Re: [gmx-users] (no) superlinear Scaling on Opterons

[David van der Spoel]

Jens Krueger wrote:
> Hello,
> 
> there have been multiple reports on the list of superlinear scaling on
> AMD Opterons of the 200 series.
> 
> We have recently purchased a small cluster with the following
> configuration for each compute node:
> - 2x Opteron 2218 (4 cores per node)
> - 2 GB RAM
> - Supermicro H8DM8 mainboard
> - Mellanox PCI-E x8 Infiniband (running with OFED-1.2 and mvapich2)
> - Rockscluster 4.3
> - Gromacs-3.3.1

try grompp -shuffle
> 
> 
> For the DPPC benchmark we achieve the following numbers:
> 
> cores ns/day speedup
> 
> 01 0.289 1.00
> 02 0.487 1.69
> 04 0.768 2.66
> 08 1.330 4.60
> 12 1.776 6.15
> 16 2.137 7.39
> 20 2.550 8.82
> 
> 
> Compared to the benchmark section
> (http://www.gromacs.org/content/view/25/38/) and other published data
> (e.g. http://biowulf.nih.gov/apps/gromacs/bench-3.3.1.html) the
> performance drops to soon when using more cpu's. In fact we are far away
> from superlinear scaling and the performance on 20 cores is only half as
> good as on the biowulf cluster.
> We systematically checked the hardware and tried different compiler and
> MPI, all giving no or only minor improvement.
> 
> Has anybody hands on an Opteron cluster with cpu's from the 2000 series?
> It would be of immense value for us to get reference data from a similar
> machine.
> 
> 
> Thanks,
> 
> Jens
> 
> 
> 
> 
> 
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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Re: [gmx-users] grompp not recognizing mdp file parameters

[David van der Spoel]

toma0052 wrote:

Hello,
 It seems that I am having a problem in that grompp is not recognizing
the parameters that I enter into an mdp file, nor is it recognizing the text
in the .top file.  When I run a simulation, the output that I get is as
follows:

ERROR: invalid enum 'md' for variable integrator, using 'md'
Next time use one of: 'md' 'steep' 'cg' 'bd' 'sd' 'nm' 'l-bfgs' 'tpi'
ERROR: invalid enum 'grid' for variable ns-type, using 'Grid'
Next time use one of: 'Grid' 'Simple'
ERROR: invalid enum 'xyz' for variable pbc, using 'xyz'
Next time use one of: 'xyz' 'no' 'full'
ERROR: invalid enum 'PME' for variable coulombtype, using 'Cut-off'
Next time use one of: 'Cut-off' 'Reaction-Field' 'Generalized-Reaction-Field'
'PME' 'Ewald' 'PPPM' 'Poisson' 'Switch' 'Shift' 'User' 'Generalized-Born'
'Reaction-Field-nec' 'Encad-shift' 'PME-User'
ERROR: invalid enum 'yes' for variable optimize_fft, using 'no'
Next time use one of: 'no' 'yes'
ERROR: invalid enum 'berendsen' for variable tcoupl, using 'No'
Next time use one of: 'No' 'Berendsen' 'Nose-Hoover' 'yes' 'Andersen'
'Andersen-interval'
ERROR: invalid enum 'berendsen' for variable Pcoupl, using 'No'
Next time use one of: 'No' 'Berendsen' 'Parrinello-Rahman' 'Isotropic'
ERROR: invalid enum 'Semiisotropic' for variable Pcoupltype, using
'Isotropic'
Next time use one of: 'Isotropic' 'Semiisotropic' 'Anisotropic'
'Surface-Tension'
ERROR: invalid enum 'all-bonds' for variable constraints, using 'none'
Next time use one of: 'none' 'h-bonds' 'all-bonds' 'h-angles' 'all-angles'
checking input for internal consistency...
sh: /lib/cpp: No such file or directory
processing coordinates...
---
Program grompp, VERSION 3.3.1
Source code file: grompp.c, line: 448

Fatal error:
number of coordinates in coordinate file (area_1.03_1.gro, 17365)
 does not match topology (dppc.top, 0)
---

 What could be the problem here?  Is this just some simple formatting
error that I've missed?  I have run simulations before, and everything seemed
to work out fine.  The run above is simply the same files from the successful
simulation copied into a new directory with a few alterations made to the mdp
file.  If my other files still run, why are essentially the same files not
recognized when put into a new directory?



maybe you have a DOS formatted file? try dos2unix or something like that.

what platform are you running on?


--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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Re: [gmx-users] human readable input for g_covar

[Tsjerk Wassenaar]

Hi Michael,

I have a modified version of trjconv to extract velocities from a .trr and
write them to a .xtc file. You can send me a mail off-list if you're
interested.

Best,

Tsjerk

On 10/4/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
>
> Hi:
> I am involving in a project to analyse the vibrational spectrum of a
> peptide. i am trying to do covariance analysis with  the velocity data in a
> .trr file using g_covar, since it doesn't take velocity by default, my plan
> is to output that in a human readable file and swat that with the coordinate
> data, but the program wouldn't take human readable input either. it is there
> a easy way to translate the data back to .trr format or it is there a
> different way to do this task?
>
> many thanks
> regards
> Michael
>
>
> ---
> 快来参加博狂终级PK，IPod Nano等你来拿！(
> http://d1.sina.com.cn/sina/limeng3/mail_zhuiyu/2007/mail_zhuiyu_20070918.html)
>
> ===
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-- 
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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[gmx-users] human readable input for g_covar

[mdaf]

Hi: 
I am involving in a project to analyse the vibrational spectrum of a peptide. i 
am trying to do covariance analysis with  the velocity data in a .trr file 
using g_covar, since it doesn't take velocity by default, my plan is to output 
that in a human readable file and swat that with the coordinate data, but the 
program wouldn't take human readable input either. it is there a easy way to 
translate the data back to .trr format or it is there a different way to do 
this task? 

many thanks 
regards 
Michael 


---
快来参加博狂终级PK，IPod Nano等你来拿！( 
http://d1.sina.com.cn/sina/limeng3/mail_zhuiyu/2007/mail_zhuiyu_20070918.html )

===
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[gmx-users] (no) superlinear Scaling on Opterons

[Jens Krueger]

Hello,

there have been multiple reports on the list of superlinear scaling on
AMD Opterons of the 200 series.

We have recently purchased a small cluster with the following
configuration for each compute node:
- 2x Opteron 2218 (4 cores per node)
- 2 GB RAM
- Supermicro H8DM8 mainboard
- Mellanox PCI-E x8 Infiniband (running with OFED-1.2 and mvapich2)
- Rockscluster 4.3
- Gromacs-3.3.1


For the DPPC benchmark we achieve the following numbers:

cores ns/day speedup

01 0.289 1.00
02 0.487 1.69
04 0.768 2.66
08 1.330 4.60
12 1.776 6.15
16 2.137 7.39
20 2.550 8.82


Compared to the benchmark section
(http://www.gromacs.org/content/view/25/38/) and other published data
(e.g. http://biowulf.nih.gov/apps/gromacs/bench-3.3.1.html) the
performance drops to soon when using more cpu's. In fact we are far away
from superlinear scaling and the performance on 20 cores is only half as
good as on the biowulf cluster.
We systematically checked the hardware and tried different compiler and
MPI, all giving no or only minor improvement.

