx C source code

set the CFLAGS environment variable with

CFLAGS="-O0 -g3"

and then installed, using

./configure

make

make install

but it seems that I'm still doing something wrong, because when I do

gdb mdrun

there appear to still be no debugging symbols in the program:

(gdb) file mdrun

Reading symbols from /usr/bin/mdrun...(no debugging symbols 
found)...done.

(gdb) file mdrun_d

Reading symbols from /usr/bin/mdrun_d...(no debugging symbols 
found)...done.

Do you have any idea what I might be doing wrong?

Thanks for all the help,

--

Inon   Sharony

ינון שרוני

+972(3)6407634

atto.TAU.ac.IL/~inonshar

Please consider your environmental responsibility before printing 
this e-mail.

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RE: [gmx-users] trying to get better performance in a Rocks cluster running GROMACS 4.0.4

2009-09-24 Thread Berk Hess


Hi,

You don't mention what kind of benchmark system tou are using for these tests.
A too small system could explain these results.

Berk


Date: Thu, 24 Sep 2009 07:01:04 -0700
From: flormart...@yahoo.com.ar
To: gmx-users@gromacs.org
Subject: [gmx-users] trying to get better performance in a Rocks cluster
running GROMACS 4.0.4

hi,

   We are about to start running GROMACS 4.0.4 with OpenMPI, in 8
nodes, quad core Rocks cluster. We made some tests, without PME and
found two notable things:

* We are getting the best speedup (6) with 2 nodes ( == 8 cores ). I read
the "Speeding Up Parallel GROMACS in High Latency networks" paper, and
thought that the culprit was the switch, but ifconfig shows no retransmits
(neither does ethtool -s or netstat -s). Does version 4 includes the
alltoall patch? Is the paper irrelevant with GROMACS 4?

* When running with the whole cluster ( 8 nodes, 32 cores ), top reports
in any node a 50% system CPU usage. Is that normal? Can it be accounted to
the use of the network? The sys usage gets a bit up when we configured the
Intel NICs with Interrupt Coalescense Off, so I'm tempted to think it
 is
just OpenMPI hammering the tcp stack, polling for packages.

Thanks in advance,

Dra.M.Florencia Martini

Laboratorio de Fisicoquímica de Membranas Lipídicas y Liposomas

Cátedra de Química General e Inorgánica

Facultad de Farmacia y Bioquímica

Universidad de Buenos Aires

Junín 956 2º (1113)

TE: 54 011 4964-8249 int 24




  
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Re: [gmx-users] Consecutive Simulations

Thanks Justin, you are very helpful as always :-)

On Thu, Sep 24, 2009 at 6:41 AM, Justin A. Lemkul  wrote:

>
>
> Jack Shultz wrote:
>
>> If I run a simulation using mdrun and then run mdrun again, does it add
>> another interval of simulation or does it just re-run the last simulation.
>> I'll elaborate so it makes a little more sense, our project has this
>> progress bar that tells users the progress of the simulation. If I run mdrun
>> for 100ps they will think it is stuck in an endless loop. If we run
>> increments of mdrun, we can update the bar at each increment. Can we go
>> straight to mdrun or do we have to prep the next increment with grompp?
>>
>>
> You have to make use of checkpointing.  This page might be useful:
>
> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
>
> -Justin
>
>  --
>> Jack
>>
>> http://drugdiscoveryathome.com
>> http://hydrogenathome.org
>>
>>
>> 
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
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>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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-- 
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org
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RE: [gmx-users] trying to get better performance in a Rocks cluster running GROMACS 4.0.4

2009-09-24 Thread FLOR MARTINI

Thanks for your question.
We are running a lipid bilayer of 128 DPPC and 3655 water molecules and the 
nstep of the mdp is a total for 10 ns. I don´t think really that our system is 
a small one...

Dra.M.Florencia Martini

Laboratorio de Fisicoquímica de Membranas Lipídicas y Liposomas

Cátedra de Química General e Inorgánica

Facultad de Farmacia y Bioquímica

Universidad de Buenos Aires

Junín 956 2º (1113)

TE: 54 011 4964-8249 int 24

--- El jue 24-sep-09, Berk Hess  escribió:

De: Berk Hess 
Asunto: RE: [gmx-users] trying to get better performance in a Rocks cluster 
running GROMACS 4.0.4
Para: "Discussion list for GROMACS users" 
Fecha: jueves, 24 de septiembre de 2009, 11:22 am




Hi,

You don't mention what kind of benchmark system tou are using for these tests.
A too small system could explain these results.

