Re: [gmx-users] GROMACS with GPU

[Jones de Andrade]

Hi!

If I may ask, but what is the gromacs version that is planned on the roadmap
to begin to work with the newer version of openmm? Specially interested due
to ATI support

Regards

Jones

On Thu, Aug 18, 2011 at 10:01 PM, Szilárd Páll wrote:

> Hi,
>
> Gromacs 4.5.x works only with OpenMM 2.x. You might be able to use
> CUDA 4.0, but you will probably have to recompile OpenMM from source.
>
> Cheers,
> --
> Szilárd
>
>
>
> On Fri, Aug 19, 2011 at 2:23 AM, Park, Jae Hyun nmn 
> wrote:
> > Dear GMX users,
> >
> >
> >
> > I am installing GMX 4.5.3 with GPU.
> >
> > But, the CUDA in my GPU machine is ver 4.0. Can I use this version of
> CUDA
> > and openmm-3.1.1? Or, do I have to re-install CUDA 3.2 and openmm-2.0 as
> > described in manual?
> >
> >
> >
> > Thank you in advance for your kind instruction.
> >
> > Jae H. Park
> >
> >
> >
> >
> >
> > ===
> >
> > Jae Hyun Park, Ph. D.
> >
> > Physics Division
> >
> > Oak Ridge National Laboratory
> >
> > PO. Box 2008, MS-6372
> >
> > Oak Ridge, TN 37831
> >
> > Phone (865) 241-1482
> >
> > E-mail pa...@ornl.gov
> >
> >
> >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] NPT - density off

[wibke . sudholt]

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[gmx-users] NPT - density off

[Elisabeth]

Dear experts,

I am intending to calculate the equilibrium density of a pure hydrocarbon at
different pressures , at 425 K. The normal boiling point of the liquid is
around 350 K. For pressures below 100 bar densities I am getting from NPT is
in accurate. I start form a structure which is compressed to above 0.6 g/cm3
density but since temperature is high density goes than to the values
below.

P = 50 bar > NPT rho=   0.344   experimental density ~ 0.54
P100  > NPT rho=  0.43  experimental density ~ 0.55

densities become more accurate for P >100 bar.

P 500>   rho=  0.56experimental density ~ 0.61

I thought maybe you have some idea on how this inaccuracy can be improved.

Thank you in advance for your invaluable help.
Best,


;Bonds
constraints = none
constraint-algorithm = lincs

;Run control
integrator  =  md
dt  =  0.001
nsteps  =  500
nstcomm =  100

;Output control
nstenergy   =  100
nstxout =  100
nstvout =  0
nstfout =  0
nstlog  =  1000
nstxtcout  =  1000

;Neighbor searching
nstlist =  10
ns_type =  grid

;Electrostatics/VdW
coulombtype =  Shift
vdw-type=  Shift
rcoulomb-switch =  0
rvdw-switch =  0.9

;Cut-offs
rlist   =  1.25
rcoulomb=  1.0
rvdw=  1.0

;Temperature coupling
Tcoupl  =  v-rescale
tc-grps =  System
tau_t   =  0.1
ref_t   =  425

;Pressure coupling
Pcoupl  =  berendsen
Pcoupltype  =  isotropic
tau_p   =  1
compressibility =  3.5e-5
ref_p   =  100

;Velocity generation
gen_vel =  no;yes
gen_temp=  425
gen_seed=  173529
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Re: [gmx-users] use of the mailing list

[Junior Nebeker]

Of course I know of Mark's contributions.  However, one's contributions, big
or small, shouldn't excuse him/her from being rude to others.  That's my
constructive feedback - take it or leave it.

