Re: [gmx-users] mdrun -c option "did not work"

[Jérôme Baffreau]

Thanks for your answer.

Actually no my run did not finish normally the first time (it has been 
stopped after 7 days because of the time limitation on the cluster it was 
running on). So I started it again (I ran the same command and added the 
option "-append yes") and this time the calculation finished normally, 
but when I look at the md.log file it looks like the second run did not 
add anything since it stops in the middle of a line (in the middle of a 
word actually!)...



Sounds like a filesystem problem.



No, that's because the Linux cluster's system terminated my calculation when 
it reached max. allowed time.



Maybe I just did not use the correct command to start this calculation 
again, that would explain the end of the md.log and the "no-generation" 
of the final structure.
What option(s) should I use with trjconv? Actually I already tried to use 
this command, but it generated a 200 MB pdb file which was not my aim!



Read trjconv -h and see how to choose the only final frame.



I have a stupid question: how do I know how many frames there are in my 
calculation?




Mark
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Jerome


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Re: [gmx-users] simulation of protein in presence of ATP

[nikhil damle]

Hi

Thanks a lot for help. I could run the EM with ATP in its right place. But 
position restrained dynamics gives warnings saying that some angles are rotated 
beyond 30 deg. So when i directly went for MD run it is running fine. What 
dis-advantages i have of not performing position restrained dynamics on my 
ATP-receptor complex system ?

Regards,
Nikhil





From: Mark Abraham 
To: Discussion list for GROMACS users 
Sent: Tuesday, 23 June, 2009 12:35:12 PM
Subject: Re: [gmx-users] simulation of protein in presence of ATP

nikhil damle wrote:
> Hi,
>  We can use max 4 coloumns for naming atoms. But .rtp file has 5 coloumn 
> atom names (AO1PG etc) That i modified to 4 letter name. But now the error is 
> "atom N not found in residue 1ATP while combining tdb and rtp"

pdb2gmx tries to cap termini of peptides automatically, but this isn't a 
peptide. So look at pdb2gmx -h and choose the option that will allow you to 
interactively choose that no terminal capping needs to take place.

Mark

> 
> *From:* Mark Abraham 
> *To:* Discussion list for GROMACS users 
> *Sent:* Tuesday, 23 June, 2009 11:16:26 AM
> *Subject:* Re: [gmx-users] simulation of protein in presence of ATP
> 
> nikhil damle wrote:
>  > Hi,
>  >
>  >Thanks a lot for the reply. I am submitting ATP crds as ATP.pdb to 
> pdb2gmx and receive the error as "No atoms found in pdb file ATP.pdb" I 
> converted HETATM tag to ATOM tag. Still same error msg. Please find ATP.pdb 
> file attached herewith.
> 
> You've broken the PDB format, which encodes the information in fixed-column 
> style. See http://www.wwpdb.org/documentation/format32/v3.2.html
> 
> Mark
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Re: [gmx-users] handling particle decomposition with distance restraints

[Chris Neale]

We are running SUSE Linux

It's best to keep all of this on the mailing list in case it becomes 
useful to somebody else.



jayant james wrote:

Hi!
thanks for your mail. I have never used pull code before and so I am a 
bit apprehensive but I do accept your suggestion and I am working on 
that. By the wat what is the OS that you are using? Is it Suse or Fedora?

Thanks
Jayant James

On Thu, Jun 25, 2009 at 4:31 PM, Chris Neale > wrote:


Let me re-emphasize that the pull code may be a good solution for you.

As per your request, I currently use the following without any
problems:

fftw 3.1.2
gromacs 3.3.1 or 4.0.4
openmpi 1.2.6

Be especially aware that openmpi 1.3.0 and 1.3.1 are broken, as I
posted here:

http://lists.gromacs.org/pipermail/gmx-users/2009-March/040844.html


To be clear, I have never experienced any openmpi-based problems
with any version of gromacs 4 and openmpi 1.2.6.