Berk


Date: Thu, 24 Sep 2009 07:01:04 -0700
From: flormart...@yahoo.com.ar
To: gmx-users@gromacs.org
Subject: [gmx-users] trying to get better performance in a Rocks cluster
running GROMACS 4.0.4

hi,

   We are about to start running GROMACS 4.0.4 with OpenMPI, in 8
nodes, quad core Rocks cluster. We made some tests, without PME and
found two notable things:

* We are getting the best speedup (6) with 2 nodes ( == 8 cores ). I read
the "Speeding Up Parallel GROMACS in High Latency networks" paper, and
thought that the culprit was the switch, but ifconfig shows no retransmits
(neither does ethtool -s or netstat -s). Does version 4 includes the
alltoall patch? Is the paper irrelevant with GROMACS 4?

* When running with the whole cluster ( 8 nodes, 32 cores ), top reports
in any node a 50% system CPU usage. Is that normal? Can it be accounted to
the use of the network? The sys usage gets a bit up when we configured the
Intel NICs with Interrupt Coalescense Off, so I'm tempted to think it
 is
just OpenMPI hammering the tcp stack, polling for packages.

Thanks in advance,

Dra.M.Florencia Martini

Laboratorio de Fisicoquímica de Membranas Lipídicas y Liposomas

Cátedra de Química General e Inorgánica

Facultad de Farmacia y Bioquímica

Universidad de Buenos Aires

Junín 956 2º (1113)

TE: 54 011 4964-8249 int 24




  
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Re: [gmx-users] Re: Re: help with gmx C source code


Inon Sharony wrote:



Hi Alex! (and everyone else)


I


  Re: help with gmx C source code

set the CFLAGS environment variable with

CFLAGS="-O0 -g3"


No, that probably doesn't set an environment variable. Read up on how 
your shell does this. Either set it properly, or follow Berk's 
suggestion of putting such a command on the configure line.


Mark


and then installed, using

./configure
make
make install

but it seems that I'm still doing something wrong, because when I do

gdb mdrun

there appear to still be no debugging symbols in the program:

(gdb) file mdrun
Reading symbols from /usr/bin/mdrun...(no debugging symbols found)...done.
(gdb) file mdrun_d
Reading symbols from /usr/bin/mdrun_d...(no debugging symbols 
found)...done.



Do you have any idea what I might be doing wrong?

Thanks for all the help,

--
Inon   Sharony
ינון שרוני
+972(3)6407634
atto.TAU.ac.IL/~inonshar
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[gmx-users] dummy atoms in planar square Pt

2009-09-24 Thread Rebeca García Fandiño


Hi,

I am trying to simulate an organic system which has a planar-square Pt center. 
I am following the methodology employed in JACS 2008, 10040 (where they use 
amber calculations). There, they use 2 dummy atoms to mantain the planar square 
geometry of the metal. 

I have built my system with no dummy atoms, using GAFF and converted it into 
Gromacs, so now I have a .gro and a .top file.

I have introduced then the dummy atoms, in the .gro and in the topology file, 
but I get errors complaining about these extra atoms has mass 0. 

I have read the manual and also looked at the GMX list, and I have found that 
other people have also found problems of these type. I have read that in case 
such as acetonitrile the advice was to redistribute the mass over N and CH3 
such that centre of mass is unchanged and inertia tensor is not modified too 
much either.

Should I do something similar in my case? Which mass should I redistribute? The 
mass of the whole molecule? 

 

Thank you very much for your help.

 

Best wishes,

 

Dr. Rebeca Garcia

Universidad de A Coruña

Spain
  
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[gmx-users] timestep fraction complete

I figured out another way to update the progress of my simulation, but I
need to report the fraction of completion at the certain intervals of mdrun.
Possibly at every time step or if that does not make sense every 100
timesteps. I don't think this is a feature currently supported, so I will
have to make some source code chages. I am looking for the variables related
to total number of time steps and where it controls the the current time
step so I can calculate the fraction of complete where current-timestep /
total-timestep

-- 
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org
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[gmx-users] BUG in GROMACS 4.0.5, related to very log total integration time

2009-09-24 Thread Daniel Adriano Silva M

Dear GROMACS users and developers.

I don known if this issued had been previously addressed, but I found
that when I try to run a MD with time-step of 2fs and 25 steps
(yes 500us!!!) the dynamics aborts with the next message (64bit-LINUX
and icc 10 compiler):


WARNING: This run will generate roughly 20576946697451257856 Mb of data

starting mdrun 'F1-ATPASE'
-1794967296 steps, -3589934.8 ps.

nodetime = 0! Infinite Giga flopses!
Parallel run - timing based on wallclock.

