Re: [gmx-users] gromacs parallel doesn't work

[Arneh Babakhani]

grompp -f ResMD1.mdp -c ../Heating/AfterHeatup.gro -p NoBadWater.top -o 
ResMD1 ;
mpirun -np 4 mdrun -s ResMD1.tpr -o ResMD1 -c AfterResMD1 -e ResMD1 -g 
ResMD1 > & ResMD1.job &




Mark Abraham wrote:

Arneh Babakhani wrote:
Hello, I'm having a similar problem, although my OS sees all 4 of my 
processors just fine.


When I run mpirun -c 4 mdrun . . .

all 4 of my processors are running, but only at 50% each.  
Furthermore, in present working directory, I see several backed up 
files:


[EMAIL PROTECTED] TEMP]$ ls
AfterResMD1.gro  #mdout.mdp.1#   ResMD1.job  ResMD1.trr
#AfterResMD1.gro.1#  NoBadWater.top  ResMD1.log  #ResMD1.trr.1#
#AfterResMD1.gro.2#  posre.itp   #ResMD1.log.1#  #ResMD1.trr.2#
dmpc.itp ResMD1.edr  #ResMD1.log.2#  #ResMD1.trr.3#
lipid.itp#ResMD1.edr.1#  #ResMD1.log.3#
lipid_posre.itp  #ResMD1.edr.2#  ResMD1.mdp
mdout.mdp#ResMD1.edr.3#  ResMD1.tpr

It's almost as if I'm running 4 identical jobs (one on each 
processor) , instead of one job in parallel using 4 processors.


Any thoughts?


You probably are. What are your full grompp and mdrun commands?

Mark
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Re: [gmx-users] gromacs parallel doesn't work

[Mark Abraham]

Arneh Babakhani wrote:
Hello, I'm having a similar problem, although my OS sees all 4 of my 
processors just fine.


When I run mpirun -c 4 mdrun . . .

all 4 of my processors are running, but only at 50% each.  Furthermore, 
in present working directory, I see several backed up files:


[EMAIL PROTECTED] TEMP]$ ls
AfterResMD1.gro  #mdout.mdp.1#   ResMD1.job  ResMD1.trr
#AfterResMD1.gro.1#  NoBadWater.top  ResMD1.log  #ResMD1.trr.1#
#AfterResMD1.gro.2#  posre.itp   #ResMD1.log.1#  #ResMD1.trr.2#
dmpc.itp ResMD1.edr  #ResMD1.log.2#  #ResMD1.trr.3#
lipid.itp#ResMD1.edr.1#  #ResMD1.log.3#
lipid_posre.itp  #ResMD1.edr.2#  ResMD1.mdp
mdout.mdp#ResMD1.edr.3#  ResMD1.tpr

It's almost as if I'm running 4 identical jobs (one on each processor) , 
instead of one job in parallel using 4 processors.


Any thoughts?


You probably are. What are your full grompp and mdrun commands?

Mark
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Re: [gmx-users] gromacs parallel doesn't work

[Arneh Babakhani]

Hello, I'm having a similar problem, although my OS sees all 4 of my 
processors just fine.


When I run mpirun -c 4 mdrun . . .

all 4 of my processors are running, but only at 50% each.  Furthermore, 
in present working directory, I see several backed up files:


[EMAIL PROTECTED] TEMP]$ ls
AfterResMD1.gro  #mdout.mdp.1#   ResMD1.job  ResMD1.trr
#AfterResMD1.gro.1#  NoBadWater.top  ResMD1.log  #ResMD1.trr.1#
#AfterResMD1.gro.2#  posre.itp   #ResMD1.log.1#  #ResMD1.trr.2#
dmpc.itp ResMD1.edr  #ResMD1.log.2#  #ResMD1.trr.3#
lipid.itp#ResMD1.edr.1#  #ResMD1.log.3#
lipid_posre.itp  #ResMD1.edr.2#  ResMD1.mdp
mdout.mdp#ResMD1.edr.3#  ResMD1.tpr

It's almost as if I'm running 4 identical jobs (one on each processor) , 
instead of one job in parallel using 4 processors.


Any thoughts?