I posted the original notice of our problems with openmpi (1.2.1)
that were solved by using lam here.
http://www.mail-archive.com/gmx-users@gromacs.org/msg08257.html

Chris

jayant james wrote:

Hi!
thanks for your mail. Could you please share what OS and
versions of fftw, openmpi and gmx you are currently using.
Thanks you
JJ

On Thu, Jun 25, 2009 at 12:28 PM, mailto:chris.ne...@utoronto.ca>
>> wrote:

   Why not use the pull code? If you haev to use distance
restraints,
   then try LAM mpi with your pd run. We had similar error
messages
   with vanilla .mdp files using openmpi with large and complex
   systems that went away when we switched to LAM MPI. Our
problems
   disappeared in gmx 4 so we went back to openmpi for all
systems as
   that mdrun_mpi version is faster in our hands.

   I admit, there is no good reason why LAM would work and openMPI
   would not, but I have seen it happen before so it's worth a
shot.

   -- original message--

   The energy minimization went on without any problem on 4
   processors but the
   problem occurs when I perform the MD run. Also, I did not
get any
   error
   message with relevance to LINCS etc...
   JJ

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-- 
Jayasundar Jayant James


www.chick.com/reading/tracts/0096/0096_01.asp

)





--
Jayasundar Jayant James

www.chick.com/reading/tracts/0096/0096_01.asp 
)




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Re: [gmx-users] handling particle decomposition with distance restraints

[Chris Neale]

Let me re-emphasize that the pull code may be a good solution for you.

As per your request, I currently use the following without any problems:

fftw 3.1.2
gromacs 3.3.1 or 4.0.4
openmpi 1.2.6

Be especially aware that openmpi 1.3.0 and 1.3.1 are broken, as I posted 
here:


http://lists.gromacs.org/pipermail/gmx-users/2009-March/040844.html


To be clear, I have never experienced any openmpi-based problems with 
any version of gromacs 4 and openmpi 1.2.6.


I posted the original notice of our problems with openmpi (1.2.1) that 
were solved by using lam here.

http://www.mail-archive.com/gmx-users@gromacs.org/msg08257.html

Chris

jayant james wrote:

Hi!
thanks for your mail. Could you please share what OS and versions of 
fftw, openmpi and gmx you are currently using.

Thanks you
JJ

On Thu, Jun 25, 2009 at 12:28 PM, > wrote:


Why not use the pull code? If you haev to use distance restraints,
then try LAM mpi with your pd run. We had similar error messages
with vanilla .mdp files using openmpi with large and complex
systems that went away when we switched to LAM MPI. Our problems
disappeared in gmx 4 so we went back to openmpi for all systems as
that mdrun_mpi version is faster in our hands.

I admit, there is no good reason why LAM would work and openMPI
would not, but I have seen it happen before so it's worth a shot.

-- original message--

The energy minimization went on without any problem on 4
processors but the
problem occurs when I perform the MD run. Also, I did not get any
error
message with relevance to LINCS etc...
JJ

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--
Jayasundar Jayant James

www.chick.com/reading/tracts/0096/0096_01.asp 
)




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[gmx-users] handling particle decomposition with distance restraints

[chris . neale]

Why not use the pull code? If you haev to use distance restraints,  
then try LAM mpi with your pd run. We had similar error messages with  
vanilla .mdp files using openmpi with large and complex systems that  
went away when we switched to LAM MPI. Our problems disappeared in gmx  
4 so we went back to openmpi for all systems as that mdrun_mpi version  
is faster in our hands.


I admit, there is no good reason why LAM would work and openMPI would  
not, but I have seen it happen before so it's worth a shot.


-- original message--

The energy minimization went on without any problem on 4 processors but the
problem occurs when I perform the MD run. Also, I did not get any error
message with relevance to LINCS etc...
JJ

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[gmx-users] angle

[Morteza Khabiri]

Dear gmxusers

I want to calculate the angle between 2 alpha helix. One of the
possibility to do, is g_bundle command. If I want to use g_bundle I have a
problem to define the groups in the index file. On a basis of which
criteria could I choose the 3 group in index file as input for g_bundle???