#

If i reduce the steps number by one order of magnitude then all goes
ok.  My MDP when I obtined this error was:


; VARIOUS PREPROCESSING OPTIONS
title= NPT simulacion
cpp  = /lib/cpp

; RUN CONTROL PARAMETERS
integrator   = md
dt   = 0.002
nsteps   = 25
nstxout  = 5000
nstvout  = 5000
nstlog   = 2500
nstenergy= 2500
nstxtcout= 2500
energygrps   = Protein Non-Protein
nstlist = 10
rlist   = 1.0
ns_type = grid
pbc = xyz
coulombtype  = pme
rcoulomb = 1.0
vdw-type = Cut-off
rvdw = 1.0
fourierspacing   =  0.12
pme_order=  4
optimize_fft =  yes
ewald_rtol   =  1e-5
tcoupl   = Berendsen
tc-grps  = Protein  Non-Protein
tau_t= 0.1  0.1
ref_t= 300  300
Pcoupl   = Parrinello-Rahman
Pcoupltype   = Isotropic
tau_p= 1.0
ref_p= 1.0
compressibility  = 4.5e-5
gen_vel  = no
constraints  = all-bonds
constraint-algorithm = Lincs
unconstrained-start  = yes
lincs-order  = 4
lincs-iter   = 1
lincs-warnangle  = 30

I known this kind of error is not a priority since the total
integration time is ridiculous big, but anyway I want to comment it to
you.
Thanks

Daniel Silva
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Re: [gmx-users] BUG in GROMACS 4.0.5, related to very log total integration time


Daniel Adriano Silva M wrote:

Dear GROMACS users and developers.

I don known if this issued had been previously addressed, but I found
that when I try to run a MD with time-step of 2fs and 25 steps
(yes 500us!!!) the dynamics aborts with the next message (64bit-LINUX
and icc 10 compiler):


WARNING: This run will generate roughly 20576946697451257856 Mb of data

starting mdrun 'F1-ATPASE'
-1794967296 steps, -3589934.8 ps.

nodetime = 0! Infinite Giga flopses!
Parallel run - timing based on wallclock.

#

If i reduce the steps number by one order of magnitude then all goes
ok.  My MDP when I obtined this error was:


; VARIOUS PREPROCESSING OPTIONS
title= NPT simulacion
cpp  = /lib/cpp

; RUN CONTROL PARAMETERS
integrator   = md
dt   = 0.002
nsteps   = 25
nstxout  = 5000
nstvout  = 5000
nstlog   = 2500
nstenergy= 2500
nstxtcout= 2500
energygrps   = Protein Non-Protein
nstlist = 10
rlist   = 1.0
ns_type = grid
pbc = xyz
coulombtype  = pme
rcoulomb = 1.0
vdw-type = Cut-off
rvdw = 1.0
fourierspacing   =  0.12
pme_order=  4
optimize_fft =  yes
ewald_rtol   =  1e-5
tcoupl   = Berendsen
tc-grps  = Protein  Non-Protein
tau_t= 0.1  0.1
ref_t= 300  300
Pcoupl   = Parrinello-Rahman
Pcoupltype   = Isotropic
tau_p= 1.0
ref_p= 1.0
compressibility  = 4.5e-5
gen_vel  = no
constraints  = all-bonds
constraint-algorithm = Lincs
unconstrained-start  = yes
lincs-order  = 4
lincs-iter   = 1
lincs-warnangle  = 30

I known this kind of error is not a priority since the total
integration time is ridiculous big, but anyway I want to comment it to
you.


Yes, it's known. IIRC there was some discussion on the developers list 
about changing the relevant data type so that it can store bigger 
numbers. It's also a non-problem inasmuch as if you are ever able to run 
a simulation that long, manually resetting the number of steps to zero 
at a suitable point will be workable.


Mark
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Re: [gmx-users] timestep fraction complete


Jack Shultz wrote:
I figured out another way to update the progress of my simulation, but I 
need to report the fraction of completion at the certain intervals of 
mdrun. Possibly at every time step or if that does not make sense every 
100 timesteps. I don't think this is a feature currently supported, so I 
will have to make some source code chages. I am looking for the 
variables related to total number of time steps and where it controls 
the the current time step so I can calculate the fraction of complete 
where current-timestep / total-timestep


Under at least some circumstances GROMACS writes the expected runtime 
remaining to stderr, but I don't recall what/when. Piping that to some 
useful script has to be a good start. You certainly don't need this data 
every time step, and don't want to be perturbing mdrun to get it.


Even if the above was unsuitable, surely progress would only need to be 
moderately accurate and for simulations that last many hours. If so, 
you'll get good enough data by grepping a gmxdump of the .tpr to get the 
expected frequencies of output and length of run, and then watching the 
growth of whichever of .log/.trr/.edr is written most frequently. I/O 
buffering will affect the numbers somewhat.