Has anybody hands on an Opteron cluster with cpu's from the 2000 series?
It would be of immense value for us to get reference data from a similar
machine.


Thanks,

Jens


-- 
Dr. Jens Krueger

Institute of Biophotonics
School of Biomedical Science and Engineering
National Yang-Ming University
155, Li-Non St., Sec. 2
Taipei, 112, Taiwan (R.O.C.)

mobile: 0921452940

http://www.ym.edu.tw/~wfischer

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version:2.1
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Re: [gmx-users] getting a good .gro file from a pdb file while the topology is ready

[Allen Smith]

In message <[EMAIL PROTECTED]> (on 3
October 2007 19:09:54 -0400), [EMAIL PROTECTED] (Allen Smith)
wrote:
>In message <[EMAIL PROTECTED]> (on 4 October 2007 04:04:05 +1000),
>[EMAIL PROTECTED] (Mark Abraham) wrote:
>>Allen Smith wrote:
>>> Umm... the atom numbers (not just the numbers of residues) are going to
>>> need to correspond between the .top and .gro files.
>>
>>I think the OP meant changing the number of molecules in the [molecules] 
>>section of the .top file. I expect that within each molecule in the 
>>structure file the order of the atoms must agree between with the 
>>topology file. Certainly the order of the molecules in the [molecules] 
>>section must correspond to that in the structure file.
>>
>>However, the atom numbers cannot (in general), match in order between 
>>structure and topology file for any system with more than one copy of a 
>>molecule (e.g. solvent). For simple solvated systems where one gets 
>>focussed on the solute, it can look like correspondence is occurring and 
>>thus might be necessary :-)
>
>However, in this case, the original poster has not only edited down the
>solvent, but the bilayer. I am reasonably certain that if I put in more than
>one copy of something which is in a .rtp file and _not_ in, say, ions.itp,
>then it will be in both times in the .top file (after all, two
>different-position glycines are in twice in the .top file...).

Correction: multiple copies of an ion present in the .pdb file input into
pdb2gmx come out multiple times in the .top file (even though the ion is in
ions.itp), at least for a case in which they're not distinguished by chain
id from the rest.

-Allen

-- 
Allen Smith http://cesario.rutgers.edu/easmith/
September 11, 2001  A Day That Shall Live In Infamy II
"They that can give up essential liberty to obtain a little temporary
safety deserve neither liberty nor safety." - Benjamin Franklin
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Re: [gmx-users] Re: getting a good .gro file from a pdb file while thetopology is ready

[Allen Smith]

In message <[EMAIL PROTECTED]> (on 3 October 2007
19:41:40 -0400), [EMAIL PROTECTED] (Justin A. Lemkul) wrote:
>You can use editconf to directly convert a .pdb file into .gro format.

Good point.

>-Justin
>
>Quoting maria goranovic <[EMAIL PROTECTED]>:
>
>>  Thank you all for the replies and help.

Quite welcome; hope my reply was at least slightly helpful...

>> The main reason I was messing with
>> pdb2gmx, editconf and genbox was mainly to convert my pdb into a nice .gro
>> format file, which I could input into grompp. I understand grompp can take a
>> pdb file for input as well. Does it not need any "box" information, like the
>> box type, or the dimensions ? If it can infer these directly from the pdb,
>> or these details can be specified in the .mdp file then my problems are
>> solved.

With regard to the box, that you are dealing with a planar system might,
again, make a difference here; this is not my area, however.

   -Allen

>> I will look more carefully into the -h ..
>>
>> Thank you !
>>
>> -Maria
>>
>>
>> Message: 6
>> > Date: Thu, 04 Oct 2007 03:51:27 +1000
>> > From: Mark Abraham <[EMAIL PROTECTED]>
>> > Subject: Re: [gmx-users] getting a good .gro file from a pdb file
>> >while the   topology is ready
>> > To: Discussion list for GROMACS users 
>> > Message-ID: <[EMAIL PROTECTED]>
>> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>> >
>> >
>> > Hydrogen takes up volume too... your equilibration will be less
>> > troublesome if your whole system "fits" at the start of the equilibration.
>> >
>> > It sounds like it might be worth your while reading the introductory
>> > part of pdb2gmx -h, editconf -h, genbox -h, etc. so you have an idea
>> > what each tool is trying to do. Following a recipe without appreciating
>> > what you're doing is fine, until you go to change the recipe, which is
>> > what you're trying to do here. :-)
>> >
>> > Mark
>> >
>> >
>> > --
>> >
>> > Message: 7
>> > Date: Thu, 04 Oct 2007 04:04:05 +1000
>> > From: Mark Abraham <[EMAIL PROTECTED]>
>> > Subject: Re: [gmx-users] getting a good .gro file from a pdb file
>> >while the   topology is ready
>> > To: Discussion list for GROMACS users 
>> > Message-ID: <[EMAIL PROTECTED]>
>> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>> >
>> > Allen Smith wrote:
>> > > In message <[EMAIL PROTECTED]>
>> > (on
>> > > 3 October 2007 19:13:51 +0200), [EMAIL PROTECTED] (maria
>> > goranovic)
>> > > wrote:
>> > >> Hi,
>> > >>
>> > >> I had a large bilayer in .gro and .top gromacs format files
>> > >
>> > > Bilayer? I believe there are some specific things for doing planar
>> > periodic
>> > > boundary conditions (or planar infinite system conditions), but I am not
>> > > familiar with them.
>> >
>> > Yeah but they're in the .mdp and not the issue here :-)


-- 
Allen Smith   http://cesario.rutgers.edu/easmith/
February 1, 2003   Space Shuttle Columbia
Ad Astra Per Aspera To The Stars Through Asperity
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Re: [gmx-users] Re: getting a good .gro file from a pdb file while thetopology is ready

[Justin A. Lemkul]

You can use editconf to directly convert a .pdb file into .gro format.