Before thanks



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Re: [gmx-users] handling particle decomposition with distance restraints

[jayant james]

The energy minimization went on without any problem on 4 processors but the
problem occurs when I perform the MD run. Also, I did not get any error
message with relevance to LINCS etc...
JJ

On Wed, Jun 24, 2009 at 6:53 PM, Justin A. Lemkul  wrote:

>
>
> jayant james wrote:
>
>> Yes my distance restraints are long because I am using FRET distances as
>> distance restraints while performing MD simulations. Upon usage of this
>> command
>>
>> mpirun -np 4  mdrun_mpi  -s pr -e pr -g md -o traj.trr -c pr.gro  -pd
>>   &
>>
>> I get the following error!!   I did try giving yes after -pd but even then
>> the same error message is repeated.
>>
>>
> Anything else printed to the screen or log file?  LINCS warnings or
> anything else?  Did energy minimization complete successfully?
>
> -Justin
>
>  Back Off! I just backed up md.log to ./#md.log.9#
>> Reading file pr.tpr, VERSION 4.0 (single precision)
>> NNODES=4, MYRANK=1, HOSTNAME=localhost.localdomain
>> NODEID=1 argc=13
>> NODEID=3 argc=13
>> [localhost:17514] *** Process received signal ***
>> [localhost:17514] Signal: Segmentation fault (11)
>> [localhost:17514] Signal code: Address not mapped (1)
>> [localhost:17514] Failing at address: 0x134
>> [localhost:17514] [ 0] /lib64/libpthread.so.0 [0x38dec0f0f0]
>> [localhost:17514] [ 1] /lib64/libc.so.6(memcpy+0x15b) [0x38de08432b]
>> [localhost:17514] [ 2]
>> /usr/lib64/openmpi/1.2.4-gcc/libmpi.so.0(ompi_convertor_pack+0x152)
>> [0x3886e45392]
>> [localhost:17514] [ 3]
>> /usr/lib64/openmpi/1.2.4-gcc/openmpi/mca_btl_sm.so(mca_btl_sm_prepare_src+0x13d)
>> [0x7f39dd118a4d]
>> [localhost:17514] [ 4]
>> /usr/lib64/openmpi/1.2.4-gcc/openmpi/mca_pml_ob1.so(mca_pml_ob1_send_request_start_rndv+0x140)
>> [0x7f39dd735230]
>> [localhost:17514] [ 5]
>> /usr/lib64/openmpi/1.2.4-gcc/openmpi/mca_pml_ob1.so(mca_pml_ob1_send+0x748)
>> [0x7f39dd72e508]
>> [localhost:17514] [ 6]
>> /usr/lib64/openmpi/1.2.4-gcc/openmpi/mca_coll_tuned.so(ompi_coll_tuned_bcast_intra_split_bintree+0x91c)
>> [0x7f39dc6f735c]
>> [localhost:17514] [ 7]
>> /usr/lib64/openmpi/1.2.4-gcc/libmpi.so.0(MPI_Bcast+0x15c) [0x3886e4c40c]
>> [localhost:17514] [ 8] mdrun_mpi(bcast_state+0x26c) [0x56d59c]
>> [localhost:17514] [ 9] mdrun_mpi(mdrunner+0x1067) [0x42b807]
>> [localhost:17514] [10] mdrun_mpi(main+0x3b4) [0x431c34]
>> [localhost:17514] [11] /lib64/libc.so.6(__libc_start_main+0xe6)
>> [0x38de01e576]
>> [localhost:17514] [12] mdrun_mpi [0x413339]
>> [localhost:17514] *** End of error message ***
>> mpirun noticed that job rank 0 with PID 17514 on node
>> localhost.localdomain exited on signal 11 (Segmentation fault).
>> 3 additional processes aborted (not shown)
>>
>>
>>
>> On Wed, Jun 24, 2009 at 6:04 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>jayant james wrote:
>>
>>
>>I just replaced the old gmx 4.0 version with the 4.0.5 version
>>and still the same problem
>>
>>NOTE: atoms involved in distance restraints should be within the
>>longest cut-off distance, if this is not the case mdrun
>>generates a fatal error, in that case use particle decomposition
>>(mdrun option -pd)
>>
>>Well, does it work with -pd?  It looks like your distance restraints
>>are indeed quite long, so this looks like it is your only option.
>>
>>-Justin
>>
>>
>>
>>WARNING: Can not write distance restraint data to energy file
>>with domain decomposition
>>
>>
>>
>>On Wed, Jun 24, 2009 at 5:10 PM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>>>> wrote:
>>
>>
>>
>>   jayant james wrote:
>>
>>   Hi!
>>   I am performing an mpi MD (on a quad core system) run with
>>   distance restraints. When I execute this command below
>> without
>>   position restraints the MD run is distributed over 4 nodes
>>   perfectly well. But when I incorporate the distance
>>restraints I
>>   hit a road block
>>mpirun -np 4  mdrun_mpi  -s pr -e pr -g md -o traj.trr
>>-c pr.gro  &
>>I get this error message (below). My pr.mdp and distance
>>   restraints files are given below the error message
>>   . *
>>   Question.* How do I handle this sitation? Do I increase
>>the long
>>   range cut off in the pr.mdp file? If you see my distance
>>   restraints file, my upper range of distances are close to
>>9nm!!
>>
>>
>>   Upgrade to the latest version (4.0.5), since there have been
>>   numerous improvements to domain decomposition throughout the
>>   development of version 4.0.
>>
>>   -Justin
>>
>>   Please guide.
>>   Thanks
>>   JJ
>>
>> -