Mark

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Re: [gmx-users] BUG in GROMACS 4.0.5, related to very log total integration time

2009-09-24 Thread Daniel Adriano Silva M

Mark,

Your are right. Thanks

Daniel

2009/9/24 Mark Abraham :
> Daniel Adriano Silva M wrote:
>>
>> Dear GROMACS users and developers.
>>
>> I don known if this issued had been previously addressed, but I found
>> that when I try to run a MD with time-step of 2fs and 25 steps
>> (yes 500us!!!) the dynamics aborts with the next message (64bit-LINUX
>> and icc 10 compiler):
>>
>> 
>> WARNING: This run will generate roughly 20576946697451257856 Mb of data
>>
>> starting mdrun 'F1-ATPASE'
>> -1794967296 steps, -3589934.8 ps.
>>
>> nodetime = 0! Infinite Giga flopses!
>>        Parallel run - timing based on wallclock.
>>
>> #
>>
>> If i reduce the steps number by one order of magnitude then all goes
>> ok.  My MDP when I obtined this error was:
>>
>>
>> ; VARIOUS PREPROCESSING OPTIONS
>> title                    = NPT simulacion
>> cpp                      = /lib/cpp
>>
>> ; RUN CONTROL PARAMETERS
>> integrator               = md
>> dt                       = 0.002
>> nsteps                   = 25
>> nstxout                  = 5000
>> nstvout                  = 5000
>> nstlog                   = 2500
>> nstenergy                = 2500
>> nstxtcout                = 2500
>> energygrps               = Protein Non-Protein
>> nstlist         = 10
>> rlist           = 1.0
>> ns_type         = grid
>> pbc             = xyz
>> coulombtype              = pme
>> rcoulomb                 = 1.0
>> vdw-type                 = Cut-off
>> rvdw                     = 1.0
>> fourierspacing       =  0.12
>> pme_order            =  4
>> optimize_fft         =  yes
>> ewald_rtol           =  1e-5
>> tcoupl                   = Berendsen
>> tc-grps                  = Protein  Non-Protein
>> tau_t                    = 0.1      0.1
>> ref_t                    = 300      300
>> Pcoupl                   = Parrinello-Rahman
>> Pcoupltype               = Isotropic
>> tau_p                    = 1.0
>> ref_p                    = 1.0
>> compressibility          = 4.5e-5
>> gen_vel                  = no
>> constraints              = all-bonds
>> constraint-algorithm     = Lincs
>> unconstrained-start      = yes
>> lincs-order              = 4
>> lincs-iter               = 1
>> lincs-warnangle          = 30
>>
>> I known this kind of error is not a priority since the total
>> integration time is ridiculous big, but anyway I want to comment it to
>> you.
>
> Yes, it's known. IIRC there was some discussion on the developers list about
> changing the relevant data type so that it can store bigger numbers. It's
> also a non-problem inasmuch as if you are ever able to run a simulation that
> long, manually resetting the number of steps to zero at a suitable point
> will be workable.
>
> Mark
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Re: [gmx-users] timestep fraction complete

I am hoping for an update every 10 minutes just to satisfy the anxieties of
volunteers crunching on my project, but every hour may be satisfactory. And
if I can do this without requiring any shell scripts it would be better in
my environment. So I started making some code modifications which apparently
did not work