-Justin

Quoting maria goranovic <[EMAIL PROTECTED]>:

>  Thank you all for the replies and help. The main reason I was messing with
> pdb2gmx, editconf and genbox was mainly to convert my pdb into a nice .gro
> format file, which I could input into grompp. I understand grompp can take a
> pdb file for input as well. Does it not need any "box" information, like the
> box type, or the dimensions ? If it can infer these directly from the pdb,
> or these details can be specified in the .mdp file then my problems are
> solved.
>
> I will look more carefully into the -h ..
>
> Thank you !
>
> -Maria
>
>
> Message: 6
> > Date: Thu, 04 Oct 2007 03:51:27 +1000
> > From: Mark Abraham <[EMAIL PROTECTED]>
> > Subject: Re: [gmx-users] getting a good .gro file from a pdb file
> >while the   topology is ready
> > To: Discussion list for GROMACS users 
> > Message-ID: <[EMAIL PROTECTED]>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> >
> > Hydrogen takes up volume too... your equilibration will be less
> > troublesome if your whole system "fits" at the start of the equilibration.
> >
> > It sounds like it might be worth your while reading the introductory
> > part of pdb2gmx -h, editconf -h, genbox -h, etc. so you have an idea
> > what each tool is trying to do. Following a recipe without appreciating
> > what you're doing is fine, until you go to change the recipe, which is
> > what you're trying to do here. :-)
> >
> > Mark
> >
> >
> > --
> >
> > Message: 7
> > Date: Thu, 04 Oct 2007 04:04:05 +1000
> > From: Mark Abraham <[EMAIL PROTECTED]>
> > Subject: Re: [gmx-users] getting a good .gro file from a pdb file
> >while the   topology is ready
> > To: Discussion list for GROMACS users 
> > Message-ID: <[EMAIL PROTECTED]>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > Allen Smith wrote:
> > > In message <[EMAIL PROTECTED]>
> > (on
> > > 3 October 2007 19:13:51 +0200), [EMAIL PROTECTED] (maria
> > goranovic)
> > > wrote:
> > >> Hi,
> > >>
> > >> I had a large bilayer in .gro and .top gromacs format files
> > >
> > > Bilayer? I believe there are some specific things for doing planar
> > periodic
> > > boundary conditions (or planar infinite system conditions), but I am not
> > > familiar with them.
> >
> > Yeah but they're in the .mdp and not the issue here :-)
> >
> > >> which I truncated to make a smaller bilayer, and added some more water
> > >> molecules, using programs other than gromacs. The final output I have
> > is a
> > >> pdb file with complete solvation, and a topology file which I obtained
> > from
> > >> the original top file by simply changing the number of residues of each
> > >> group in the last section.
> > >
> > > Umm... the atom numbers (not just the numbers of residues) are going to
> > need
> > > to correspond between the .top and .gro files.
> >
> > I think the OP meant changing the number of molecules in the [molecules]
> > section of the .top file. I expect that within each molecule in the
> > structure file the order of the atoms must agree between with the
> > topology file. Certainly the order of the molecules in the [molecules]
> > section must correspond to that in the structure file.
> >
> > However, the atom numbers cannot (in general), match in order between
> > structure and topology file for any system with more than one copy of a
> > molecule (e.g. solvent). For simple solvated systems where one gets
> > focussed on the solute, it can look like correspondence is occurring and
> > thus might be necessary :-)
> >
> > Mark
> >
> >
> > --
> >
> > ___
> > gmx-users mailing list
> > gmx-users@gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> >
> > End of gmx-users Digest, Vol 42, Issue 11
> > *
> >
>
>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
>



==

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/

==
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Re: [gmx-users] getting a good .gro file from a pdb file while the topology is ready

[Allen Smith]

In message <[EMAIL PROTECTED]> (on 4 October 2007 04:04:05 +1000),
[EMAIL PROTECTED] (Mark Abraham) wrote:
>Allen Smith wrote:
>> In message <[EMAIL PROTECTED]> (on
>> 3 October 2007 19:13:51 +0200), [EMAIL PROTECTED] (maria goranovic)
>> wrote:
>>> Hi,
>>>
>>> I had a large bilayer in .gro and .top gromacs format files
>> 
>> Bilayer? I believe there are some specific things for doing planar periodic
>> boundary conditions (or planar infinite system conditions), but I am not
>> familiar with them.
>
>Yeah but they're in the .mdp and not the issue here :-)

Ah, thank you.

>
>>> which I truncated to make a smaller bilayer, and added some more water
>>> molecules, using programs other than gromacs. The final output I have is a
>>> pdb file with complete solvation, and a topology file which I obtained from
>>> the original top file by simply changing the number of residues of each
>>> group in the last section.
>> 
>> Umm... the atom numbers (not just the numbers of residues) are going to need
>> to correspond between the .top and .gro files.
>
>I think the OP meant changing the number of molecules in the [molecules] 
>section of the .top file. I expect that within each molecule in the 
>structure file the order of the atoms must agree between with the 
>topology file. Certainly the order of the molecules in the [molecules] 
>section must correspond to that in the structure file.
>
>However, the atom numbers cannot (in general), match in order between 
>structure and topology file for any system with more than one copy of a 
>molecule (e.g. solvent). For simple solvated systems where one gets 
>focussed on the solute, it can look like correspondence is occurring and 
>thus might be necessary :-)

However, in this case, the original poster has not only edited down the
solvent, but the bilayer. I am reasonably certain that if I put in more than
one copy of something which is in a .rtp file and _not_ in, say, ions.itp,
then it will be in both times in the .top file (after all, two
different-position glycines are in twice in the .top file...). There may be
some dependence on chain labels from the original .pdb file, however, from
observations; I suppose that it's possible that it would partially depend on
whether the name is in aminoacid.dat or something like that, although that
seems a bit weird. It doesn't sound like the original poster is using
something that's in an .itp file that the original poster has constructed.

-Allen

P.S. Incidentally, I note the irritating habit of pdb2gmx (including in
3.3.2) of converting what is already labeled as SOL to HOH, even though
genbox inserts water molecules as SOL.

-- 
Allen Smith  http://cesario.rutgers.edu/easmith/
There is only one sound argument for democracy, and that is the argument
that it is a crime for any man to hold himself out as better than other men,
and, above all, a most heinous offense for him to prove it. - H. L. Mencken
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[gmx-users] Re: getting a good .gro file from a pdb file while the topology is ready

[maria goranovic]

 Thank you all for the replies and help. The main reason I was messing with
pdb2gmx, editconf and genbox was mainly to convert my pdb into a nice .gro
format file, which I could input into grompp. I understand grompp can take a
pdb file for input as well. Does it not need any "box" information, like the
box type, or the dimensions ? If it can infer these directly from the pdb,
or these details can be specified in the .mdp file then my problems are
solved.

I will look more carefully into the -h ..

Thank you !

