[gmx-users] Potential energy problem

[madhumita das]

Hi Gromacs users,

I am doing the protein lipid system packing step and thus shrinking and
minimizing the system alternately but after first minimization rest of all
minimization steps show E pot=nan and no minimization step occurs in the
em.log file. How to get rid of this problem? Please help.


Yours faithfully,

Madhumita Das.
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Re: [gmx-users] Potential energy problem

[Mark Abraham]

On 14/09/2011 5:29 PM, madhumita das wrote:

Hi Gromacs users,

I am doing the protein lipid system packing step and thus shrinking 
and minimizing the system alternately but after first minimization 
rest of all minimization steps show E pot=nan and no minimization step 
occurs in the em.log file. How to get rid of this problem? Please help.


It is likely that your system is 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up


Mark
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[gmx-users] simulation with amber10 and gromacs 4.5.1

[vijayaraj ramadoss]

Hello Users,

Previous I have done simulation of small protein using Amber10 with ff99sb 
force field. I did the same calculation using the gromacs 4.5.1 with amber 
ff99sb force field. I found a loop segment takes much more fluctuation with 
gromacs simulation and which was not observed with the amber10 simulation. can 
anyone explain me why this happens. 

regards,
vrk.
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Re: [gmx-users] simulation with amber10 and gromacs 4.5.1

[Justin A. Lemkul]

vijayaraj ramadoss wrote:

Hello Users,

Previous I have done simulation of small protein using Amber10 with 
ff99sb force field. I did the same calculation using the gromacs 4.5.1 
with amber ff99sb force field. I found a loop segment takes much more 
fluctuation with gromacs simulation and which was not observed with the 
amber10 simulation. can anyone explain me why this happens.




Did you run replicates of each system, or are you basing your observations on a 
single trajectory?  You need to compare properly sampled systems.  A single 
trajectory is generally not enough to make reliable conclusions.


-Justin

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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] Re: Gromacs_trouble

[Justin A. Lemkul]

Please keep this discussion on the gmx-users list.  I have only limited 
experience with MARTINI, but there are others on the list more experienced than 
I.  See comments below.


Du Jiangfeng (BIOCH) wrote:

Dear Justin,

Thank you very much again of your help.

So far, I appended some sentences to make carboxylated residues in Martini 
force field and I got my protein model. However, no matter how to perform EM, 
the MD simulation was always blown up because of too many links warnings.

I presume the problem is still in the values of the modified residues in the itp file. 


What I did is :
1   the usage of "atom2cg_v2.1.awk" converting my GLA domain into coarse grained model. 
(In "atom2cg_v2.1.awk", I added new lines for GLA).
2  the usage of "seq2itp.pl" making itp file for my GLA domain. (In 
"seq2itp,pl", I appended some lines for GLA residue).

That's it.

But it seems not to work. 

Does my way is correct? Or should I shift to another method to figure it out? 



There is nothing wrong with the way you've constructed the topology, from what I 
can see.  That's the standard MARTINI protocol for proteins, anyway.  What's 
more likely the problem is the values you've assigned either for bonded or 
nonbonded interactions of your new species.  You said earlier you assigned some 
arbitrary values, but you haven't provided any of that information.



I also attach some files that I changed and the GLA domain. (In the files of "atom2cg"  and 
"seq2itp", the things what I added were marked with "#append", so you can track them 
easily).



The structure file emcgmR.gro shows that residue CGU-26 is especially strange. 
It appears as if it is shearing apart.  I suspect that may be part of your problem.


-Justin


Thank you in advance,
Best Wishes,
Jiang. 

 



Du Jiangfeng (BIOCH) wrote:

Hi Guys,

I want to run a protein which contains some carboxylated residues into a 
membrane. I have had to add a special residue into itp file since there is no 
any description in normal itp for GLA residue. I admit some values I added for 
GLA residue were ambiguous because I don't know the exact values.