On Fri, Aug 19, 2011 at 9:51 AM, Amit Choubey  wrote:

>
>
> On Fri, Aug 19, 2011 at 8:13 AM, Junior Nebeker 
> wrote:
>
>> Sure Mark.  If your interest is in patrolling the Gromacs mailing list,
>> then I'll leave you to it.
>>
>
> I think before you type your response you should consider that Mark has
> helped several hundred times over this mailing list.
>
>
>> On Thu, Aug 18, 2011 at 9:40 PM, Mark Abraham wrote:
>>
>>>  On 19/08/2011 1:41 PM, Junior Nebeker wrote:
>>>
>>> Correct.  Other people (who are new to this list) need your help, and
>>> unless their requests are way out of line, there's no reason to adopt a
>>> haughty attitude in responding.
>>>
>>>
>>> There's never a case for rudeness, but when (for example) people have
>>> been asking questions on the mailing list for years and still haven't
>>> absorbed the advice available here http://www.gromacs.org/Support, then
>>> one can get frustrated. Expressing a little of that can help people realise
>>> how to participate more effectively in the discussion. One's family doctor
>>> can ask a lot of patient questions about what is wrong because you're paying
>>> them a lot of money. If people who might give free help don't feel that
>>> their time is valued, they might stop giving it. One way of demonstrating
>>> this is to ask questions that show one's willingness to work on the problem
>>> by providing lots of relevant diagnostic information. See
>>> http://www.catb.org/~esr/faqs/smart-questions.html
>>>
>>> Mark
>>>
>>> P.S. I'm not intending to express particular criticism of the original
>>> poster in this thread
>>>
>>>
>>> On Thu, Aug 18, 2011 at 5:05 PM, Mark Abraham 
>>> wrote:
>>>
 On 19/08/2011 9:32 AM, Junior Nebeker wrote:

>
> Hey mark,
>
> If you are really sick of asking people for such information, why do
> you even care to respond to this mailing list?
>

  Because I'd rather teach someone to fish than either give them fish or
 watch them starve.


 Mark
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>>>
>>>
>>>
>>>
>>>
>>> --
>>>
>>> gmx-users mailing listgmx-users@gromacs.org
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>>
>>
>> --
>>
>> gmx-users mailing listgmx-users@gromacs.org
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>
>
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Re: [gmx-users] h-bonds constraints

[Dr. Vitaly V. Chaban]

Thanks! That's reasonable.


On Fri, Aug 19, 2011 at 2:31 PM, Bogdan Costescu  wrote:
> On Fri, Aug 19, 2011 at 20:02, Dr. Vitaly V. Chaban  
> wrote:
>> What criterion does the grompp utility use to identify H-atoms when it
>> is requested in the MDP file to apply constraints=h-bonds? Thanks.
>
> Any atom name starting with H or h (so case-insensitive).
>
> Cheers,
> Bogdan
>
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Re: [gmx-users] h-bonds constraints

[Bogdan Costescu]

On Fri, Aug 19, 2011 at 20:02, Dr. Vitaly V. Chaban  wrote:
> What criterion does the grompp utility use to identify H-atoms when it
> is requested in the MDP file to apply constraints=h-bonds? Thanks.

Any atom name starting with H or h (so case-insensitive).

Cheers,
Bogdan
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[gmx-users] h-bonds constraints

[Dr. Vitaly V. Chaban]

What criterion does the grompp utility use to identify H-atoms when it
is requested in the MDP file to apply constraints=h-bonds? Thanks.

-- 
Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA
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Re: [gmx-users] use of the mailing list

[Amit Choubey]

On Fri, Aug 19, 2011 at 8:13 AM, Junior Nebeker wrote:

> Sure Mark.  If your interest is in patrolling the Gromacs mailing list,
> then I'll leave you to it.
>

I think before you type your response you should consider that Mark has
helped several hundred times over this mailing list.


> On Thu, Aug 18, 2011 at 9:40 PM, Mark Abraham wrote:
>
>>  On 19/08/2011 1:41 PM, Junior Nebeker wrote:
>>
>> Correct.  Other people (who are new to this list) need your help, and
>> unless their requests are way out of line, there's no reason to adopt a
>> haughty attitude in responding.
>>
>>
>> There's never a case for rudeness, but when (for example) people have been
>> asking questions on the mailing list for years and still haven't absorbed
>> the advice available here http://www.gromacs.org/Support, then one can
>> get frustrated. Expressing a little of that can help people realise how to
>> participate more effectively in the discussion. One's family doctor can ask
>> a lot of patient questions about what is wrong because you're paying them a
>> lot of money. If people who might give free help don't feel that their time
>> is valued, they might stop giving it. One way of demonstrating this is to
>> ask questions that show one's willingness to work on the problem by
>> providing lots of relevant diagnostic information. See
>> http://www.catb.org/~esr/faqs/smart-questions.html
>>
>> Mark
>>
>> P.S. I'm not intending to express particular criticism of the original
>> poster in this thread
>>
>>
>> On Thu, Aug 18, 2011 at 5:05 PM, Mark Abraham wrote:
>>
>>> On 19/08/2011 9:32 AM, Junior Nebeker wrote:
>>>