-Maria


Message: 6
> Date: Thu, 04 Oct 2007 03:51:27 +1000
> From: Mark Abraham <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] getting a good .gro file from a pdb file
>while the   topology is ready
> To: Discussion list for GROMACS users 
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
> Hydrogen takes up volume too... your equilibration will be less
> troublesome if your whole system "fits" at the start of the equilibration.
>
> It sounds like it might be worth your while reading the introductory
> part of pdb2gmx -h, editconf -h, genbox -h, etc. so you have an idea
> what each tool is trying to do. Following a recipe without appreciating
> what you're doing is fine, until you go to change the recipe, which is
> what you're trying to do here. :-)
>
> Mark
>
>
> --
>
> Message: 7
> Date: Thu, 04 Oct 2007 04:04:05 +1000
> From: Mark Abraham <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] getting a good .gro file from a pdb file
>while the   topology is ready
> To: Discussion list for GROMACS users 
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Allen Smith wrote:
> > In message <[EMAIL PROTECTED]>
> (on
> > 3 October 2007 19:13:51 +0200), [EMAIL PROTECTED] (maria
> goranovic)
> > wrote:
> >> Hi,
> >>
> >> I had a large bilayer in .gro and .top gromacs format files
> >
> > Bilayer? I believe there are some specific things for doing planar
> periodic
> > boundary conditions (or planar infinite system conditions), but I am not
> > familiar with them.
>
> Yeah but they're in the .mdp and not the issue here :-)
>
> >> which I truncated to make a smaller bilayer, and added some more water
> >> molecules, using programs other than gromacs. The final output I have
> is a
> >> pdb file with complete solvation, and a topology file which I obtained
> from
> >> the original top file by simply changing the number of residues of each
> >> group in the last section.
> >
> > Umm... the atom numbers (not just the numbers of residues) are going to
> need
> > to correspond between the .top and .gro files.
>
> I think the OP meant changing the number of molecules in the [molecules]
> section of the .top file. I expect that within each molecule in the
> structure file the order of the atoms must agree between with the
> topology file. Certainly the order of the molecules in the [molecules]
> section must correspond to that in the structure file.
>
> However, the atom numbers cannot (in general), match in order between
> structure and topology file for any system with more than one copy of a
> molecule (e.g. solvent). For simple solvated systems where one gets
> focussed on the solute, it can look like correspondence is occurring and
> thus might be necessary :-)
>
> Mark
>
>
> --
>
> ___
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>
> End of gmx-users Digest, Vol 42, Issue 11
> *
>



-- 
Maria G.
Technical University of Denmark
Copenhagen
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RE: [gmx-users] protein in membrane

[Itamar Kass]

Shalom,

The easy way is to remove lipids such that a hole in the membrane will form, 
put your protein in in run. Or you can try the protocol in Faraldo-Gomez, J. 
D., Smith, G. R., and Sansom, M. S. (2002) "Setting up and optimization of 
membrane protein  
simulations. European Biophysics Journal" 31(3), 217-227.

You will probably need mdrun_make_hole.tar.gz which is used as a modifier of 
gromacs 3.1.4.

Best,
Itamar


-Original Message-
From: [EMAIL PROTECTED] on behalf of mahbubeh zarrabi
Sent: Thu 04/10/2007 06:52
To: gmx-users@gromacs.org
Subject: [gmx-users] protein in membrane
 
Dear all
i want to insert protein in popc.which practical
protocol in gromacs is useful for me?
thanks


  

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Yahoo! TV.
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[gmx-users] grompp not recognizing mdp file parameters

[toma0052]

Hello,
 It seems that I am having a problem in that grompp is not recognizing
the parameters that I enter into an mdp file, nor is it recognizing the text
in the .top file.  When I run a simulation, the output that I get is as
follows:

ERROR: invalid enum 'md' for variable integrator, using 'md'
Next time use one of: 'md' 'steep' 'cg' 'bd' 'sd' 'nm' 'l-bfgs' 'tpi'
ERROR: invalid enum 'grid' for variable ns-type, using 'Grid'
Next time use one of: 'Grid' 'Simple'
ERROR: invalid enum 'xyz' for variable pbc, using 'xyz'
Next time use one of: 'xyz' 'no' 'full'
ERROR: invalid enum 'PME' for variable coulombtype, using 'Cut-off'
Next time use one of: 'Cut-off' 'Reaction-Field' 'Generalized-Reaction-Field'
'PME' 'Ewald' 'PPPM' 'Poisson' 'Switch' 'Shift' 'User' 'Generalized-Born'
'Reaction-Field-nec' 'Encad-shift' 'PME-User'
ERROR: invalid enum 'yes' for variable optimize_fft, using 'no'
Next time use one of: 'no' 'yes'
ERROR: invalid enum 'berendsen' for variable tcoupl, using 'No'
Next time use one of: 'No' 'Berendsen' 'Nose-Hoover' 'yes' 'Andersen'
'Andersen-interval'
ERROR: invalid enum 'berendsen' for variable Pcoupl, using 'No'
Next time use one of: 'No' 'Berendsen' 'Parrinello-Rahman' 'Isotropic'
ERROR: invalid enum 'Semiisotropic' for variable Pcoupltype, using
'Isotropic'
Next time use one of: 'Isotropic' 'Semiisotropic' 'Anisotropic'
'Surface-Tension'
ERROR: invalid enum 'all-bonds' for variable constraints, using 'none'
Next time use one of: 'none' 'h-bonds' 'all-bonds' 'h-angles' 'all-angles'
checking input for internal consistency...
sh: /lib/cpp: No such file or directory
processing coordinates...
---
Program grompp, VERSION 3.3.1
Source code file: grompp.c, line: 448

Fatal error:
number of coordinates in coordinate file (area_1.03_1.gro, 17365)
 does not match topology (dppc.top, 0)
---

 What could be the problem here?  Is this just some simple formatting
error that I've missed?  I have run simulations before, and everything seemed
to work out fine.  The run above is simply the same files from the successful
simulation copied into a new directory with a few alterations made to the mdp
file.  If my other files still run, why are essentially the same files not
recognized when put into a new directory?

Thanks,
Mike

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Re: [gmx-users] getting a good .gro file from a pdb file while the topology is ready

[Xavier Periole]

On Wed, 3 Oct 2007 19:13:51 +0200
 "maria goranovic" <[EMAIL PROTECTED]> wrote:

Hi,

I had a large bilayer in .gro and .top gromacs format files which I
truncated to make a smaller bilayer, and added some more water molecules,
using programs other than gromacs. The final output I have is a pdb file
with complete solvation, and a topology file which I obtained from the
original top file by simply changing the number of residues of each group in
the last section. My goal is now to obtain a proper input to the grompp
program, which is a good .gro and a .top file. The latter I already have.

pdb2gmx is not working for me with the error:

%Fatal error:
%Residue 'DPP' not found in residue topology database



This is because the pdb file truncates the name of your DPPC
(I guess) molecules. just edit the pdb file you have and change
the "DPP " to "DPPC". in vi you can do this by typing:
:1,$ s/DPP /DPPC/

then editconf would allwo you to get a gro file but the pdb should
be ok.


Q1. How do I add my topology file to the database ?


you have it already.


Q2. The second question is regarding the use of genbox and editconf. How can
I specify the box size such that no more solvent is added to the system ?


just add the box size at the end of the gro file.


Using the following two options adds more solvent to the system, which I do
not really need

% editconf -f solvated-fully-vmd.pdb -box 12.3 12.3 17.3 -angles 90 90 90
-bt triclinic -o input.gro -c -center 0 0 0
% genbox -cp input.gro -o output.gro -cs spc216.gro


no need.