After that, the system was blowing up when MD simulation with the following 
warning:

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.029057, max 0.152326 (between atoms 81 and 82)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 43 44   37.00.0145   0.0148  0.0145
 81 82   67.50.0078   0.0090  0.0078
 89 90   34.70.0059   0.0060  0.0059

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.056864, max 0.359219 (between atoms 81 and 82)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 43 44   35.60.0145   0.0147  0.0145
 81 82   78.60.0078   0.0106  0.0078
 89 90   34.30.0059   0.0060  0.0059


Apparently, some values about GLA residue are wrong in itp file. But I really 
don't know how to set a correct value for it.



Without seeing what you actually did and knowing what force field you're using, 
it's impossible to help.  Missing parameters need to be derived in a manner 
compatible with the original force field (no small task).


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

-Justin



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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] building GROMACS 4.5.4 on Power6 with CMAKE

[Rossen Apostolov]

Hi,

On 9/13/11 4:27 PM, Mark Abraham wrote:

On 14/09/2011 12:20 AM, Marcin Zielinski wrote:

Ok,

Using -DGMX_ACCELERATION=Power6 brings a plethora of new errors 
during the compilation.


Firstly, including config.h inside the fortran .F kernel files for 
power6 is causing problems with
their parsing using xlf. adding -WF,-qfpp didn't help. Had to provide 
a modified xlf.cfg config file

for XLF (cppoptions = -P, instead of -C)
and pass it on with -F option and then add -qarch=pwr6 (all passed 
manually) for compilation of
each power6 kernel .F file. That fixed the problem with the 
compilation of Power6 kernels part.


Is there any more handy way of doing that? I've noticed that upon 
using Power6, cmake generates
Fortran_DEFINES and Fortran_FLAGS inside 
src/gmxlib/CMakeFiles/gmx.dir/flags.make file.
They somehow can not be modified from the command line. Same goes for 
the preprocessor flags.

(-DCMAKE_CPP_FLAGS do not work?).



You can also modify flags by editing CMakeCache.txt and rerunning cmake 
- if you don't pass options it should preserve what's been already found 
in the cache file.




Secondly, now I get something else:
Linking C shared library libmd.so
xlc: 1501-218 (W) file ../gmxlib/libgmx.so.6 contains an incorrect 
file suffix

../gmxlib/libgmx.so.6: In function `__bss_start':
(*ABS*+0x1025cb00): multiple definition of `_edata'
../gmxlib/libgmx.so.6: In function `__data_start':
(.data+0x8): multiple definition of `__dso_handle'
/usr/lib64/gcc/powerpc64-suse-linux/4.3/crtbeginS.o:(.data.rel+0x0): 
first defined here

../gmxlib/libgmx.so.6: In function `_fini':
(.opd+0x30): multiple definition of `_fini'
/usr/lib64/gcc/powerpc64-suse-linux/4.3/../../../../lib64/crti.o:initfini.c:(.opd+0x18): 
first defined here

../gmxlib/libgmx.so.6: In function `_init':
(.opd+0x18): multiple definition of `_init'
/usr/lib64/gcc/powerpc64-suse-linux/4.3/../../../../lib64/crti.o:initfini.c:(.opd+0x0): 
first defined here

../gmxlib/libgmx.so.6: In function `_end':
(*ABS*+0x10268b20): multiple definition of `_end'
../gmxlib/libgmx.so.6: In function `__bss_start':
(*ABS*+0x1025cb00): multiple definition of `__bss_start'
/usr/lib64/gcc/powerpc64-suse-linux/4.3/crtendS.o:(.dtors+0x0): 
multiple definition of `__DTOR_END__'

../gmxlib/libgmx.so.6:(.dtors+0x8): first defined here
/usr/bin/ld: error in ../gmxlib/libgmx.so.6(.eh_frame); no 
.eh_frame_hdr table will be created.

make[2]: *** [src/mdlib/libmd.so.6] Error 1
make[1]: *** [src/mdlib/CMakeFiles/md.dir/all] Error 2
make: *** [all] Error 2


Beats me, sorry.



me too :(

Rossen


Mark

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[gmx-users] equilibration: run time or number of steps?