Re: [gmx-users] use of LAN for parallel processing

[Mark Abraham]

Alexandre Suman de Araujo wrote:

Hi Mark

Do you know any site/paper/book which clearly discuss the use of other 
network paradigms (infiniband, myrinet, etc) to perform fair parallel MD 
simulations?


No. GROMACS will work over any network across which you can run MPI. For 
MD, you are likely to get what you pay for with that network. You can 
search the archives of gmx-users for some discussion here.


Mark
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Re: [gmx-users] use of LAN for parallel processing

[Alexandre Suman de Araujo]

Hi Mark

Do you know any site/paper/book which clearly discuss the use of other 
network paradigms (infiniband, myrinet, etc) to perform fair parallel MD 
simulations?


Thanks!

**
Alexandre Suman de Araujo*
Faculdade de Ciências Farmacêuticas de Ribeirão Preto*
Universidade de São Paulo*
Dep. de Física e Química *
Grupo de Física Biológica * e-mail: asara...@fcfrp.usp.br*
Av. do Café, s/n° * e-mail: ale.su...@gmail.com  *
CEP: 14040-903* Phone: +55 (16) 3602-4172*
Ribeirão Preto, SP, Brasil* Phone: +55 (16) 3602-4222*
** 




Mark Abraham escreveu:

akalabya bissoyi wrote:

Thanks gromacs
for you replay, can any body provide tutorial/standard protocol   how 
to use of LAN for parallel processing.


The canonical guide for doing installations of MPI versions of GROMACS 
can be found here http://oldwww.gromacs.org/content/view/19/32/


Mark
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Re: [gmx-users] angle

[Mark Abraham]

Morteza Khabiri wrote:

Dear gmxusers

I want to calculate the angle between 2 alpha helix. One of the
possibility to do, is g_bundle command. If I want to use g_bundle I have a
problem to define the groups in the index file. On a basis of which
criteria could I choose the 3 group in index file as input for g_bundle???


Does the contents of g_bundle -h help?

Mark
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[gmx-users] angle

[Morteza Khabiri]

Dear gmxusers

I want to calculate the angle between 2 alpha helix. One of the
possibility to do, is g_bundle command. If I want to use g_bundle I have a
problem to define the groups in the index file. On a basis of which
criteria could I choose the 3 group in index file as input for g_bundle???

Before thanks

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[gmx-users] Re: How to freeze the atoms?

[Vitaly V. Chaban]

I do not see topology file in your archive.