I chose the box size based on the maximum and minimum coordinates of the
heavy atoms of the system. Does one have to do the above procedure by
iteratively changing the box size until genbox adds no more solvent ?


just add the box size at the end of the gro file:
boxX boxX boxZ



Please do not be  ruthless, I am new to gromacs :)

Thank you,


--
Maria G.
Technical University of Denmark
Copenhagen


-
XAvier Periole - PhD

1- Institute of Molecular Assemblies
 City University of New York - USA
2- Molecular Dynamics-Group
 University of Groningen - The Netherlands
http://md.chem.rug.nl/~periole
-
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[gmx-users] protein in membrane

[mahbubeh zarrabi]

Dear all
i want to insert protein in popc.which practical
protocol in gromacs is useful for me?
thanks


  

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Re: [gmx-users] getting a good .gro file from a pdb file while the topology is ready

[Mark Abraham]

Allen Smith wrote:

In message <[EMAIL PROTECTED]> (on
3 October 2007 19:13:51 +0200), [EMAIL PROTECTED] (maria goranovic)
wrote:

Hi,

I had a large bilayer in .gro and .top gromacs format files


Bilayer? I believe there are some specific things for doing planar periodic
boundary conditions (or planar infinite system conditions), but I am not
familiar with them.


Yeah but they're in the .mdp and not the issue here :-)


which I truncated to make a smaller bilayer, and added some more water
molecules, using programs other than gromacs. The final output I have is a
pdb file with complete solvation, and a topology file which I obtained from
the original top file by simply changing the number of residues of each
group in the last section.


Umm... the atom numbers (not just the numbers of residues) are going to need
to correspond between the .top and .gro files.


I think the OP meant changing the number of molecules in the [molecules] 
section of the .top file. I expect that within each molecule in the 
structure file the order of the atoms must agree between with the 
topology file. Certainly the order of the molecules in the [molecules] 
section must correspond to that in the structure file.


However, the atom numbers cannot (in general), match in order between 
structure and topology file for any system with more than one copy of a 
molecule (e.g. solvent). For simple solvated systems where one gets 
focussed on the solute, it can look like correspondence is occurring and 
thus might be necessary :-)


Mark
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Re: [gmx-users] getting a good .gro file from a pdb file while the topology is ready

[Mark Abraham]

maria goranovic wrote:

Hi,

I had a large bilayer in .gro and .top gromacs format files which I 
truncated to make a smaller bilayer, and added some more water 
molecules, using programs other than gromacs. The final output I have is 
a pdb file with complete solvation, and a topology file which I obtained 
from the original top file by simply changing the number of residues of 
each group in the last section. My goal is now to obtain a proper input 
to the grompp program, which is a good .gro and a .top file. The latter 
I already have.


pdb2gmx is not working for me with the error:


The purpose of pdb2gmx is to infer topologies from structures. Since you 
have a working topology you don't need this step.



%Fatal error:
%Residue 'DPP' not found in residue topology database

Q1. How do I add my topology file to the database ?


Well, as above, you don't need it. Otherwise, you need to read chapter 5 
of the manual and figure out how it is done.


Q2. The second question is regarding the use of genbox and editconf. How 
can I specify the box size such that no more solvent is added to the 
system ?


I don't understand your objective. If you don't want to add more 
solvent, don't use genbox.


Using the following two options adds more solvent to the system, which I 
do not really need


% editconf -f solvated-fully-vmd.pdb -box 12.3 12.3 17.3 -angles 90 90 
90 -bt triclinic -o input.gro -c -center 0 0 0  
% genbox -cp input.gro -o output.gro -cs spc216.gro


I chose the box size based on the maximum and minimum coordinates of the 
heavy atoms of the system.


Hydrogen takes up volume too... your equilibration will be less 
troublesome if your whole system "fits" at the start of the equilibration.


It sounds like it might be worth your while reading the introductory 
part of pdb2gmx -h, editconf -h, genbox -h, etc. so you have an idea 
what each tool is trying to do. Following a recipe without appreciating 
what you're doing is fine, until you go to change the recipe, which is 
what you're trying to do here. :-)


Mark
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Re: [gmx-users] getting a good .gro file from a pdb file while the topology is ready

[Allen Smith]

In message <[EMAIL PROTECTED]> (on
3 October 2007 19:13:51 +0200), [EMAIL PROTECTED] (maria goranovic)
wrote:
>Hi,
>
>I had a large bilayer in .gro and .top gromacs format files

Bilayer? I believe there are some specific things for doing planar periodic
boundary conditions (or planar infinite system conditions), but I am not
familiar with them.

>which I truncated to make a smaller bilayer, and added some more water
>molecules, using programs other than gromacs. The final output I have is a
>pdb file with complete solvation, and a topology file which I obtained from
>the original top file by simply changing the number of residues of each
>group in the last section.

Umm... the atom numbers (not just the numbers of residues) are going to need
to correspond between the .top and .gro files.

>My goal is now to obtain a proper input to the
>grompp program, which is a good .gro and a .top file. The latter I already
>have.
>
>pdb2gmx is not working for me with the error:
>
>%Fatal error:
>%Residue 'DPP' not found in residue topology database
>
>Q1. How do I add my topology file to the database ?

What is DPP? Perhaps it's under another name in the original .top and .gro
files, in which case you should change the name in the .pdb file input to
that name?

>Q2. The second question is regarding the use of genbox and editconf. How can
>I specify the box size such that no more solvent is added to the system ?
>
>Using the following two options adds more solvent to the system, which I do
>not really need
>
>% editconf -f solvated-fully-vmd.pdb -box 12.3 12.3 17.3 -angles 90 90 90
>-bt triclinic -o input.gro -c -center 0 0 0

I tend to use -princ, to align the longest axis of the input with the
longest axis of the box (17.3 in your case). Not sure if that would be
advisable with a bilayer system, however.

>% genbox -cp input.gro -o output.gro -cs spc216.gro
>
>I chose the box size based on the maximum and minimum coordinates of the
>heavy atoms of the system.

Do heavy atoms include the oxygens in the waters? If so, then I would think
that that should be an adequate size (I trust you allowed for gromacs using
nanometers while PDB files use angstroms?); I would suspect things would be
too crowded otherwise. However, if you use -princ, you will probably need to
check to see exactly what dimensions it comes out to have prior to putting
it into the box, since it may align it differently than it is already
aligned.

>Does one have to do the above procedure by
>iteratively changing the box size until genbox adds no more solvent ?

If you don't want more solvent added, don't use genbox. The question will be
how to do this while making sure you don't have any vacuum spaces.

   -Allen

-- 
Allen Smith  http://cesario.rutgers.edu/easmith/
There is only one sound argument for democracy, and that is the argument
that it is a crime for any man to hold himself out as better than other men,
and, above all, a most heinous offense for him to prove it. - H. L. Mencken
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[gmx-users] getting a good .gro file from a pdb file while the topology is ready

[maria goranovic]

Hi,

I had a large bilayer in .gro and .top gromacs format files which I
truncated to make a smaller bilayer, and added some more water molecules,
using programs other than gromacs. The final output I have is a pdb file
with complete solvation, and a topology file which I obtained from the
original top file by simply changing the number of residues of each group in
the last section. My goal is now to obtain a proper input to the grompp
program, which is a good .gro and a .top file. The latter I already have.

pdb2gmx is not working for me with the error:

%Fatal error:
%Residue 'DPP' not found in residue topology database

Q1. How do I add my topology file to the database ?