[Juliette N.]

Hello,

For the equilibration one usually looks at the total energy or the
observable of interest to be independent of time. I wanted to figure out
when we are referring to equilibration which of the run time or n_steps
parameters are important. One could run 1,000,000 steps with dt of 0.001 ps
or 0.002 ps ending up with 1 and 2 ns simulation times. Can we infer that 2
ns trial is closer to equilibration or one needs to look at the n_steps
regardless of total run time. I hope my question in clear to receive your
feedback.

Thanks,
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Re: [gmx-users] equilibration: run time or number of steps?

[Justin A. Lemkul]

Juliette N. wrote:

Hello,

For the equilibration one usually looks at the total energy or the 
observable of interest to be independent of time. I wanted to figure out 
when we are referring to equilibration which of the run time or n_steps 
parameters are important. One could run 1,000,000 steps with dt of 0.001 
ps or 0.002 ps ending up with 1 and 2 ns simulation times. Can we infer 
that 2 ns trial is closer to equilibration or one needs to look at the 
n_steps regardless of total run time. I hope my question in clear to 
receive your feedback.
 


I would say time is more important than the number of steps (if dt is altered 
accordingly).  With dt = 0.1 I can run a billion steps and only achieve 
1 ps of simulation time, which is not nearly enough for any relevant quantity to 
converge.  Stability, of course, is an issue and hence we cannot simply run a 
million steps with dt = 0.01 ps and expect an atomistic simulation to be stable.


Proper equilibration is done such that the observables of interest have 
converged.  What those observables are depend entirely upon the system in 
question, but you certainly have to have stable energy, temperature, pressure, 
etc (depending on the ensemble).


-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] building GROMACS 4.5.4 on Power6 with CMAKE

[Szilárd Páll]

Hi,

I have not followed the entire discussion so I might be completely
wrong, I might be fill in some gaps.

> Firstly, including config.h inside the fortran .F kernel files for power6 is
> causing problems with
> their parsing using xlf. adding -WF,-qfpp didn't help. Had to provide a
> modified xlf.cfg config file
> for XLF (cppoptions = -P, instead of -C)
> and pass it on with -F option and then add -qarch=pwr6 (all passed manually)
> for compilation of
> each power6 kernel .F file. That fixed the problem with the compilation of
> Power6 kernels part.
>
> Is there any more handy way of doing that? I've noticed that upon using
> Power6, cmake generates
> Fortran_DEFINES and Fortran_FLAGS inside
> src/gmxlib/CMakeFiles/gmx.dir/flags.make file.
> They somehow can not be modified from the command line. Same goes for the
> preprocessor flags.
> (-DCMAKE_CPP_FLAGS do not work?).

If you want to pass *global* flags to the the C++ compiler you can do
that through CMAKE_CXX_FLAGS variable (note: CXX not CPP!). However,
if you happen to need flags only for certain files or internal
libraries, it's slightly more tricky; it requires the file/target
property COMPILE_FLAGS to be modified fron inside the CMake scripts.