2009/6/25 

> The input files for EM of the job are in the attachment.
>
>
>
> Thank you for your time!
>
>
> - 原始邮件 -
> 发件人：Vitaly V. Chaban 
> 收件人：toby10222...@sina.com, gmx-users@gromacs.org
> 主题：Re: 回复：Re: 回复：[gmx-users] Re: How to freeze the atoms?
> 日期：2009-6-24 19:10:19
>
>
> It's difficult to say anything definite about your problem based on the
> provided information. If the effect is critical for your job you may send me
> all the input files of your system and hopefully I will try to look at them
> on these days.
>
> 2009/6/24 
>
>> I checke the ndx file and the numbers of atoms in that file are the same
>> as in the corresponding residues.
>>
>> The atoms only move in EM and they stay still during equilibrium process.
>> I have not run MD yet. So I don't know whether the atoms will move or not
>> during MD run.
>>
>> Thank you!
>>
>>
>> - 原始邮件 -
>> 发件人：Vitaly V. Chaban 
>> 收件人：toby10222...@sina.com, gmx-users@gromacs.org
>> 主题：Re: 回复：[gmx-users] Re: How to freeze the atoms?
>> 日期：2009-6-24 13:00:20
>>
>>
>> I do not know such effect although work with the 'freeze' option for a
>> number of years in many gromacs versions.
>>
>> Are you sure that the numbers of the atoms in your ndx file are the same
>> as in the corresponding residues? I suggest that you should look for a
>> problem there.
>>
>> Do the atoms move only when EM is performed or during MD run as well?
>>
>> - Vitaly
>>
>>
>>   2009/6/24 
>>
>>> Dear all
>>>
>>> The CNT itself does not move. Only C and O in carbonyl groups move and
>>> the distance of movement is not large. As I wrote, Each carbonyl group (C
>>> and O ) is considered as a residue named "Car" and the group name of
>>> carbonyl in the ndx file is "Car", too. Is there anything wrong with the
>>> groups?
>>>
>>> Is it possible that the frozen atoms move a short distance due to the
>>> strong electrostatic forces. C in the CNT has no charge, while atoms in
>>> carbonyl groups take charges.
>>>
>>> Thank you for your time!
>>>
>>>
>>> - 原始邮件 -
>>> 发件人：Vitaly V. Chaban 
>>> 收件人：gmx-us...@gromacs.org
>>> 主题：[gmx-users] Re: How to freeze the atoms?
>>> 日期：2009-6-23 18:04:35
>>>
>>> >
>>> > Dear all
>>> > I attach 8 carbonyl groups onto a
>>> > carbon nanotube (CNT). Each carbonyl group is considered as a residue
>>> named
>>> > "Car" and each carbon atom in the CNT is considered as a residue named
>>> > "Gr1". In the mdp file, the freezegrps are Gr1 and Car, and the
>>> freezedim
>>> > are Y Y Y Y Y Y. Does it mean that all the C in the CNT and C and O in
>>> the
>>> > carbonyl groups are fixed in three dimensions and they can not move in
>>> any
>>> > direction. However, when I made the energy minimization, the
>>> coordinates of
>>> > C and O in carbonyl groups changed.
>>> > How can I really fix the atoms? Look forward
>>> > for your suggestions!
>>> >
>>>
>>> All the atoms which relate to your frozen groups should be non-movable
>>> during MD.
>>>
>>> >the coordinates of C and O in carbonyl groups changed.
>>>
>>> Only ones of CHO changed? And the CNT itself is nonmovable? Check your
>>> groups please.
>>>
>>
>>
>> --
>> Vitaly V. Chaban, Ph.D. (ABD)
>> School of Chemistry
>> V.N. Karazin Kharkiv National University
>> Svoboda sq.,4, Kharkiv 61077, Ukraine
>> email: cha...@univer.kharkov.ua,vvcha...@gmail.com
>> skype: vvchaban, mob.: +38-097-8259698
>>
>
>
>
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Re: [gmx-users] use of LAN for parallel processing

[Mark Abraham]

akalabya bissoyi wrote:

Thanks gromacs
for you replay, can any body provide tutorial/standard protocol   how to 
use of LAN for parallel processing.