 Hey mark,

 If you are really sick of asking people for such information, why do you
 even care to respond to this mailing list?

>>>
>>>  Because I'd rather teach someone to fish than either give them fish or
>>> watch them starve.
>>>
>>>
>>> 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/Support/Mailing_Lists/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/Support/Mailing_Lists
>>>
>>
>>
>>
>>
>>
>> --
>>
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
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>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
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Re: [gmx-users] the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure

[Amit Choubey]

On Fri, Aug 19, 2011 at 8:50 AM, KONG Xian  wrote:

> I have sent this email days ago, but I got no answer.
>
> Hope someone would saw it this time. 
>
> Sorry for disturbing.
>
> Dear all:
>
>  I am using gromacs-4.0.2_localpressure to calculate the local
> pressure of my system.
>
>  I have a question.
>
>  When rerun the mdrun from gromacs-4.0.2_localpressure I used a new
> .mdp file. There are some changes of the new .mdp file according the
> original one. I have 2 questions:
>
> **1.  **I changed the The coulomb interaction type from PME to
> reaction field with epsilon_r=1 epsilon_rf=78;  Is this change feasible?
>
Yes, you have to switch to cutoff for coulomb interaction. I have seen in
other publications that they use a regular coulomb  with cutoff as large as
2 nm. I am not sure whether there is any advantage in using Reaction field.

> 
>
> **2.  **I used LINCS for all bonds in the simulation, and I still use
> the LINCS for all bonds when calculate the local pressure. Is this way
> right?
>
 I have had no problems in using LINCS during local pressure calculation.

> 
>
> ** **
>
> Thanks for any reply.
>
> ** **
>
> Best wishes, 
>
> KONG Xian
>
> Tsinghua, Beijing, China****
>
>
>
> 
>
>
> __ Information from ESET NOD32 Antivirus, version of virus
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>
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Re: [gmx-users] parameters for CH1 -- S -- CH2 ?

[Mark Abraham]

On 20/08/2011 1:57 AM, Yun Shi wrote:

Hi all,

I have a small molecule with a part like:

CH1 --- CH1 --- S --- CH2 --- CH1
 |
 CH1

I first tried PRODRG, and it turned out PRODRG assigned bond, angle, 
and dihedral parameters according what are already present in the 
gromos53a6.ff/ffbonded.itp file. Since this file does not contain 
information regarding this CH1 --- S --- CH2 pattern, PRODRG just 
assigned bond (gb_31),angle (ga_4) as if my molecule has CH3 --- S --- 
CH2 pattern, and dihedral parameters for CH1 -- CH1 -- S -- CH2 as if 
it was CH1 -- CH2 -- S -- CH2.


So I guess I have to do this manually. But as no corresponding 
parameters defined in ffbonded.itp file, should I derive these 
parameters via chemical intuition and try validate them in some way?


Or is there an easier alternative way to do this?


Parameterizing new species is not easy. See 
http://www.gromacs.org/Documentation/How-tos/Parameterization. Be sure 
to check the literature for existing approaches - and particularly how 
the thioether parameters that do exist were derived.


Mark

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[gmx-users] parameters for CH1 -- S -- CH2 ?