> Secondly, now I get something else:
> Linking C shared library libmd.so
> xlc: 1501-218 (W) file ../gmxlib/libgmx.so.6 contains an incorrect file
> suffix
> ../gmxlib/libgmx.so.6: In function `__bss_start':
> (*ABS*+0x1025cb00): multiple definition of `_edata'
> ../gmxlib/libgmx.so.6: In function `__data_start':
> (.data+0x8): multiple definition of `__dso_handle'
> /usr/lib64/gcc/powerpc64-suse-linux/4.3/crtbeginS.o:(.data.rel+0x0): first
> defined here
> ../gmxlib/libgmx.so.6: In function `_fini':
> (.opd+0x30): multiple definition of `_fini'
> /usr/lib64/gcc/powerpc64-suse-linux/4.3/../../../../lib64/crti.o:initfini.c:(.opd+0x18):
> first defined here
> ../gmxlib/libgmx.so.6: In function `_init':
> (.opd+0x18): multiple definition of `_init'
> /usr/lib64/gcc/powerpc64-suse-linux/4.3/../../../../lib64/crti.o:initfini.c:(.opd+0x0):
> first defined here
> ../gmxlib/libgmx.so.6: In function `_end':
> (*ABS*+0x10268b20): multiple definition of `_end'
> ../gmxlib/libgmx.so.6: In function `__bss_start':
> (*ABS*+0x1025cb00): multiple definition of `__bss_start'
> /usr/lib64/gcc/powerpc64-suse-linux/4.3/crtendS.o:(.dtors+0x0): multiple
> definition of `__DTOR_END__'
> ../gmxlib/libgmx.so.6:(.dtors+0x8): first defined here
> /usr/bin/ld: error in ../gmxlib/libgmx.so.6(.eh_frame); no .eh_frame_hdr
> table will be created.
> make[2]: *** [src/mdlib/libmd.so.6] Error 1
> make[1]: *** [src/mdlib/CMakeFiles/md.dir/all] Error 2
> make: *** [all] Error 2

That unfortunately looks like a nasty symbol multiple definition
issue. My guess is that the symbols xlc is complaining about are
defined in libgmx.so.6 and when the linker tries to do the final
linking stage it ends up choking due to conflicts with symbols is some
library where the respective symbols are defined (or in fact originate
from).

AFAIK this could happen when one provides a linker option
"-lsomething" to a compile-only command iso a [compile+] link command:
$ g++ -c foo.cpp -o foo.o -lbar
$ g++ foo.o -o foobar

Let me know if this makes sense, you could look at the verbose make
output (make VERBOSE=1) and maybe you notice something like this.

Cheers,
--
Szilárd

> cheers,
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Re: [gmx-users] equilibration: run time or number of steps?

[Mark Abraham]

On 15/09/2011 5:13 AM, Juliette N. wrote:

Hello,

For the equilibration one usually looks at the total energy or the 
observable of interest to be independent of time. I wanted to figure 
out when we are referring to equilibration which of the run time or 
n_steps parameters are important. One could run 1,000,000 steps with 
dt of 0.001 ps or 0.002 ps


Your use of constraints is a critical factor in determining the largest 
time step that will lead to simulation stability.


Mark

ending up with 1 and 2 ns simulation times. Can we infer that 2 ns 
trial is closer to equilibration or one needs to look at the n_steps 
regardless of total run time. I hope my question in clear to receive 
your feedback.


Thanks,





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[gmx-users] Fwd: Gromacs_trouble

[Mark Abraham]

Hi,

Please keep discussions on the mailing list. I have no experience of 
Martini, and don't have the ability to give my time for individual help. 
I would advise you to simplify your system as much as you can. Get a 
stable simulation of a single glutamate residue working, then change to 
a singly-carboxylated residue, and slowly work up. Now when things go 
wrong you can work out what is wrong.


Mark

 Original Message 
Subject:Gromacs_trouble
Date:   Wed, 14 Sep 2011 17:19:01 +0200
From:   Du Jiangfeng (BIOCH) 
To: mark.abra...@anu.edu.au 



Hi Mark,

Thanks for your attention.

In fact, i appended the carboxylated Glutamate values into martini force field, 
and I got my protein model. However, no matter how to perform EM, the MD 
simulation was brown up because of too many links warns.

I presume the problem is still in the values of the modified residues in the 
itp file. Could you help me more? If you don't mind, I would like to attach the 
method of how I did it.

Thank you in advance,

Best Wishes,

Jiang.





On 8/09/2011 6:29 PM, Du Jiangfeng (BIOCH) wrote:

 Dear Everyone,

 I am going to simulate the interaction of prothrombin's Gla domain with 
membrane in martini force field. Here I encountered a problem: there are 10 
modified GLUs in GLA domain. Martini force field can't recognize them. How 
should I overcome this problem?