The canonical guide for doing installations of MPI versions of GROMACS 
can be found here http://oldwww.gromacs.org/content/view/19/32/


Mark
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RE: [gmx-users] pullx.xvg Meaning of output?

[Berk Hess]

Hi,

As I said, if you set a reference group (any name/group for pull_group0),
you apply a potential between two groups group0 and group1.
These two groups are treated completely equivalently (they both
experience the same force, but with opposite sign and they will both move
under influence of the force).

If you use an absolute reference (no name for pull_group0),
the reference is (0,0,0) plus pull_init. There is only pull group,
so only one group will move. But remember that the rest of the system
will move in the other direction if you remove COM motion.

Berk

> Date: Thu, 25 Jun 2009 14:08:48 +0200
> From: ilona.bal...@bioquant.uni-heidelberg.de
> To: gmx-users@gromacs.org
> Subject: RE: [gmx-users] pullx.xvg  Meaning of output?
> 
> What is meant by absolute reference? Can it be the Origin (0, 0, 0).
> Does it assume a random reference point for the pullx.xvg? I get a  
> negative value for my first pulling group, even though it is inside  
> the box and above the origin. Furthermore 0-Zcoord(pullgrp) doesn't  
> fit either.
> Does it make any difference if I use reference_group = system or no  
> reference group at all? Or what else do you usually use as a reference  
> group? What does the reference group do during the simulation? I  
> understand that pulling from both sides, Gromacs puts a spring at each  
> pullgroup. Is there any restraint on the reference group?
> 
> Cheers, Ilona
> 
> 
> 
> Quoting Berk Hess :
> 
> >
> > Hi,
> >
> > In most cases you shoud NOT use an absolute reference.
> > In plain MD there is not absolute reference, therefore pulling
> > without a reference group is a recipe for trouble.
> > By default center of mass motion removal will be turned on,
> > in which case you are pulling against the center of mass of
> > the whole system. If you have solvent, thermodynamically
> > the pulling will have no effect, since the protein can move
> > along, if you pull slow enough. If you pull too fast (which is
> > very likely), you will get horrendous artifacts.
> >
> > Berk
> >
> >> Date: Thu, 25 Jun 2009 11:02:41 +0200
> >> From: ilona.bal...@bioquant.uni-heidelberg.de
> >> To: g...@hotmail.com
> >> Subject: RE: [gmx-users] pullx.xvg  Meaning of output?
> >>
> >>
> >> Hi Berk,
> >>
> >> I am trying to unfold a protein by stretching/pulling it from both
> >> sides in Z (and -Z) direction. To this end, I am trying to figure out
> >> the best parameters. If I understand you correctly, it should not make
> >> any difference to the pulling itself, i.e. the forces the protein
> >> experiences, whether a reference group is chosen or not.
> >> Unfortunately, my simulations show something different: I did exactly
> >> the same pulling simulation twice, using a backbone atom as reference
> >> group in the first case and no reference group in the second case. The
> >> differences I found are as follows:
> >> When I use no reference group, the molecule center moves less along
> >> the Z axis than in case of a defined reference group. The reason I do
> >> bother about that fact is that  I do not want my molecule to leave the
> >> box on one end due to pulling effects even though the box is more than
> >> 3 nm longer than the unfolded protein.
> >> Also, pullf.xvg shows quite similar values for the simulation without
> >> reference group whereas forces differ more if a reference group is
> >> used. (see attached files). Why is that so?
> >>
> >> Best wishes, Ilona
> >>
> >>
> >>
> >>
> >>
> >> Quoting Berk Hess :
> >>
> >> >
> >> > Hi,
> >> >
> >> > Everything depends on what you want to accomplish, which you
> >> > do not write.
> >> > I don't see why you would want to look at single atoms.
> >> > Since you pull on COM's, only the COM coordinates are relevant.
> >> > If you want to look at single atoms, simply store them in the xtc file.
> >> >
> >> > If you have only two groups, there is no physical difference between
> >> > the reference group and  the first pull group. They are simply two
> >> > groups between which the distance is calculated and the forces act.
> >> > If you used an absolute reference, 0Z is the absolute reference   
> >> coordinate,
> >> > not the coordinate of a group.
> >> >
> >> > Berk
> >> >
> >> >> Date: Tue, 23 Jun 2009 14:39:48 +0200
> >> >> From: ilona.bal...@bioquant.uni-heidelberg.de
> >> >> To: gmx-users@gromacs.org
> >> >> Subject: RE: [gmx-users] pullx.xvg  Meaning of output?
> >> >>
> >> >>
> >> >> Dear Berk,
> >> >>
> >> >> Thanks for the quick reply. That leads me to my next questions:
> >> >> *I used the whole N and C residues for pulling. Is there any way of
> >> >> reconstructing the values for the single atoms? Or do you recommend
> >> >> only to pull N and C in the first place?
> >> >> *What does the reference group actually do? Can I simply leave it out?
> >> >> Does it influence pulling?  What would be a good reference group? A
> >> >> random backbone atom from the middle of the protein?
> >> >>
> >> >> I'm looking forward to your reply. Thank you