[Yun Shi]

Hi all,

I have a small molecule with a part like:

CH1 --- CH1 --- S --- CH2 --- CH1
 |
 CH1

I first tried PRODRG, and it turned out PRODRG assigned bond, angle, and
dihedral parameters according what are already present in the
gromos53a6.ff/ffbonded.itp file. Since this file does not contain
information regarding this CH1 --- S --- CH2 pattern, PRODRG just assigned
bond (gb_31),angle (ga_4) as if my molecule has CH3 --- S --- CH2 pattern,
and dihedral parameters for CH1 -- CH1 -- S -- CH2 as if it was CH1 -- CH2
-- S -- CH2.

So I guess I have to do this manually. But as no corresponding parameters
defined in ffbonded.itp file, should I derive these parameters via chemical
intuition and try validate them in some way?

Or is there an easier alternative way to do this?

Thanks for any suggestion!

Yun
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Re: [gmx-users] Possible bug in g_hbond with implicit solvent

[Mark Abraham]

On 20/08/2011 1:45 AM, Justin A. Lemkul wrote:



Mark Abraham wrote:

On 20/08/2011 1:26 AM, Justin A. Lemkul wrote:


Hi All,

I wanted to solicit some feedback on what I think may be a bug 
related to periodicity handling and/or implicit solvent 
simulations.  I ran some simulations of a few model peptides (some 
helices, hairpins, etc) and I got what I believed to be very 
inflated results for backbone hydrogen bonds.  For instance, a 
helical peptide with only 17 residues had, on average, 23.5 hydrogen 
bonds within the backbone alone, which, judging from the 
configurations, couldn't really be possible.


Does the structure file input to g_hbond have a spuriously small box?



It does, and I suspect this is where the problem ultimately lies.  For 
the simulation, with "pbc = no" the box vectors get ignored and 
everything is fine.  For analysis, however, it seems that the PBC 
routines are still trying to fit everything into that tiny box and 
thus basically all possible H-bonds are detected as being present 
because the distances are so small.


Sure. In your case, mdrun learns to ignore the box from the .mdp file 
setting, but I presume the box values still get copied around in the 
same fashion as for NVT PBC... A pre-emptive work-around might be to 
generate the simulation .tpr with a spurious large box, which then gets 
transferred everywhere else.


Better file formats would be the only reasonable fix, and that would not 
be all that reasonable...


I don't know how to avoid people rediscovering this phenomenon in the 
future.


Mark



Re-generating the .tpr file with a new, larger, box does not fix the 
problem, likely because the .xtc still has the tiny box.  Manipulating 
the trajectory with trjconv -box -center seems to work, though.  So I 
suppose this is an acceptable workaround, though it still may be a 
problem worth looking into.


Thanks for the inspiration; hadn't thought about trying to change the 
box after the fact :)


-Justin



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Re: [gmx-users] g_rdf

[Justin A. Lemkul]

Nilesh Dhumal wrote:

Hello,

I run a 5ns simulation for a single glucose molecule in gas phase.

I tried to plot radial distribution function for O---H intramolecular
interactions using following command.

g_rdf -f 6.trr -s 6.tpr -n index -o

In rdf.xvg file there is no data.

Can you tell what could be the reason.




Probably due to exclusions in the topology, as g_rdf -h indicates.  There are 
several possible workarounds discussed in the same paragraph.


-Justin


I am using Gromacs 4.0.7 version.


Thanks

Nilesh














--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure

[KONG Xian]

I have sent this email days ago, but I got no answer.

Hope someone would saw it this time. 

Sorry for disturbing.

Dear all:

 I am using gromacs-4.0.2_localpressure to calculate the local
pressure of my system.

 I have a question.

 When rerun the mdrun from gromacs-4.0.2_localpressure I used a new
.mdp file. There are some changes of the new .mdp file according the
original one. I have 2 questions:

1.  I changed the The coulomb interaction type from PME to reaction
field with epsilon_r=1 epsilon_rf=78;  Is this change feasible?

2.  I used LINCS for all bonds in the simulation, and I still use the
LINCS for all bonds when calculate the local pressure. Is this way right? 

 

Thanks for any reply.

 

Best wishes, 

KONG Xian

Tsinghua, Beijing, China





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[gmx-users] g_rdf

[Nilesh Dhumal]

Hello,

I run a 5ns simulation for a single glucose molecule in gas phase.