 What I want to do now is to add this modified residue into martini force 
field, but I do not know whether it is feasible or logical? What's worse, I 
really don't know what is BNLN, BNKB or ANGL? Where can I get some references 
about this story?


Depending on the details of the modified GLU, you will need to consider
the points made at
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field,
http://www.gromacs.org/Documentation/How-tos/Parameterization and in the
Martini documentation.

Mark


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[gmx-users] Re: strangeness in gro file

[Sweta Iyer]

> 
> Hi Mark,
I did a grompp without the temperature coupling and generated a .tpr file. From 
that I generated a .gro file using editconf. What it looks like now is it 
starts numbering from 1 -29, which is where the first monomer ends, again 1-29 
for the second monomer and then its continuous numbering from then on! DMPC 
starts from 30 and its continuous till the end of the coordinate file! This 
still wouldnt let me generate an index file as the numbering still overlaps 
between the two protein chains. :(
Would it have a made a difference if, instead of including a TER after one 
chain of the complex, I just changed the chain id to distinguish them as  
separate entities in the original pdb file that i used to begin with? I would 
have thought it shouldnt make a difference and has nothing to do with this 
issue!

Cheers
Sweta
> 
> Message: 1
> Date: Tue, 13 Sep 2011 16:12:49 +1000
> From: Mark Abraham 
> Subject: Re: [gmx-users] Strangeness in gro file
> To: Discussion list for GROMACS users 
> Message-ID: <4e6ef461.7000...@anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> On 13/09/2011 3:27 PM, Sweta Iyer wrote:
>> Hi all,
>> I am trying to use the g_membed tool to insert my protein into a DMPC 
>> membrane.
>> My protein is a dimer and hence I separated the two monomers by a TER card 
>> in the original pdb file before pdb2gmx step for gromacs to identify it as 
>> teo separate entities.. I then merged my protein file with that of the 
>> membrane and added water and ions to it. Then when I went ahead to make an 
>> index file I notice that the numbering of residues is not continuous in my 
>> gro file, ie, it starts from residue 1-29 of a monomer, then again 1-29 of 
>> the second monomer, 1-128 for the DMPC moleculaes and similarly for the SOL 
>> and ions as well. As a result, I cannot exactly specify residue number for 
>> my index file to specify the two protein groups as different as the residue 
>> numbers overlap. Even when i try to do it, i get an error message saying 
>> Atom 1 in multiple T-Coupling groups  Is there a way to re number them so 
>> that there is continuity or is there another way around to making the index 
>> file? I have not seen this the previously when I have made an index file. I 
>> am using gmx ver
> sion 4.5.4 and the 53a6 forcefield. I am not attaching the gro file here as 
> it is quite lengthy.
> 
> Only atom numbering within a [moleculetype] is relative to that atom. 
> Index files need atom numbers from the whole system. These are 
> constructed from the first [molecules] entry being 1 to n, then the 
> second [molecules] entry n+1 to n+n (if that entry is the same 
> [moleculetype], etc. The numbers assigned to atoms and residues in the 
> coordinate file supplied to grompp are ignored. Only the atom and 
> molecule ordering is significant (and must match the .top).
> 
> Do a grompp using an .mdp file that does not use any index groups (e.g. 
> disable T-coupling), and pass that resulting .tpr to editconf to get a 
> coordinate file back out. I expect the atom numbering will now be from 1 
> to N where N is the number of atoms in the system. Use that coordinate 
> file to work out your index groups (with make_ndx or otherwise). Later, 
> you and grompp will be talking the same language. :)
> 
> Mark
> 
> 
> 
> --
> 
> Message: 2
> Date: Tue, 13 Sep 2011 11:44:52 +0530
> From: aiswarya pawar 
> Subject: Re: [gmx-users] g_dist error
> To: Discussion list for GROMACS users 
> Message-ID:
>   
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Mark,
> 
> the command line goes like this-
> 
> g_dist -f md.xtc -s md.tpr -dist 0.5 -e 500
> 
> the index file has group1- a_1322 ( this is just a single atom from a
> protein. its in sidechain)
>  group2- a_OW ( this is water atoms)
> 
> now as per the utility it should give me and output as-
> 
> t:1 1322 a 54119 OW 0.389
> 
> but am getting something different
> 
> On Tue, Sep 13, 2011 at 11:24 AM, Mark Abraham wrote:
> 
>> On 13/09/2011 3:40 PM, aiswarya pawar wrote:
>> 
>> 
>> Hi Mark,
>> 
>> The -dist option says- print all the atoms in group 2 that are closer than
>> a certain distance to the center of mass of group 1.
>> That means it should give me the distance from OW to protein atom.
>> 
>> 
>> If you choose correct groups that are correctly defined with respect to
>> your trajectory and use a large enough distance cutoff.
>> 
>> 
>> 
>> And when am already specifying only one atom from protein ie say 1322. why
>> do i get this kind of output-
>> 
>> 
>> We can't tell. We don't know what your command line is, what's in your
>> simulation system, the contents of your index groups, or which groups you've
>> selected for which role. Clearly something is not working properly, and our
>> time constraints mean that we're going to assume you've done something
>> wrong, in the absence of evidence to the contrary.
>> 
>> Mark
>> 
>>