src/mdlib/sim_util.c:93:void print_time(FILE *out,time_t start,int
step,t_inputrec *ir)
src/mdlib/sim_util.c-94-{
src/mdlib/sim_util.c-95-  static real time_per_step;
src/mdlib/sim_util.c-96-  static time_t end;
src/mdlib/sim_util.c-97-  time_t finish;
src/mdlib/sim_util.c-98-  double dt, fc;
src/mdlib/sim_util.c-99-  char buf[48];
src/mdlib/sim_util.c-100-  FILE *progress="progress.txt";
src/mdlib/sim_util.c-101-
src/mdlib/sim_util.c-102-  if (!gmx_parallel_env)
src/mdlib/sim_util.c-103-fprintf(out,"\r");
src/mdlib/sim_util.c-104-  fprintf(out,"step %d",step);
src/mdlib/sim_util.c-105-  if ((step >= ir->nstlist)) {
src/mdlib/sim_util.c-106-if ((ir->nstlist == 0) || ((step % ir->nstlist)
== 0)) {
src/mdlib/sim_util.c-107-  /* We have done a full cycle let's update
time_per_step */
src/mdlib/sim_util.c-108-  end=time(NULL);
src/mdlib/sim_util.c-109-  dt=difftime(end,start);
src/mdlib/sim_util.c-110-  time_per_step=dt/(step - ir->init_step + 1);
src/mdlib/sim_util.c-111-}
src/mdlib/sim_util.c-112-dt=(ir->nsteps + ir->init_step -
step)*time_per_step;
src/mdlib/sim_util.c-113-
src/mdlib/sim_util.c-114-if (dt >= 300) {
src/mdlib/sim_util.c-115-  finish = end+(time_t)dt;
src/mdlib/sim_util.c-116-  sprintf(buf,"%s",ctime(&finish));
src/mdlib/sim_util.c-117-  buf[strlen(buf)-1]='\0';
src/mdlib/sim_util.c-118-  fprintf(out,", will finish %s",buf);
src/mdlib/sim_util.c-119-}
src/mdlib/sim_util.c-120-else
src/mdlib/sim_util.c-121-  fprintf(out,", remaining runtime: %5d
s  ",(int)dt);
src/mdlib/sim_util.c-122-  fc = (int)dt / ir->nstlist;
src/mdlib/sim_util.c-123-  fprintf(stderr, "Fraction complete: %d \n",
fc);
src/mdlib/sim_util.c-124-  }
src/mdlib/sim_util.c-125-  if (gmx_parallel_env)
src/mdlib/sim_util.c-126-fprintf(out,"\n");
src/mdlib/sim_util.c-127-
src/mdlib/sim_util.c-128-  fflush(out);
src/mdlib/sim_util.c-129-}

Back Off! I just backed up md.edr to ./#md.edr.4#
starting mdrun 'Protein in water'
500 steps,  1.0 ps.
step 100, remaining runtime:   122 s  Fraction complete: 0
step 200, remaining runtime:92 s  Fraction complete: 0


On Thu, Sep 24, 2009 at 6:34 PM, Mark Abraham wrote:

> Jack Shultz wrote:
>
>> I figured out another way to update the progress of my simulation, but I
>> need to report the fraction of completion at the certain intervals of mdrun.
>> Possibly at every time step or if that does not make sense every 100
>> timesteps. I don't think this is a feature currently supported, so I will
>> have to make some source code chages. I am looking for the variables related
>> to total number of time steps and where it controls the the current time
>> step so I can calculate the fraction of complete where current-timestep /
>> total-timestep
>>
>
> Under at least some circumstances GROMACS writes the expected runtime
> remaining to stderr, but I don't recall what/when. Piping that to some
> useful script has to be a good start. You certainly don't need this data
> every time step, and don't want to be perturbing mdrun to get it.
>
> Even if the above was unsuitable, surely progress would only need to be
> moderately accurate and for simulations that last many hours. If so, you'll
> get good enough data by grepping a gmxdump of the .tpr to get the expected
> frequencies of output and length of run, and then watching the growth of
> whichever of .log/.trr/.edr is written most frequently. I/O buffering will
> affect the numbers somewhat.
>
> Mark
>
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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>



-- 
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org
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Re: [gmx-users] timestep fraction complete

Ah of course!
 fc = (int)dt / ir->nstlist;
I should cast these as data types that support decimals right?

On Thu, Sep 24, 2009 at 6:44 PM, Jack Shultz 
wrote:

> I am hoping for an update every 10 minutes just to satisfy the anxieties of
> volunteers crunching on my project, but every hour may be satisfactory. And
> if I can do this without requiring any shell scripts it would be better in
> my environment. So I started making some code modifications which apparently
> did not work
>
> src/mdlib/sim_util.c:93:void print_time(FILE *out,time_t start,int
> step,t_inputrec *ir)
> src/mdlib/sim_util.c-94-{
> src/mdlib/sim_util.c-95-  static real time_per_step;
> src/mdlib/sim_util.c-96-  static time_t end;
> src/mdlib/sim_util.c-97-  time_t finish;
> src/mdlib/sim_util.c-98-  double dt, fc;
> src/mdlib/sim_util.c-99-  char buf[48];
> src/mdlib/sim_util.c-100-  FILE *progress="progress.txt";
> src/mdlib/sim_util.c-101-
> src/mdlib/sim_util.c-102-  if (!gmx_parallel_env)
> src/mdlib/sim_util.c-103-fprintf(out,"\r");
> src/mdlib/sim_util.c-104-  fprintf(out,"step %d",step);
> src/mdlib/sim_util.c-105-  if ((step >= ir->nstlist)) {
> src/mdlib/sim_util.c-106-if ((ir->nstlist == 0) || ((step %
> ir->nstlist) == 0)) {
> src/mdlib/sim_util.c-107-  /* We have done a full cycle let's update
> time_per_step */
> src/mdlib/sim_util.c-108-  end=time(NULL);
> src/mdlib/sim_util.c-109-  dt=difftime(end,start);
> src/mdlib/sim_util.c-110-  time_per_step=dt/(step - ir->init_step + 1);
> src/mdlib/sim_util.c-111-}
> src/mdlib/sim_util.c-112-dt=(ir->nsteps + ir->init_step -
> step)*time_per_step;
> src/mdlib/sim_util.c-113-
> src/mdlib/sim_util.c-114-if (dt >= 300) {
> src/mdlib/sim_util.c-115-  finish = end+(time_t)dt;
> src/mdlib/sim_util.c-116-  sprintf(buf,"%s",ctime(&finish));
> src/mdlib/sim_util.c-117-  buf[strlen(buf)-1]='\0';
> src/mdlib/sim_util.c-118-  fprintf(out,", will finish %s",buf);
> src/mdlib/sim_util.c-119-}
> src/mdlib/sim_util.c-120-else
> src/mdlib/sim_util.c-121-  fprintf(out,", remaining runtime: %5d
> s  ",(int)dt);
> src/mdlib/sim_util.c-122-  fc = (int)dt / ir->nstlist;
> src/mdlib/sim_util.c-123-  fprintf(stderr, "Fraction complete: %d \n",
> fc);
> src/mdlib/sim_util.c-124-  }
> src/mdlib/sim_util.c-125-  if (gmx_parallel_env)
> src/mdlib/sim_util.c-126-fprintf(out,"\n");
> src/mdlib/sim_util.c-127-
> src/mdlib/sim_util.c-128-  fflush(out);
> src/mdlib/sim_util.c-129-}
>
> Back Off! I just backed up md.edr to ./#md.edr.4#
> starting mdrun 'Protein in water'
> 500 steps,  1.0 ps.
> step 100, remaining runtime:   122 s  Fraction complete: 0
> step 200, remaining runtime:92 s  Fraction complete: 0
>
>
>   On Thu, Sep 24, 2009 at 6:34 PM, Mark Abraham 
> wrote:
>
>> Jack Shultz wrote:
>>
>>> I figured out another way to update the progress of my simulation, but I
>>> need to report the fraction of completion at the certain intervals of mdrun.
>>> Possibly at every time step or if that does not make sense every 100
>>> timesteps. I don't think this is a feature currently supported, so I will
>>> have to make some source code chages. I am looking for the variables related
>>> to total number of time steps and where it controls the the current time
>>> step so I can calculate the fraction of complete where current-timestep /
>>> total-timestep
>>>
>>
>> Under at least some circumstances GROMACS writes the expected runtime
>> remaining to stderr, but I don't recall what/when. Piping that to some
>> useful script has to be a good start. You certainly don't need this data
>> every time step, and don't want to be perturbing mdrun to get it.
>>
>> Even if the above was unsuitable, surely progress would only need to be
>> moderately accurate and for simulations that last many hours. If so, you'll
>> get good enough data by grepping a gmxdump of the .tpr to get the expected
>> frequencies of output and length of run, and then watching the growth of
>> whichever of .log/.trr/.edr is written most frequently. I/O buffering will
>> affect the numbers somewhat.
>>
>> Mark
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
>
>
>  --
> Jack
>
> http://drugdiscoveryathome.com
> http://hydrogenathome.org
>



-- 
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org
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Re: [gmx-users] timestep fraction complete


Jack Shultz wrote:
I am hoping for an update every 10 minutes just to satisfy the anxieties 
of volunteers crunching on my project, but every hour may be 
satisfactory. And if I can do this without requiring any shell scripts 
it would be better in my environment. So I started making some code 
modifications which apparently did not work
 
src/mdlib/sim_util.c:93:void print_time(FILE *out,time_t start,int 
step,t_inputrec *ir)

src/mdlib/sim_util.c-94-{
src/mdlib/sim_util.c-95-  static real time_per_step;
src/mdlib/sim_util.c-96-  static time_t end;
src/mdlib/sim_util.c-97-  time_t finish;
src/mdlib/sim_util.c-98-  double dt, fc;
src/mdlib/sim_util.c-99-  char buf[48];
src/mdlib/sim_util.c-100-  FILE *progress="progress.txt";
src/mdlib/sim_util.c-101-
src/mdlib/sim_util.c-102-  if (!gmx_parallel_env)
src/mdlib/sim_util.c-103-fprintf(out,"\r");
src/mdlib/sim_util.c-104-  fprintf(out,"step %d",step);
src/mdlib/sim_util.c-105-  if ((step >= ir->nstlist)) {
src/mdlib/sim_util.c-106-if ((ir->nstlist == 0) || ((step % 
ir->nstlist) == 0)) {
src/mdlib/sim_util.c-107-  /* We have done a full cycle let's update 
time_per_step */