Thanks,

Arneh






Beniamino Sciacca wrote:

OK!!!
now it works.
I installed a kernel-image smp (for my kernel 2.6)
and now with "-c 2" it works!!!
I've two processes running at nearly 100%, and the simulation time is 
reduced at 50%!
But now i don't understand why before (one week ago without smp it 
worked) mah

I thank all you very much

regards
Beniamino

2006/6/4, Yang Ye <[EMAIL PROTECTED] 
>:


So, the kernel you used from Debian could be a non-SMP one. Change
another in the boot screen if there is.
\
Yang Ye

David van der Spoel wrote:
> Beniamino Sciacca wrote:
>> with "-c 2" I've two processes, each one running at nearly 50%.
>> with "-c 4" I've four processes, each one running at nearly 25%
>> with "-c 1" I've only one process wich runs at nearly 99%
>> I tried also with mdrun_Nmpi (compiled without enabling mpi),
and it
>> runs at nearly 99%.
>> Is it possible that the software sees only one core?
>
> I think your OS only sees one processor.
> if Linux try:
> cat /proc/cpuinfo
>
>
>>
>> Beniamino
>>
>> Yang Ye ha scritto:
>>
>>> Use top to check, you shall have two processes running at nearly
>>> 100% with "-c 2"
>>>
>>> Yang Ye
>>>
>>> Beniamino Sciacca wrote:
>>>
 I've just tried "mpirun -c 2 mdrun..." (34 h/ns).
 It works, but the problem is the same... the simulation time
 In fact I also tried "mpirun -c 1 mdrun" (32 h/ns)
and  "mpirun -c
 4 mdrun" (34 h/ns), but the simulation time remain the same!


 Yang Ye ha scritto:

> Beniamino Sciacca wrote:
>
>> I never used mprun -np 2, and I had not problem. Before I
didn't
>> use "mprun -np 2", now I don't use "mprun -np 2" but simulation
>> time now is twice. It has changed from a day to the other.
>> However I've just tried, like you suggested,  to use " -np
2" (in
>> grompp and in mdrun) but I obtain an error:
>> ---
>> "Program mdrun_d, VERSION 3.3.1
>> Source code file: init.c, line: 69
>>
>> Fatal error:
>> run input file DNA8_mdEq.tpr was made for 2 nodes,
>>  while mdrun_d expected it to be for 1 nodes.
>> "
>> ---
>> In fact I've only one node.
>
> Try David's mpirun -c 2 mdrun
>
>>
>> Laptop should be running in top speed, I never modified the
>> configuration of energy profile.
>> Beniamino
>>
>>
>> 2006/6/3, Yang Ye <[EMAIL PROTECTED]

>> mailto:[EMAIL PROTECTED]>>>:
>>
>> First, make sure that you used mdrun -np 2.
>> Second, check your energy profile. Is your laptop
running in top
>> speed?
>> or does it have sleep time?
>>
>> Yang Ye
>>
>> Beniamino Sciacca wrote:
>> > I don't understand what you talking about...
>> > I didn't write any hostfile I'm not in a cluster. I
>> only use my
>> > notebook with the two cores.
>> > In fact I type "lamboot" without -v...
>> >
>> > Beniamino
>> >
>> > Mark Abraham ha scritto:
>> >> Did your default LAM hostfile configuration (or whatever
>> it is)
>> >> change from 2 processors to one?
>> >>
>> >> Mark
>> >> ___
>> >> gmx-users mailing list gmx-users@gromacs.org

>> >
>> >> http://www.gromacs.org/mailman/listinfo/gmx-users
>> >> Please don't post (un)subscribe requests to the
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>> the www

[gmx-users] Capped Carbon nanotube

[Rahul Godawat]

Hi Users,

 

I am looking for a capped (one or both ends) carbon nanotube
structure and/or topology. I shall be grateful if you can send me to [EMAIL PROTECTED] or hint me the location online.


Thanks

 

 

Rahul Godawat

Graduate Student,

Department of Chemical and Biological Engineering,

Rensselaer Polytechnic Institute, 

110 8th Street,

Troy NY 12180 3590

 






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Re: [gmx-users] gromos87 to gromos96

[Mark Abraham]

Anthony Cruz wrote:

Hi:
How to convert gromos87 ferric iron heme l-j parameters:

4.30115e-5(kJ nm^-12 mol^-1) and 8.86909e-3(kJ nm^-6 mol^-1)

to use it in gromos96 FF?


Find the functional forms in which these parameters are applied and do 
something intelligent. Then, sacrifice a goat and hope the force field 
deities are kind and they are compatible. Better still, find out how the 
gromos87 parameters were derived, and repeat that process for gromos96.


Mark
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RE: [gmx-users] Protein is out the box

[Dallas B. Warren]

To center and put things back into the box with a trajectory, use
trjconv -center

Catch ya,

Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
[EMAIL PROTECTED]
+61 3 9903 9524
-
When the only tool you own is a hammer, every problem begins to resemble
a nail.
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[gmx-users] manual-3.3.pdf

[Akshay Patny]

Hi GMX Team

 

Can anyone send me the PDF copy of ‘manual-3.3.pdf’
as I am having trouble downloading it online?