Q2. The second question is regarding the use of genbox and editconf. How can
I specify the box size such that no more solvent is added to the system ?

Using the following two options adds more solvent to the system, which I do
not really need

% editconf -f solvated-fully-vmd.pdb -box 12.3 12.3 17.3 -angles 90 90 90
-bt triclinic -o input.gro -c -center 0 0 0
% genbox -cp input.gro -o output.gro -cs spc216.gro

I chose the box size based on the maximum and minimum coordinates of the
heavy atoms of the system. Does one have to do the above procedure by
iteratively changing the box size until genbox adds no more solvent ?

Please do not be  ruthless, I am new to gromacs :)

Thank you,


-- 
Maria G.
Technical University of Denmark
Copenhagen
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Re: [gmx-users] Re: Is there a test set for GROMACS 3.3.1 ?

[David van der Spoel]

maria goranovic wrote:
I could not see any obvious errors in either the log files or the out 
files in angles1 or angles125. grompp.out reports no warning or error 
either, do I did not change the maxwarn parameter anyway. Any other 
suggestions ? Or should I post the output or log files ?


Any other out files? checktpr.out or checkedr.out?
You can send the out files from one directory to me directly (off-list).

 


Then you have to do as it says and check the files in for example
angles1. Check whether grompp failed and if so why ( grompp.out).
You may
have to change the maxwarn parameter in the gmxtest.pl script.




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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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[gmx-users] Re: Is there a test set for GROMACS 3.3.1 ?

[maria goranovic]

I could not see any obvious errors in either the log files or the out files
in angles1 or angles125. grompp.out reports no warning or error either, do I
did not change the maxwarn parameter anyway. Any other suggestions ? Or
should I post the output or log files ?


Then you have to do as it says and check the files in for example
> angles1. Check whether grompp failed and if so why (grompp.out). You may
> have to change the maxwarn parameter in the gmxtest.pl script.
>
>
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Re: [gmx-users] g_rms

[Mark Abraham]

andrea carotti wrote:

So does the -Rmat option not produce a human-readable text file?

Hi, unfortunately I can't see this option in g_rms.
I'm using the v 3.3.1 and also on the reference page online there is not
-Rmat. Am i missing something?


Hmm, you're right. Installations that I know are 3.3.1 don't have this 
-Rmat option, but the g_rms in the GROMACS installation on my desktop 
machine reports itself as 3.3.1 and has this -Rmat option. Probably, I'm 
still running a beta 3.3.1 (and since I don't use this for more than 
manual checking I've never bothered to update the version!) and this 
option never made it to the production version. I can't think of any way 
to check this, however. Do the developers know?


Please accept my apologies for the misunderstanding.

Mark
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Re: [gmx-users] mdrun error after 2.6nS

[Mark Abraham]

Blaise Mathias-Costa wrote:
Hello Mark and Tsjerk, Thanks a lot for your suggestions. I have gone 
through that web site and it doesn't say anything very specific, for 
example if the system is not minimized properly it should have 
complained at the beginning, but the problem arises after 2.6nS!


No. The numerical equations are well-defined whether or not you 
minimize. Whether the system is numerically or physically stable is 
another matter, and things could fairly easily take many picoseconds to 
nanoseconds in a feedback loop to get bad enough to cause LINCS warnings.


The website can't be more specific, because proper system preparation is 
a bit of dark art and system-dependent.


I have searched in the archive, when somebody had similar problem with 
PR run David suggested to look for the "center-of-mass motion removal", 
to give POPC+Protein, but I dont have POPC in my system. In another case 
advised to reduce the time step, does it mean that I should reduce the 
time step from 0.002 to 0.001 and do the simulations from the beginning?


Yes. Making the integration time step smaller can help you relax away 
from bad numerical space into good ones... once equilibrated you can 
then try relaxing the time step back to 2fs.


Another suggestion was the computing power may not be sufficient, but I 
don't think this will be applicable for me, b'se I am running in 8 nodes 
each node is with 4 processors, and the unit cell size is ~96000 atoms 
in total.
 
What could be the most appropriate way to solve this problem?  Many 
thanks in  advance!


Find a reasonable equilibration protocol in the literature for a system 
similar to yours, try it out, and experiment.


Mark
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Re: [gmx-users] g_rms

[andrea carotti]

> So does the -Rmat option not produce a human-readable text file?
Hi, unfortunately I can't see this option in g_rms.
I'm using the v 3.3.1 and also on the reference page online there is not
-Rmat. Am i missing something?
Thanks
Andrea


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Re: [gmx-users] mdrun error after 2.6nS

[Tsjerk Wassenaar]

Hi Blaise,

Check for the first occurrence of the error in the log file and match the
atom numbers against your .gro file to see which residue is involved from
the beginning. Also, do you have non-standard residues/metal ions? Tell more
about the system and what you're trying to do.

Best,

Tsjerk

On 10/3/07, Blaise Mathias-Costa <[EMAIL PROTECTED]> wrote:
>
> Hello Mark and Tsjerk, Thanks a lot for your suggestions. I have gone
> through that web site and it doesn't say anything very specific, for example
> if the system is not minimized properly it should have complained at the
> beginning, but the problem arises after 2.6nS!
> I have searched in the archive, when somebody had similar problem with PR
> run David suggested to look for the "center-of-mass motion removal", to give
> POPC+Protein, but I dont have POPC in my system. In another case advised to
> reduce the time step, does it mean that I should reduce the time step from
> 0.002 to 0.001 and do the simulations from the beginning?
>
> Another suggestion was the computing power may not be sufficient, but I
> don't think this will be applicable for me, b'se I am running in 8 nodes
> each node is with 4 processors, and the unit cell size is ~96000 atoms in
> total.
>
> What could be the most appropriate way to solve this problem?  Many thanks
> in  advance!
>
> Kind Regards,
> Blaise
>
> Blaise Mathias Costa, PhD
> Department of Pharmacology and Experimental Neuroscience
> University of Nebraska Medical Center
> Omaha, NE 68198-5800, USA.
> Tel: 001 402 559 7132
>
> [EMAIL PROTECTED] wrote: -
>
> To: Discussion list for GROMACS users 
> From: Mark Abraham <[EMAIL PROTECTED]>
> Sent by: [EMAIL PROTECTED]
> Date: 10/02/2007 12:29PM
> Subject: Re: [gmx-users] mdrun error after 2.6nS
>
> Blaise Mathias-Costa wrote:
> > Hi all,
> >
> > The mdrun stopped  after 2.6nS  after writing this error:
> > Step 1321571, time 2643.14 (ps)  LINCS WARNING
>
> See http://wiki.gromacs.org/index.php/Errors#LINCS_warnings
>
> Mark
> ___
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>



-- 
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] mdrun error after 2.6nS

[Blaise Mathias-Costa]