src/mdlib/sim_util.c-108-  end=time(NULL);
src/mdlib/sim_util.c-109-  dt=difftime(end,start);
src/mdlib/sim_util.c-110-  time_per_step=dt/(step - ir->init_step + 1);
src/mdlib/sim_util.c-111-}
src/mdlib/sim_util.c-112-dt=(ir->nsteps + ir->init_step - 
step)*time_per_step;

src/mdlib/sim_util.c-113-
src/mdlib/sim_util.c-114-if (dt >= 300) {   
src/mdlib/sim_util.c-115-  finish = end+(time_t)dt;

src/mdlib/sim_util.c-116-  sprintf(buf,"%s",ctime(&finish));
src/mdlib/sim_util.c-117-  buf[strlen(buf)-1]='\0';
src/mdlib/sim_util.c-118-  fprintf(out,", will finish %s",buf);
src/mdlib/sim_util.c-119-}
src/mdlib/sim_util.c-120-else
src/mdlib/sim_util.c-121-  fprintf(out,", remaining runtime: %5d 
s  ",(int)dt);

src/mdlib/sim_util.c-122-  fc = (int)dt / ir->nstlist;
src/mdlib/sim_util.c-123-  fprintf(stderr, "Fraction complete: %d 
\n", fc);


You're doing integer division and writing an integer. That won't get you 
fraction complete, even if the ratio of dt (the remaining runtime in 
seconds) and ir->nstlist (the number of steps between neighboursearches) 
meant anything! Use


fprintf(stderr, "Fraction complete: %g\n", (step - ir->init_step) / 
(float) ir->nsteps);


Mark


src/mdlib/sim_util.c-124-  }
src/mdlib/sim_util.c-125-  if (gmx_parallel_env)
src/mdlib/sim_util.c-126-fprintf(out,"\n");
src/mdlib/sim_util.c-127-
src/mdlib/sim_util.c-128-  fflush(out);
src/mdlib/sim_util.c-129-}
 
Back Off! I just backed up md.edr to ./#md.edr.4#

starting mdrun 'Protein in water'
500 steps,  1.0 ps.
step 100, remaining runtime:   122 s  Fraction complete: 0
step 200, remaining runtime:92 s  Fraction complete: 0


On Thu, Sep 24, 2009 at 6:34 PM, Mark Abraham > wrote:


Jack Shultz wrote:

I figured out another way to update the progress of my
simulation, but I need to report the fraction of completion at
the certain intervals of mdrun. Possibly at every time step or
if that does not make sense every 100 timesteps. I don't think
this is a feature currently supported, so I will have to make
some source code chages. I am looking for the variables related
to total number of time steps and where it controls the the
current time step so I can calculate the fraction of complete
where current-timestep / total-timestep


Under at least some circumstances GROMACS writes the expected
runtime remaining to stderr, but I don't recall what/when. Piping
that to some useful script has to be a good start. You certainly
don't need this data every time step, and don't want to be
perturbing mdrun to get it.

Even if the above was unsuitable, surely progress would only need to
be moderately accurate and for simulations that last many hours. If
so, you'll get good enough data by grepping a gmxdump of the .tpr to
get the expected frequencies of output and length of run, and then
watching the growth of whichever of .log/.trr/.edr is written most
frequently. I/O buffering will affect the numbers somewhat.

Mark

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--
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org