 

Kind Regards

Akshay

 

Akshay Patny



Graduate Research Assistant
Faser Hall 417, Department of Medicinal Chemistry

Research Institute of Pharmaceutical
Sciences
University
 of Mississippi
University,
 MS 38677
E-mail: [EMAIL PROTECTED]
Tel: 662-915-1286 (office);
Web: www.olemiss.edu


 






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[gmx-users] Protein is out the box

[Edgar Mixcoha Hernández]

I want to make a molecular dynamic with a protein, I make the .gro and .top
with pdb2gmx, after I put the protein inside a box with editconf, I put
water to the box with genbox, I check the archive in VMD and protein is
inside together with waters molecules.
When I execute grompp to make to get the .tpr file and I feed it to mdrun I
get an archive trr and other gro with the coordinates of my protein. I
visualize the archive gro and the trayectory with VMD and my protein is out
the box, and the water is inside it, I can see the shape of the protein
arounded with water molecules but is out.
What can I do?

In the other hand, I work with a Powerbook I get install GROMACS but grompp
doesn't work, for all proteins gets out an error.

---
Program grompp, VERSION 3.3.1
Source code file: grompp.c, line: 448

Fatal error:
number of coordinates in coordinate file (Msaab3-1w.gro, 27339)
 does not match topology (Msaab3-1.top, 0)
---

But when I check the topology and the gro archive, both are Ok..
And allways says that topology archive have 0 coordinates

I'll thank for help... I need to finish it to graduate...

=)
-- 
Edgar Mixcoha Hernández, Chemist, BSc
Laboratorio de Bioquímica, Edificio de Posgrado
Escuela Nacional de Medicina y Homeopatía, IPN
Lab +52 55 5729 6000 ext 55562
Mobile +52 55 2955 2219
__



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[gmx-users] B-factor calculations

[Jon Ellis]

Hello users

I am using B-factors to look at protein flexibility, using g_rmsf. I  
have a 3-ns simulation of an RNA strand bound to a 30-mer peptide. I  
did g_rmsf on the complex using the -oq option to obtain the bfac.pdb  
file, which gives me the B-factors averaged over the entire  
trajectory (I think).


Is it reasonable and physically valid to calculate b-factors varying  
over time, say by computing g_rmsf for smaller segments of my  
trajectory? If so, what would be a reasonable time interval for the  
averaging?


Thanks in advance for your help

Cheers
Jon




Jon Ellis
PhD Candidate, Thompson Group
Institute of Biomaterials and Biomedical Engineering/Dept of Chemistry
University of Toronto
Lash Miller 147
(416) 978-6568
[EMAIL PROTECTED]






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[gmx-users] gromos87 to gromos96

[Anthony Cruz]

Hi:
How to convert gromos87 ferric iron heme l-j parameters:

4.30115e-5(kJ nm^-12 mol^-1) and 8.86909e-3(kJ nm^-6 mol^-1)

to use it in gromos96 FF?

Anthony
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[gmx-users] lincs error

[Beniamino Sciacca]

Hi!
this is my problem: after a few step (from 1 to 20) mdrun stops because 
of  lincs
"...LINCS WARNING - Relative constraint deviation after lincs: max 
103.684275 (between atoms 7941 and 7942) rms 1.227871 bonds that rotated 
more than 180 degrees..."

7941 e  7942 should be two water atoms.
There are more than one WARNING
If I use a smaller time step (1fs instead of 4 fs or 2 fs) there is no 
problem, and it works well!

What can I do?
Beniamino
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[gmx-users] A problem with periodic boundary conditions

[Olli Lehtonen]

Hi all,

While running an energy minimization with mdrun 3.3.1, I observed that
different peptide units in the simulation box were translated in y
direction out of the box, each by N*Ly, N=1,5 (N is peptide unit and Ly is
the box y-dimension). The final structure (confout.gro) is a kind of
staircase instead of beta sheet which I'm trying to simulate.

Only one peptide and all solvent (water and Cl-) remain in the original
box. This happens even after setting nsteps=1. My system is probably quite
far from equilibrium but this kind of behaviour seems anyway unexpected.

I used genconf to generate the initial structure (which looks fine) and it
is these generated units which become translated with mdrun. Any
suggestions how to solve this problem are welcome.

best regards,

Olli
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Re: [gmx-users] pdb2gmx error, How to generate the gro and top file for a small molecular?

[TJ Piggot]

By hand for the topology, check chapter five of the manual.

For the gro file use editconf to convert the pdb

Hope that helps

Tom

--On Tuesday, June 13, 2006 17:40:41 +0800 "SUN, Jian" 
<[EMAIL PROTECTED]> wrote:




Dear all,

I am doing the simulation of a protein with a small molecular in its
active site.
But unfortunately, pdb2gmx cannot generate the gro and top file for the
small molecualr?
I am using the oplsaa force field, who can tell me how to generate the
gro and top files?