Re: [gmx-users] Re: strangeness in gro file

[Mark Abraham]

On 15/09/2011 11:23 AM, Sweta Iyer wrote:





Hi Mark,
I did a grompp without the temperature coupling and generated a .tpr 
file. From that I generated a .gro file using editconf. What it looks 
like now is it starts numbering from 1 -29, which is where the first 
monomer ends, again 1-29 for the second monomer and then its 
continuous numbering from then on!


That looks weird.

DMPC starts from 30 and its continuous till the end of the coordinate 
file! This still wouldnt let me generate an index file as the 
numbering still overlaps between the two protein chains. :(


As I said last time, the atom numbers in the coordinate file are not 
significant. You can make them all zero, and make_ndx will still let you 
make an index file that will work. Only the ordering is significant. The 
contortions that I thought would regularize the numbers were only to 
help you double check what is happening.


Would it have a made a difference if, instead of including a TER after 
one chain of the complex, I just changed the chain id to distinguish 
them as  separate entities in the original pdb file that i used to 
begin with? I would have thought it shouldnt make a difference and has 
nothing to do with this issue!


I don't know.

Mark
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Re: [gmx-users] Re: strangeness in gro file

[Justin A. Lemkul]

Mark Abraham wrote:

  On 15/09/2011 11:23 AM, Sweta Iyer wrote:





Hi Mark,
I did a grompp without the temperature coupling and generated a .tpr 
file. From that I generated a .gro file using editconf. What it looks 
like now is it starts numbering from 1 -29, which is where the first 
monomer ends, again 1-29 for the second monomer and then its 
continuous numbering from then on!


That looks weird.



I've seen this for dimeric proteins where the chains are identical.  A little 
annoying to deal with.


DMPC starts from 30 and its continuous till the end of the coordinate 
file! This still wouldnt let me generate an index file as the 
numbering still overlaps between the two protein chains. :(


As I said last time, the atom numbers in the coordinate file are not 
significant. You can make them all zero, and make_ndx will still let you 
make an index file that will work. Only the ordering is significant. The 
contortions that I thought would regularize the numbers were only to 
help you double check what is happening.


Would it have a made a difference if, instead of including a TER after 
one chain of the complex, I just changed the chain id to distinguish 
them as  separate entities in the original pdb file that i used to 
begin with? I would have thought it shouldnt make a difference and has 
nothing to do with this issue!


I don't know.



genconf -renumber solves all of this rather easily, I think.

-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] how to handle different atom names between pdb and rtp files.

[Jianguo Li]

You can either use -ighn option in pdb2gmx or mannualy rename the atom names in 
the pdb file.