Hello Mark and Tsjerk, Thanks a lot for your suggestions. I have gone through that web site and it doesn't say anything very specific, for example if the system is not minimized properly it should have complained at the beginning, but the problem arises after 2.6nS! I have searched in the archive, when somebody had similar problem with PR run David suggested to look for the "center-of-mass motion removal", to give POPC+Protein, but I dont have POPC in my system. In another case advised to reduce the time step, does it mean that I should reduce the time step from 0.002 to 0.001 and do the simulations from the beginning?  Another suggestion was the computing power may not be sufficient, but I don't think this will be applicable for me, b'se I am running in 8 nodes each node is with 4 processors, and the unit cell size is ~96000 atoms in total. What could be the most appropriate way to solve this problem?  Many thanks in  advance! Kind Regards,BlaiseBlaise Mathias Costa, PhDDepartment of Pharmacology and Experimental NeuroscienceUniversity of Nebraska Medical CenterOmaha, NE 68198-5800, USA.Tel: 001 402 559 7132 [EMAIL PROTECTED] wrote: -To: Discussion list for GROMACS users From: Mark Abraham <[EMAIL PROTECTED]>Sent by: [EMAIL PROTECTED]Date: 10/02/2007 12:29PMSubject: Re: [gmx-users] mdrun error after 2.6nSBlaise Mathias-Costa wrote:> Hi all,> > The mdrun stopped  after 2.6nS  after writing this error:> Step 1321571, time 2643.14 (ps)  LINCS WARNINGSee http://wiki.gromacs.org/index.php/Errors#LINCS_warningsMark___gmx-users mailing list    gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease 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 [EMAIL PROTECTED]Can't post? Read http://www.gromacs.org/mailing_lists/users.php___
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Re: [gmx-users] g_rms

[Mark Abraham]

andrea carotti wrote:

Hi again,

If you read g_rms -h like I suggested last time, you'll see that -f2 and 
-s serve the same purpose with the former using a trajectory and the 
latter a single structure. That document doesn't say what happens when 
you use both... but the operation you're trying to do doesn't need both!

the -h option is my standard first step when i use all the gmx-tools and I've 
read and done it like every time.


So does the -Rmat option not produce a human-readable text file?

Mark
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Re: [gmx-users] g_rms

[andrea carotti]

Hi again,

> If you read g_rms -h like I suggested last time, you'll see that -f2 and 
> -s serve the same purpose with the former using a trajectory and the 
> latter a single structure. That document doesn't say what happens when 
> you use both... but the operation you're trying to do doesn't need both!
the -h option is my standard first step when i use all the gmx-tools and I've 
read and done it like every time.
I've tried to use -f2 option without using the -s and it comes out with the 
error "topol.tpr not found" so it's not "so optional", but it's needed also 
when using the -f2 option..
I've alsto tried to use the -s with my traj without using the -f2 option but it 
creates a matrix 2200x2200.
However the problem still remain unsolved or misunderstanded.
If i use the my only working command line
g_rms -f 2200.pdb -f2 33.pdb -s ref.pdb -n -o -m -bin 

I obtain a rmsd.xvg with 2 columns. So, which is the meaning of that value? a 
mean of all the rmsd calculated for that frame in respect to the other 33 refs?
Thanks
Andrea

-- 

Andrea Carotti
Dipartimento di Chimica e Tecnologia del Farmaco
Via del Liceo, 1
06123 Perugia, Italy
phone: +39 075 585 5169
fax: +39 075 585 5161
www http://rpg.unipg.it
personal www http://iris.chimfarm.unipg.it/users/andcar

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Re: [gmx-users] g_rms

[Mark Abraham]

andrea carotti wrote:

Hi,
You should be getting such a 2200x33 matrix. My guess is that the 
command line or files that you're using are not what you think they

are :-)
my command line is 

g_rms -f 2200.pdb -f2 33.pdb -s ref.pdb -n -o -m -bin 


If you read g_rms -h like I suggested last time, you'll see that -f2 and 
-s serve the same purpose with the former using a trajectory and the 
latter a single structure. That document doesn't say what happens when 
you use both... but the operation you're trying to do doesn't need both!



Note that the pdbs (traj and ref) have the same number of atoms (same
structure).
During the calculation i can see that it is creating the 2200x33 matrix,
but on the rmsd.xvg i find only two columns. From the xpm and dat files
i can't extract the matrix (i don't know) to a text file.


There's an option to g_rms that writes a text matrix for importing into 
R. Look it up.


Mark
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Re: [gmx-users] g_rms

[andrea carotti]

Hi,
> You should be getting such a 2200x33 matrix. My guess is that the 
> command line or files that you're using are not what you think they
> are :-)
my command line is 

g_rms -f 2200.pdb -f2 33.pdb -s ref.pdb -n -o -m -bin 

Note that the pdbs (traj and ref) have the same number of atoms (same
structure).
During the calculation i can see that it is creating the 2200x33 matrix,
but on the rmsd.xvg i find only two columns. From the xpm and dat files
i can't extract the matrix (i don't know) to a text file.
I hope this could clarify better my question
Thanks
Andrea



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Re: [gmx-users] Re: Re: Is there a test set for GROMACS 3.3.1 ? (David van der Spoel)

[David van der Spoel]

maria goranovic wrote:

Hi,

I did the following, please let me know if more details are required 
regarding the architecture etc.


- installed 3.3.1 as per instructions
- downloaded the test set for 3.3.2 from the ftp site
- source ~/gromacs-3.3.1/bin/GMXRC
- cd gmxtest
- ./gmxtest.pl simple

The output for this is:

FAILED. Check files in angles1
FAILED. Check files in angles125
FAILED. Check files in bham
FAILED. Check files in bonds1
FAILED. Check files in bonds125
FAILED. Check files in dih1
FAILED. Check files in dih125
FAILED. Check files in g96angles1
FAILED. Check files in g96angles125
FAILED. Check files in g96bonds1
FAILED. Check files in g96bonds125
FAILED. Check files in imp1
FAILED. Check files in imp36
FAILED. Check files in morse
FAILED. Check files in rb1
FAILED. Check files in rb125
16 out of 16 simple tests FAILED




Then you have to do as it says and check the files in for example 
angles1. Check whether grompp failed and if so why (grompp.out). You may 
have to change the maxwarn parameter in the gmxtest.pl script.