Thanks a lot
Jian




--
TJ Piggot
[EMAIL PROTECTED]
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Re: [gmx-users] special molecule

[Tamas Horvath]

Does it mean, that the itp file, generated by the PRODRG server should only used with  the gmx forcefield, or may it be combined with the other gromos frocefields, like the G43a2?On 6/13/06, 
Mark Abraham <[EMAIL PROTECTED]> wrote:
Dongsheng Zhang wrote:> Sear Mark,>> Since PRODRG server only generates a itp file by using gromos type force> field, do I have to use gromos force field for my whole protein-ligand> system if my ligand force field parameters are got from PRODRG? In
> another word, can I mix two different force field (one for protein, one> for ligand) in one system? Thanks!It's technically possible, if fiddly, but I'd strongly advise againstit. Force fields are mathematical constructs that are optimized to
produce reasonable model physics as an interacting unit. There is noreason to suppose that a bond stretching parameter is a measure of bondstrength, for example, because the other parameters in this force field
might have some quirk that this parameter is compensating for because ofthe optimization procedure. A force field is merely a point in ahigh-dimensional space which when used the right way has been shown to
produce a useful physical model. Thus there is no reason to suppose thata few of those high-dimensional space coordinates plus some others fromsome other force field will combine to produce a useful physical model.
Mark___gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] special molecule

[Tamas Horvath]

What I asked is, if I have to reorganise the pdb file, or renumber the residues, etc.On 6/13/06, Mark Abraham <
[EMAIL PROTECTED]> wrote:Tamas Horvath wrote:> So if I generate an .itp with PRODRG, and link it in the .top file, then
> grompp can use the original .pdb file? Or it's not that simple?The order of the [ molecules ] section will have to correspond to theorder in the structure file you supply with -c to grompp, but if you
read the grompp manpage it is obvious that the format of that structurefile is irrelevant.Mark___gmx-users mailing list
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[gmx-users] pdb2gmx error, How to generate the gro and top file for a small molecular?

[SUN, Jian]

Dear all,
 
I am doing the simulation of a protein with a small molecular in its active site.
But unfortunately, pdb2gmx cannot generate the gro and top file for the small molecualr?
I am using the oplsaa force field, who can tell me how to generate the gro and top files?
 
Thanks a lot
Jian
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[gmx-users] problem with selenomethionine residues

[Sridhar Acharya]

Hi,
When I am running the mdrun for position restrain the program terminates 
giving the following error. The protein molecule contains 16 selenomethionine residues,

the topology for which was got from the PRODRG server.

When run in GROMACS 3.2.1 version
===
Wrote pdb files with previous and current coordinates
Fatal error: ci = -2147483648 should be in 0 .. 6782 [FILE nsgrid.c, LINE 
218] 


When run in GROMACS 3.3.1 version
===
Fatal error:
Too many LINCS warnings (12461) - aborting to avoid logfile runaway.
This normally happens when your system is not sufficiently equilibrated,or 
if you are changing lambda too fast in free energy simulations. 
If you know what you are doing you can adjust the lincs warning threshold 
in your mdp file, but normally it is better to fix the problem.


Looking forward for ur response,
regards


sridhar

--
Sridhar Acharya, M
Senior Research Fellow
Lab of Computational Biology
CDFD, Gandipet Campus
Hyderabad. AP. INDIA
http://www.cdfd.org.in
email: [EMAIL PROTECTED]
Phone: Lab: 08413-235467*2044
Mobile: 9866147193


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org:CDFD;Computational Biology
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title:Senior Research Fellow
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Re: [gmx-users] regarding visualizing the output

[Tsjerk Wassenaar]

Hi Lali,In VMD you can view .xtc files directly. Check the gromacs archive or the VMD manual. Besides, you can use trjconv with -b and -e to extract a certain time frame. Please check the Gromacs manual or try trjconv -h (also to find out what else is possible).
Best regards,TsjerkOn 6/13/06, lalitha selvam <[EMAIL PROTECTED]> wrote:
hello sir,1.i ran simulation for 2 ns.i want to view the structure from 1500 to
2000 frames at every 25 ps.how to get it in pdb strucutres of the abovewanted frames.2.with the use of trjconv i had one pdb file converted from one frame. i'mviewing that structure with VMD, but when i'm trying to load in NOC software
i'm not able to view.cant we view that pdb structures converted from gromacsin other visualization software.please anyone explain me.regardslali.s_
Cox & Kings presents 'Win a trip for 2 to Austria' Contest. Click herehttp://www.coxandkings.com/cms/products/specialpromotions/?link=view&CM_ID=78
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http://www.gromacs.org/mailing_lists/users.php-- Tsjerk A. Wassenaar, M.Sc.Groningen Biomolecular Sciences and Biotechnology Institute (GBB)Dept. of Biophysical Chemistry
University of GroningenNijenborgh 49747AG Groningen, The Netherlands+31 50 363 4336
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