I tried to plot radial distribution function for O---H intramolecular
interactions using following command.

g_rdf -f 6.trr -s 6.tpr -n index -o

In rdf.xvg file there is no data.

Can you tell what could be the reason.


I am using Gromacs 4.0.7 version.


Thanks

Nilesh












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Re: [gmx-users] Possible bug in g_hbond with implicit solvent

[Justin A. Lemkul]

Mark Abraham wrote:

On 20/08/2011 1:26 AM, Justin A. Lemkul wrote:


Hi All,

I wanted to solicit some feedback on what I think may be a bug related 
to periodicity handling and/or implicit solvent simulations.  I ran 
some simulations of a few model peptides (some helices, hairpins, etc) 
and I got what I believed to be very inflated results for backbone 
hydrogen bonds.  For instance, a helical peptide with only 17 residues 
had, on average, 23.5 hydrogen bonds within the backbone alone, which, 
judging from the configurations, couldn't really be possible.


Does the structure file input to g_hbond have a spuriously small box?



It does, and I suspect this is where the problem ultimately lies.  For the 
simulation, with "pbc = no" the box vectors get ignored and everything is fine. 
 For analysis, however, it seems that the PBC routines are still trying to fit 
everything into that tiny box and thus basically all possible H-bonds are 
detected as being present because the distances are so small.


Re-generating the .tpr file with a new, larger, box does not fix the problem, 
likely because the .xtc still has the tiny box.  Manipulating the trajectory 
with trjconv -box -center seems to work, though.  So I suppose this is an 
acceptable workaround, though it still may be a problem worth looking into.


Thanks for the inspiration; hadn't thought about trying to change the box after 
the fact :)


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] -ter option with pdb2gmx

[Mark Abraham]

On 20/08/2011 1:27 AM, Vijayaraj wrote:
"-ter" or "-inter" options of pdb2gmx are working fine with all force 
fields except amber force field. I cant select the terminal groups 
when I use amber ff, it directly goes through the generation of top 
files without asking any options for terminal group selection. I just 
want to use the none option for the terminals (with amber ff). any 
suggestion?


AMBER treats charges on terminal residues differently, so the -ter 
mechanism doesn't work in the way that it can for other force fields. 
See http://ffamber.cnsm.csulb.edu/#usage.


You'd have found this out faster if your earlier email had had a 
one-sentence description of your simulation objective. :)


Mark



Regards,
Vijay


Date: Fri, 19 Aug 2011 15:31:04 +0200
From: Vijayaraj mailto:vijayara...@gmail.com>>
Subject: [gmx-users] -ter option with pdb2gmx
To: gmx-users@gromacs.org 
Message-ID:
mailto:vaj4...@mail.gmail.com>>
Content-Type: text/plain; charset="iso-8859-1"

Hello,

I am trying to use "-ter" with the pdb2gmx command, seems its not
working
fine.

>pdb2gmx -f  -o  -p  -ter

I also used "-inter" option, its not working.
I am using 4.5.4 version. any help would be greatly appreciated.

Regards,
vijay






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Re: [gmx-users] Possible bug in g_hbond with implicit solvent

[Mark Abraham]

On 20/08/2011 1:26 AM, Justin A. Lemkul wrote:


Hi All,

I wanted to solicit some feedback on what I think may be a bug related 
to periodicity handling and/or implicit solvent simulations.  I ran 
some simulations of a few model peptides (some helices, hairpins, etc) 
and I got what I believed to be very inflated results for backbone 
hydrogen bonds.  For instance, a helical peptide with only 17 residues 
had, on average, 23.5 hydrogen bonds within the backbone alone, which, 
judging from the configurations, couldn't really be possible.


Does the structure file input to g_hbond have a spuriously small box?

Mark



The simulations use infinite cutoffs and a nonperiodic unit cell.  
g_hbond identifies 26 backbone hydrogen bonds at time zero of the 
trajectory.  If, however, I create a .tpr file from a configuration 
with a large box (i.e., 10-nm cube) and run g_hbond on just that 
configuration (.gro file), I get a far more sensible result - 8 
hydrogen bonds.