Cheers,
Jianguo 





From: KONG Xian 
To: gmx-users@gromacs.org
Sent: Tuesday, 13 September 2011 15:36:41
Subject: [gmx-users] how to handle different atom names between pdb and rtp 
files.

 
Hello, I’ve got a pdb file,but while I convert it to gro files, I met such 
problem:
 
Atom HA in residue MET 1 was not found in rtp entry MET with 11 atoms while 
sorting atoms
 
I find that in the rtp files of the ff files, the H atom linked with C-alpha is 
called H, but in the pdb file, the same hydrogen atom is called HA, I think 
this 
may be the problem. 

 
So, my problem is, how to convert my pdb files to make the atom names 
consistent 
between the pdb and rtp files?
 
 
KONG Xian
Tsinghua University, Beijing, China
2011/9/13

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[gmx-users] Re: amb2gmx.pl to convert GLYCAM topology

[Yun Shi]

Hi Alan,

For example, in the Glycam_06g.dat file, you can find:

OH-CG-CG-OS   1   -1.10  0.0-1


So this dihedral parameter has a force constant of -1.10, and this is what I
mean by "GLYCAM force field assigns negative force constants to some
dihedrals".

I did try the GMX45 approach, and using the conversion factor 4.184, I got a
difference of about 0.05%.  I am not sure if this is caused not setting step
size in the sander minimization.

Regards,
Yun







Date: Tue, 13 Sep 2011 12:03:10 +0100
From: Alan 
Subject: Re: [gmx-users] Re: amb2gmx.pl to convert GLYCAM topology
To: Discussion list for GROMACS users 
Message-ID:
   
Content-Type: text/plain; charset="utf-8"

Hi Yun,

Have you read http://ambermd.org/formats.html?

In particular, this note:

"""
NOTE: *the atom numbers in the following arrays that describe bonds, angles,
and dihedrals are coordinate array indexes for runtime speed. The true atom
number equals the absolute value of the number divided by three, plus one.
In the case of the dihedrals, if the fourth atom is negative, this implies
that the dihedral is an improper. If the third atom is negative, this
implies that the end group interations are to be ignored. End group
interactions are ignored, for example, in dihedrals of various ring systems
(to prevent double counting of 1-4 interactions) and in multiterm dihedrals.
*
"""

I may be failing to understand what you mean by "GLYCAM force field assigns
negative force constants to some dihedrals".

Anyway, since GMX 4.5 can go without RB convertions, you can do this:

acpype -x disac.inpcrd -p disac.prmtop --gmx45

If you have sander, you can do just one step of EM and compare against one
step EM with GMX. Do the proper conversions and Energies diff should be <
0.001%.

Cheers,

Alan

On 12 September 2011 21:21, Yun Shi  wrote:

> Hi all,
>
> I am not a CS person, but I did find something in acpype.py as
>
> .
> if phase in [0, 180]:
> properDihedralsGmx45.append([
>
> item[0].atoms, phaseRaw,
> > kPhi, period])
> > if not self.gmx45:
> > if kPhi > 0: V[period] = 2 * kPhi * cal
> > if period == 1:
> > C[0] += 0.5 * V[period]
> > if phase == 0:
> > C[1] -= 0.5 * V[period]
> > else:
> > C[1] += 0.5 * V[period]
> > elif period == 2:
> > ..
> >
> > kPhi here seems to be the dihedral force constant, and it seems if kPhi <
> > 0, no value will be assigned to C[0], C[1], C[2] ...
> >
> > I wonder if the negative dihedral force constants problem could be solved
> > by changing 'kPhi > 0' to 'kPhi != 0' for acpype?
> >
> > Thanks,
> >
> > Yun
> >
> > --
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>
>
>
> --
> Alan Wilter SOUSA da SILVA, DSc
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> CB10 1SD, Hinxton, Cambridge, UK
> +44 1223 49 4588
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> Date: Tue, 13 Sep 2011 16:46:44 +0530
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Re: [gmx-users] g_rms matrix between wt and mutant

[Shay Teaching]

Thanks Mark and Justin for your input. it works. For progeny, here's how:

1. In case of multiple, separate chains of protein, generate a *new* tpr X
that does not include chain information.
2. From X generate a new tpr file Y, consisting now only of the group under
scrutiny (for example, backbone. Use tpbconv).
3. Make new index file for Y.
4. Now use trjconv to make xtc1  and xtc2 that consist only on that group.
5. Use g_rms with Y tpr, the generate xtcs, and the new index group.