___

[gmx-users] Re: Re: Re: Re: Re: Re: Re: umbrella potential

2009-09-24 Thread Stefan Hoorman

>
>
> >
> > > I will ty Justin's suggestion. I should have the answer by tomorrow.
> > > As for Thomas' suggestion, well, my mdp file didn't even have the
> > > "pull_start" flag. So I assume gromacs though I had set it to "no". But
> > > anyway, I checked the force in each window as you mentioned andfound
> > > something quite strange. The original pull_pf.xvg file, is an eve
> > > increasing line starting at -43 kj/mol/nm. So when I check a specific
> > > time frame, the pull force is, for example 93 kj/mol/nm at time frame
> > > 4000. But when I checked the pull force on the pull_pf.xvg file at that
> > > specific window, well, the pull force was something around -42
> > > kj/mol/nm. Now I am really confused. It seems I am doing something
> > > really wrong, but actually quite simple to solve. I will try setting
> > > "pull_start = yes" and see what happens.
> >
> > Because you're looking at two entirely different things.  In your initial
> > pulling simulation to separate your species, the force will continually
> > change,
> > building up until the two dissociate, then probably level off to some
> > roughly
> > constant value until the simulation stops (when the species are no longer
> > interacting).
> >
> > In umbrella sampling, the force imposed on the pull group is used to
> > restrain it
> > within a window, and will not necessarily have anything to do with the
> > values
> > obtained in the original separation simulation.  Apples to oranges, if
> you
> > will.
> >
> > Setting "pull_start = yes" is appropriate for the umbrella sampling.  In
> > conjunction with "pull_init1 = 0" the original distance between the two
> > species
> > should be taken as the distance to be restrained during umbrella sampling
> > simulations.
> >
> > > One other thing. I checked my pull_px.xvg file for the initial
> > > separation trajectory. It looks like a a rollercoaster with a tendency
> > > to going down. So the final value of distance PULL_COM is 1.5nm lower
> > > than the initial value. The values on each of my windows are the same
> > > for the individual values pf the separation trajectory from which they
> > > were taken. And again, the values on the pull_px,xvg files all
> decrease.
> > >
> >
> > Not a steady increase as the two species separate?  Is your box size
> > sufficient
> > to accommodate the distance you are pulling, or are you experiencing
> > periodicity
> > artefacts?
> >
> >
> > I am sorry. Correcting. The px values increase for my simulation. The
> files
> I checked were for a simulation with a smaller box periodicity does occur.
> With my actual system (larger box) the px values increase. I have started a
> new run for my windows setting "pull_start = yes" with "pull_init1 = 0".
> Once I have some of the simulations finished I should have an idea of what
> is happening.
> Thank you
>
> Hi again. I have finished my wham analysis and here is what came out. Well,
first let me remind you of what we have already talked about. I have
simulated my system, comprised of protein and ligand, with the pull code set
to umbrella in order to obtain the entry structures for the sampling
simulations for my wham analysis. Now, after several suggestions I have
finally come up with a set of parameters that seemed to work. I have
included the "pull_start = yes " in my windows' parameter  file and have
also increased the "pull_force" from 35 to 2000. This increase seems to be
sufficient to maintain my structures restrained in the initial position, so
now my distance between groups float around a given value, which is quite
close to the initial one. The structures obtained for the wham windows were
obtained selecting frames in which a given distance between the structures
was met. The structures were obtained with a 0.1nm distance delta.
The problem now is the following. According to my .edr file, I should have
no more interaction (LJ-SR and Coul-SR) between my structures starting from
2.5nm distance between them. So I would expect that my profile.xvg file
resulting from g_wham would give my values that would, from 2.5nm on, kind
of stabilize. My profile.xvg resulting from g_wham gives me increasing
values of umbrella potential starting in -1.1kcal mol\S-1\N until +90kcal
mol\S-1\N.
It does not look like anything I have seen for similar studies on the
literature. It has no minimum valey, i.e., the minimum value is the first
one and then the values just increase from there.
Thank you
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Re: [gmx-users] Re: Re: Re: Re: Re: Re: Re: umbrella potential




Stefan Hoorman wrote:

Hi again. I have finished my wham analysis and here is what came out. 
Well, first let me remind you of what we have already talked about. I 
have simulated my system, comprised of protein and ligand, with the pull 
code set to umbrella in order to obtain the entry structures for the 
sampling simulations for my wham analysis. Now, after several 
suggestions I have finally come up with a set of parameters that seemed 
to work. I have included the "pull_start = yes " in my windows' 
parameter  file and have also increased the "pull_force" from 35 to 
2000. This increase seems to be sufficient to maintain my structures 
restrained in the initial position, so now my distance between groups 
float around a given value, which is quite close to the initial one. The 
structures obtained for the wham windows were obtained selecting frames 
in which a given distance between the structures was met. The structures 
were obtained with a 0.1nm distance delta.
The problem now is the following. According to my .edr file, I should 
have no more interaction (LJ-SR and Coul-SR) between my structures 
starting from 2.5nm distance between them. So I would expect that my 
profile.xvg file resulting from g_wham would give my values that would, 
from 2.5nm on, kind of stabilize. My profile.xvg resulting from g_wham 
gives me increasing values of umbrella potential starting in -1.1kcal 
mol\S-1\N until +90kcal mol\S-1\N.
It does not look like anything I have seen for similar studies on the 
literature. It has no minimum valey, i.e., the minimum value is the 
first one and then the values just increase from there.

Thank you



How long are you sampling in each window?  How many total windows do you have? 
What do the histograms look like?


-Justin





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--


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


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Re: [gmx-users] timestep fraction complete