I can't recall anyone reporting anything like this before, but it 
seems to be that it's a fairly important issue.  Before I posted to 
redmine, I wanted to see if anyone had encountered this, too.  The 
version I'm using is 4.5.4; I haven't tested the latest 
release-4-5-patches yet, but I can if that would be useful.


-Justin



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[gmx-users] -ter option with pdb2gmx

[Vijayaraj]

"-ter" or "-inter" options of pdb2gmx are working fine with all force fields
except amber force field. I cant select the terminal groups when I use amber
ff, it directly goes through the generation of top files without asking any
options for terminal group selection. I just want to use the none option for
the terminals (with amber ff). any suggestion?

Regards,
Vijay


Date: Fri, 19 Aug 2011 15:31:04 +0200
> From: Vijayaraj 
> Subject: [gmx-users] -ter option with pdb2gmx
> To: gmx-users@gromacs.org
> Message-ID:
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello,
>
> I am trying to use "-ter" with the pdb2gmx command, seems its not working
> fine.
>
> >pdb2gmx -f  -o  -p  -ter
>
> I also used "-inter" option, its not working.
> I am using 4.5.4 version. any help would be greatly appreciated.
>
> Regards,
> vijay
>
>
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[gmx-users] Possible bug in g_hbond with implicit solvent

[Justin A. Lemkul]

Hi All,

I wanted to solicit some feedback on what I think may be a bug related to 
periodicity handling and/or implicit solvent simulations.  I ran some 
simulations of a few model peptides (some helices, hairpins, etc) and I got what 
I believed to be very inflated results for backbone hydrogen bonds.  For 
instance, a helical peptide with only 17 residues had, on average, 23.5 hydrogen 
bonds within the backbone alone, which, judging from the configurations, 
couldn't really be possible.


The simulations use infinite cutoffs and a nonperiodic unit cell.  g_hbond 
identifies 26 backbone hydrogen bonds at time zero of the trajectory.  If, 
however, I create a .tpr file from a configuration with a large box (i.e., 10-nm 
cube) and run g_hbond on just that configuration (.gro file), I get a far more 
sensible result - 8 hydrogen bonds.


I can't recall anyone reporting anything like this before, but it seems to be 
that it's a fairly important issue.  Before I posted to redmine, I wanted to see 
if anyone had encountered this, too.  The version I'm using is 4.5.4; I haven't 
tested the latest release-4-5-patches yet, but I can if that would be useful.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] use of the mailing list

[Mark Abraham]

On 20/08/2011 1:13 AM, Junior Nebeker wrote:
Sure Mark.  If your interest is in patrolling the Gromacs mailing 
list, then I'll leave you to it.


If you have something constructive to contribute, please do. Otherwise, 
please don't.


Mark
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Re: [gmx-users] use of the mailing list

[Junior Nebeker]

Sure Mark.  If your interest is in patrolling the Gromacs mailing list, then
I'll leave you to it.

On Thu, Aug 18, 2011 at 9:40 PM, Mark Abraham wrote:

>  On 19/08/2011 1:41 PM, Junior Nebeker wrote:
>
> Correct.  Other people (who are new to this list) need your help, and
> unless their requests are way out of line, there's no reason to adopt a
> haughty attitude in responding.
>
>
> There's never a case for rudeness, but when (for example) people have been
> asking questions on the mailing list for years and still haven't absorbed
> the advice available here http://www.gromacs.org/Support, then one can get
> frustrated. Expressing a little of that can help people realise how to
> participate more effectively in the discussion. One's family doctor can ask
> a lot of patient questions about what is wrong because you're paying them a
> lot of money. If people who might give free help don't feel that their time
> is valued, they might stop giving it. One way of demonstrating this is to
> ask questions that show one's willingness to work on the problem by
> providing lots of relevant diagnostic information. See
> http://www.catb.org/~esr/faqs/smart-questions.html
>
> Mark
>
> P.S. I'm not intending to express particular criticism of the original
> poster in this thread
>
>
> On Thu, Aug 18, 2011 at 5:05 PM, Mark Abraham wrote:
>
>> On 19/08/2011 9:32 AM, Junior Nebeker wrote:
>>
>>>
>>> Hey mark,
>>>
>>> If you are really sick of asking people for such information, why do you
>>> even care to respond to this mailing list?
>>>
>>
>>  Because I'd rather teach someone to fish than either give them fish or
>> watch them starve.
>>
>>
>> Mark
>> --
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>>
>
>
>
>
>
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RE: [gmx-users] more than 100% CPU

[Park, Jae Hyun nmn]

Thank you so much, all.