--
Maria G.
Technical University of Denmark
Copenhagen


Message: 2
Date: Tue, 02 Oct 2007 20:48:09 +0200
From: David van der Spoel < [EMAIL PROTECTED]
>
Subject: Re: [gmx-users] Is there a test set for GROMACS 3.3.1 ?
To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>
Message-ID: <[EMAIL PROTECTED]
>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

maria goranovic wrote:
 > Hi,
 >
 > The wiki refers to a test set for the upcoming 3.3.2 version. Is
there a
 > test set for the 3.3.1 version as well ?
 >
 > I tried running the test set for 3.3.2 after installing 3.3.1 and
ran
 > into a host of errors, but that is probably because of the different
 > version ?

these errors could indeed be related to the version differences. 3.3.1
is correct except for some funky bonded potential though.
however if I test it I get:

[miro:~] % source vanilla-3.3.1/bin/GMXRC

[miro:~/GROMACS/gmxtest] % ./gmxtest.pl simple
All 16 simple tests PASSED

Please give some more detailed report on what you've tried.
 >
 > Here are some of the errors anyway:
 >
 > No topol.tpr file in angles1. grompp failed
 > FAILED. Check files in angles1
 > No topol.tpr file in angles125. grompp failed
 > FAILED. Check files in angles125
 > No topol.tpr file in bham. grompp failed
 > FAILED. Check files in bham
 > No topol.tpr file in bonds1. grompp failed
 > FAILED. Check files in bonds1
 >
 >
 > Thank you for the help,
 >
 > --
 > Maria G.
 > Technical University of Denmark
 > Copenhagen
 >
 >
 >

 >
 > ___
 > gmx-users mailing listgmx-users@gromacs.org

 > http://www.gromacs.org/mailman/listinfo/gmx-users
 > Please search the archive at http://www.gromacs.org/search before
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 > www interface or send it to [EMAIL PROTECTED]
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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]
[EMAIL PROTECTED]
   http://folding.bmc.uu.se






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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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Re: [gmx-users] g_order in GROMACS 3.3.2 and 3.3.1

[Justin A. Lemkul]

The g_order tool requires a unique sort of index group.  There's lots of
discussion about it documented in the list archives.  In short, you need to use
make_ndx to generate an index file that contains _only_ groups pertaining to the
carbon atoms you want to analyze, separated by chain (i.e., sn1.ndx/sn2.ndx). 
Each atom type should be in a separate group.

-Justin

Quoting ªL´­µ½ <[EMAIL PROTECTED]>:

> Hello, gmx developer and users:
>
>   After modifying the source code of g_order in GROMACS 3.3.1 with Bug
> #84 and compiling again, I got the error message when using g_order to
> calculate order parameteters of POPC bilayer.
>   The error message is : grp 1 does not have same number of elements as
> grp1.
>   Command line about generating .ndx file and using g_order are listed
> below :
>
>   make_ndx -f  XXX.pdb -o index.ndx  (XXX.pdb is the original
> structure of the system)  (I chose system or POP as my index group)
>
>   g_order  -f YYY.pdb -n index.ndx -s ZZZ.tpr -o -od
>
>
>It will be gotten the same error message when using GROMACS 3.3.2
> version.
>
>Is something wrong in my process ?
>
>Thank you.



==

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/

==
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[gmx-users] Re: Re: Is there a test set for GROMACS 3.3.1 ? (David van der Spoel)

[maria goranovic]

Hi,

I did the following, please let me know if more details are required
regarding the architecture etc.

- installed 3.3.1 as per instructions
- downloaded the test set for 3.3.2 from the ftp site
- source ~/gromacs-3.3.1/bin/GMXRC
- cd gmxtest
- ./gmxtest.pl simple

The output for this is:

FAILED. Check files in angles1
FAILED. Check files in angles125
FAILED. Check files in bham
FAILED. Check files in bonds1
FAILED. Check files in bonds125
FAILED. Check files in dih1
FAILED. Check files in dih125
FAILED. Check files in g96angles1
FAILED. Check files in g96angles125
FAILED. Check files in g96bonds1
FAILED. Check files in g96bonds125
FAILED. Check files in imp1
FAILED. Check files in imp36
FAILED. Check files in morse
FAILED. Check files in rb1
FAILED. Check files in rb125
16 out of 16 simple tests FAILED


-- 
Maria G.
Technical University of Denmark
Copenhagen
>
>
> Message: 2
> Date: Tue, 02 Oct 2007 20:48:09 +0200
> From: David van der Spoel <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] Is there a test set for GROMACS 3.3.1 ?
> To: Discussion list for GROMACS users 
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> maria goranovic wrote:
> > Hi,
> >
> > The wiki refers to a test set for the upcoming 3.3.2 version. Is there a
> > test set for the 3.3.1 version as well ?
> >
> > I tried running the test set for 3.3.2 after installing 3.3.1 and ran
> > into a host of errors, but that is probably because of the different
> > version ?
>
> these errors could indeed be related to the version differences. 3.3.1
> is correct except for some funky bonded potential though.
> however if I test it I get:
>
> [miro:~] % source vanilla-3.3.1/bin/GMXRC
>
> [miro:~/GROMACS/gmxtest] % ./gmxtest.pl simple
> All 16 simple tests PASSED
>
> Please give some more detailed report on what you've tried.
> >
> > Here are some of the errors anyway:
> >
> > No topol.tpr file in angles1. grompp failed
> > FAILED. Check files in angles1
> > No topol.tpr file in angles125. grompp failed
> > FAILED. Check files in angles125
> > No topol.tpr file in bham. grompp failed
> > FAILED. Check files in bham
> > No topol.tpr file in bonds1. grompp failed
> > FAILED. Check files in bonds1
> >
> >
> > Thank you for the help,
> >
> > --
> > Maria G.
> > Technical University of Denmark
> > Copenhagen
> >
> >
> > 
> >
> > ___
> > gmx-users mailing listgmx-users@gromacs.org
> > http://www.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 [EMAIL PROTECTED]
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> --
> David.
> 
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  75124 Uppsala, Sweden
> phone:  46 18 471 4205  fax: 46 18 511 755
> [EMAIL PROTECTED][EMAIL PROTECTED]   http://folding.bmc.uu.se
> 
>
>
>
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[gmx-users] g_order in GROMACS 3.3.2 and 3.3.1

[林揚善]

Hello, gmx developer and users:

  After modifying the source code of g_order in GROMACS 3.3.1 with Bug #84 
and compiling again, I got the error message when using g_order to calculate 
order parameteters of POPC bilayer.
  The error message is : grp 1 does not have same number of elements as 
grp1.
  Command line about generating .ndx file and using g_order are listed 
below :

  make_ndx -f  XXX.pdb -o index.ndx  (XXX.pdb is the original 
structure of the system)  (I chose system or POP as my index group)
  
  g_order  -f YYY.pdb -n index.ndx -s ZZZ.tpr -o -od 


   It will be gotten the same error message when using GROMACS 3.3.2 
version.

   Is something wrong in my process ?

   Thank you.___
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Re: [gmx-users] g_rms

[Mark Abraham]

andrea carotti wrote:

Hi and thanks for answering to my previous question.
Now I'm calculating the rmsd between two trajectories (-f2 option).
One is made by 2200 frames and the other has 33 frames..Now I've some
doubt about the output (rmsd.xvg), cause this file has only two columns
with 2200 rows ...i was imaging that it should have 2200 rows and 33
columns, am I wrong? 


You should be getting such a 2200x33 matrix. My guess is that the 
command line or files that you're using are not what you think they are :-)



The second question is something that is already been asked before..it
could be usefull to obtain the matrix 2200 x 33 in a human readable
file. Is it possible without hacking the code? Perhaps using external
scripts? 


There's a human readable matrix form that can already be written. Check 
out g_rms -h


Mark
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