This should work and avoid the notorious segmentation fault (as long as you
make sure the group you choose, backbone for example, has identical number
of atoms in both xtc1 and xtc2).

-SA
On Tue, Sep 13, 2011 at 11:17 AM, Mark Abraham wrote:

>  On 13/09/2011 6:11 PM, Shay Teaching wrote:
>
> Ok I tried that and it doesn't work:
> There's a fundamental difference between chains/no-chains topology, namely
> the existence of peptide bond between chains, and the different protonation
> state on the termini.
> In the chain-based topology there are several termini, and less peptide
> bonds.
>
> This causes the no-chains-tpr to have different number of atoms, and
> different protonation states.
> I tried using tpbconv to make a backbone-tpr, but it still gets me to
> segmentation fault.
>
>
> The idea behind Justin's original solution is still right. You need to
> provide two sets of corresponding atoms and those sets have to have the same
> size. So you need to construct two index groups that suit what you actually
> want to compare - say, the backbone atoms that are common to the two forms.
> That will require some thought, and playing around with make_ndx (or a text
> editor). Then use those to create subset .tpr and trajectory files as Justin
> suggested. Each form is likely to need its own customized index group to
> make the subset that is correct for it.
>
> Mark
>
>
>
> So thanks, but I don't think it would work.
> -SA
>
> On Mon, Sep 12, 2011 at 11:47 PM, Shay Teaching 
> wrote:
>
>> Thanks, I'll try that, and post again if it works.
>>
>>
>> On Mon, Sep 12, 2011 at 6:20 PM, Justin A. Lemkul wrote:
>>
>>>
>>>
>>> Shay Teaching wrote:
>>>
 When I try to work the command on a small portion of the backbone it
 seems to work just fine. But when I try the entire backbone (which is
 composed of several _separate_ chains) I am getting segmentation fault.
 Any workaround for that, so I can use the entire backbone?

>>>
>>>  Are there chain identifiers separating the proteins?  I don't know if
>>> that would cause the problem, but it's possible.  In that case, I'd suggest
>>> you start with a coordinate file and topology without chain identifiers and
>>> generate a new .tpr file (and then take the backbone atoms only with
>>> tpbconv).
>>>
>>> -Justin
>>>
>>>  Thanks again,
 -Shay


 On Mon, Sep 12, 2011 at 5:29 PM, Justin A. Lemkul >>> jalem...@vt.edu>> wrote:



Shay Teaching wrote:

Hi all,
(Gromacs 4.0.7): I am trying to make rms matrix between one Wt
trajectory and one mutant trajectory using the following command:

g_rms -f wt.xtc -f2 mutant.xtc -s wt.tpr -m -fit rot+trans -n
wt_backbone.ndx

The file wt_backbone.ndx contains the backbone of the protein
(Backbone indices are identical between wt and mutant).

The result is that I am getting a well deserved error saying
that wt.xtc and mutant.xtc has different number of atoms (the
tpr itself):
Fatal error:
Second trajectory (76128 atoms) does not match the first one
(76129 atoms)

So the question becomes: Is there a (convenient) way to produce
rms-matrix between wt and mutant?
Or perhaps circumvent this problem in some other way?


Use trjconv to write out new trajectories containing only backbone
atoms of each protein, then use tpbconv to write a .tpr file with
only backbone atoms in it (using index groups, if necessary).  Then
run g_rms again with these new trajectories and .tpr file.
 Everything should match if the indices are chosen correctly.

-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<%28540%29%20231-9080>


http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin


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