Jae H. Park

-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Szilárd Páll
Sent: Thursday, August 18, 2011 9:19 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] more than 100% CPU

It is true that on Intel CPUs with HT supported and on you get an up
to 10-15% speedup if you also use all virtual cores wrt to running
only as many threads as real cores. Additionally, as the OS reports
all virtual processors, by Gromacs will use all of them by default,
i.e. will run with 8 threads on a 4-core CPU with HT.

However, this is not the case on AMD and other CPU without
simultaneous multithreading. There you'll loose performance if you
overload CPUs.

--
Szilárd



On Fri, Aug 19, 2011 at 3:52 AM,   wrote:
> Slightly off-topic, but for all but the smallest systems, I get a further
> 10% efficiency by running a 16-process mpi job on an 8-core machine. I
> suspect that the story is the same with threads. Thus, on a 16-core node,
> you could try starting 32 threads. Note that this will report a 2x larger
> "efficiency" as you were discussing before, but by checking the ns.day you
> will see that the benefit is between 5% and 16%
>
> Chris.
>
> It means you are running a lot of parallel processes, but that does not
> translate into a linear increase in speed.  So faster, but not 16X.
>
> Warren Gallin
>
> On 2011-08-18, at 5:36 PM, Park, Jae Hyun nmn wrote:
>
>> Thank you, Warren.
>> Does that mean 16 times faster ?
>>
>> Jae H. Park
>>
>> -Original Message-
>> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at
>> gromacs.org] On Behalf Of Warren Gallin
>> Sent: Thursday, August 18, 2011 7:26 PM
>> To: Discussion list for GROMACS users
>> Subject: Re: [gmx-users] more than 100% CPU
>>
>> I believe that the current version of GROMACS supports threading, which
>> does not require mpi.
>>
>> So mdrun is running threads at 100% of the activity of each of your 16
>> nodes, hence 1600%.
>>
>> Warren Gallin
>>
>> On 2011-08-18, at 5:19 PM, Park, Jae Hyun nmn wrote:
>>
>>> Hi GMX users,
>>>
>>> I installed GMX 4.5.3 recently.
>>> But, when I just execute mdrun (without mpi, I did not installed
>>> mpi-version of mdrun), the use of CPU appears more than 100% ("top" command
>>> in LINUX). How is it possible?
>>> For example, I am using 16-node machine. And if I simply run "mdrun",
>>> then  use of CPU is 1600%!!.
>>> The simulation runs well and the results looks reasonable.
>>> Is there anybody who can teach me what is happening? I would deeply
>>> appreciate.
>>>
>
>
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Re: [gmx-users] -ter option with pdb2gmx

[Justin A. Lemkul]

Vijayaraj wrote:

Hello,

I am trying to use "-ter" with the pdb2gmx command, seems its not 
working fine.


 >pdb2gmx -f  -o  -ter



If this is your command line it is severely broken.


I also used "-inter" option, its not working.


Please define "not working."  It's working fine for me.


I am using 4.5.4 version. any help would be greatly appreciated.



We can assist you only if you provide useful diagnostics of what (actual) 
command you entered, what the output was, and why it was not what you expected.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] -ter option with pdb2gmx

[Vijayaraj]

Hello,

I am trying to use "-ter" with the pdb2gmx command, seems its not working
fine.

>pdb2gmx -f  -o  -ter

I also used "-inter" option, its not working.
I am using 4.5.4 version. any help would be greatly appreciated.

Regards,
vijay
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Re: [gmx-users] Regarding generating topology file.

[Bruce D. Ray]

On Tuesday, August 2, 2011 at 5:17 AM, Ravi Kumar Venkatraman 
 wrote:
> I have got some topology and parameter file 
for some small organic molecules from swissparam in *.mol2 format.
> I am 
trying to generate *.top, *.gro & *.itp files using topolbuild. But I
 dont know how to do. So can anybody
> give me a link or some materials 
related to this.

I'm not sure what the problem is.  The topolbuild 1.3.1 download does include 
documentation
on how to use it.  Is there something specific you have tried that you are 
having difficulties
with?

Of course, for use with gromacs 4.5.*, one does have edit the *.top with a text 
editor to change
the initial include lines in the topology file to reflect the re-organization 
of the force field files.
Furthermore, the current topolbuild version does not support CHARMm force 
fields.

Also, I believe that swissparam gives those files.

 
-- 
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St.
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[gmx-users] calculate residence time for a protein complex

[aiswarya pawar]

Hi,

I have simulated a protein complex and now i would like to know the residing
water molecules between the protein complex. g_hbond and trjorder helps in
giving the number of hydrogen bonds and distance. but is this the residence
time calculation. please help me with this. there few posts given in the
archives regarding the residence time which is not very clear to me. but
will the residence time calculation same for single protein and complex

Thank you,
Aiswarya
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Re: [Fwd: Re: [gmx-users] VSMP cluster performance changes with time]

[Mark Abraham]

On 19/08/2011 5:07 PM, Anupam Nath Jha wrote:

Is it the problem with the gromacs?



Probably not. Assuming you have kept everything else constant, it is likely that
other activity on the machine or file system is delaying you somehow.


This is still likely to be true. Other activity (other users jobs, heavy 
I/O demand etc.) can starve GROMACS for resources. If you are doing 
everything the same, then something you are not controlling must be 
different.


Mark
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[Fwd: Re: [gmx-users] VSMP cluster performance changes with time]

[Anupam Nath Jha]

I am using 24 processors and it is same for all steps.
this is the command in use:


tpbconv_mpi -f run.trr -s run.tpr -e run.edr -extend 1000 -o ext_11
nohup /opt/ScaleMP/mpich2/1.0.8/bin/mpirun -machinefile $PBS_NODEFILE -np 24
/opt/gromacs4/bin/mdrun_mpi -v -deffnm ext_11
--

similar for next steps.

regards
anupam



> On 18/08/11, Anupam Nath Jha  wrote:
>
>>
>>
>> Dear all
>>
>> I am running a MD (Gromacs - 4.5.3) in VSMP cluster with 24nodes.
>>
>> I am writing log files for different ns (1-10) in different files i.e.
>> different
>> files for each nano second . The performance goes like following:
>>
>> --
>> for 1st ns:
>>
>>(Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
>> Performance:   1444.719 85.902  3.946  6.082
>> Finished mdrun on node 0 Tue Aug 16 21:46:02 2011
>>
>> at 2nd ns:
>>
>> (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
>> Performance:560.393 33.322  1.531 15.679
>> Finished mdrun on node 0 Wed Aug 17 13:27:38 2011
>> --
>>
>> and in case of 3rd ns:
>>  it didn't complete the all steps and went in next.
>>
>> Is it the problem with the gromacs?
>>
>
>
> Probably not. Assuming you have kept everything else constant, it is likely 
> that
> other activity on the machine or file system is delaying you somehow. However,
> in the absence of much basic information (like how many processors you are
> trying to use) we can't suppose much. Copying and pasting command lines is
> useful.
>
> Mark
>
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-- 
Science is facts; just as houses are made of stone, so is science is made of
facts; but a pile of stones is not a house, and  a collection of facts is not
necessarily science.

Anupam Nath Jha
Saraswathi Vishveshwara Lab
Molecular Biophysics Unit
IISc,Bangalore-560012
Karnataka
Ph. no.-22932611



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-- 
Science is facts; just as houses are made of stone, so is science is made of
facts; but a pile of stones is not a house, and  a collection of facts is not
necessarily science.

Anupam Nath Jha
Saraswathi Vishveshwara Lab
Molecular Biophysics Unit
IISc,Bangalore-560012
Karnataka
Ph. no.-22932611



-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
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