[gmx-users] use of LAN for parallel processing

[akalabya bissoyi]

Thanks gromacs
for you replay, can any body provide tutorial/standard protocol   how to use
of LAN for parallel processing.




 AKALABYA  BISSOYI
N.I.T.Rourkela
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Re: [gmx-users] Re: Re: Re: Re: problems with some calculated trajectories

[Erik Marklund]

Bernhard Knapp skrev:


The whole complex consists of 5 chains (MHC-alpha, MHC-beta, epitope, 
T-cell receptor alpa, T-cell receptor beta).

What you can see in
http://www.meduniwien.ac.at/msi/biosim/bk/4afterNoJump1767.jpg
http://www.meduniwien.ac.at/msi/biosim/bk/4afterNoJump1768.jpg
is exactly the same angle. The two MHC chains "jump" away from each 
other and from the T-cell receptor. I have already simulated some of 
these complexes before with slightly different amino acid sequences 
but with an overall similar structure and this "jumping" never occured.


I did the following conversion:

trjconv -f 1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.trr -o 
1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.noJump.xtc -s 
1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.tpr -n index.ndx -pbc nojump 
-novel -fit progressive -skip 10


As Tsjerk stated earlier, fitting prior to jump-removal can mess up the 
trajectory.  Try without -fit. g_rms will superimpose the structures for 
you anyway.

and the rmds calculation with
g_rms -f 1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.noJump.xtc -s 
1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.tpr -o 
rmsd.TcrCdrs.noJump.fitpMHC.xvg -n index.cdrsAndStrands.ndx -ng 7



but also if I calculate the rmsd directly from the trr-file the jumps 
are inside and the same as from the xtc file without  "-pbc nojump"
g_rms -f 1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.trr -s 
1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.tpr -o 
rmsd.TcrCdrs.fitpMHC.FromOriginalTRR.xvg -n index.cdrsAndStrands.ndx 
-ng 7



cheers
Bernhard




Today's Topics:

  1. Re: Re: Re: problems with some calculated trajectories
 (Tsjerk Wassenaar)
  2. Re: Re: Re: problems with some calculated trajectories
 (Mark Abraham)
  3. RE: Re: Re: problems with some calculated trajectories (Berk Hess)

 


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--
---
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys

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RE: [gmx-users] pullx.xvg Meaning of output?

[ilona . baldus]

What is meant by absolute reference? Can it be the Origin (0, 0, 0).
Does it assume a random reference point for the pullx.xvg? I get a  
negative value for my first pulling group, even though it is inside  
the box and above the origin. Furthermore 0-Zcoord(pullgrp) doesn't  
fit either.
Does it make any difference if I use reference_group = system or no  
reference group at all? Or what else do you usually use as a reference  
group? What does the reference group do during the simulation? I  
understand that pulling from both sides, Gromacs puts a spring at each  
pullgroup. Is there any restraint on the reference group?


Cheers, Ilona



Quoting Berk Hess :



Hi,

In most cases you shoud NOT use an absolute reference.
In plain MD there is not absolute reference, therefore pulling
without a reference group is a recipe for trouble.
By default center of mass motion removal will be turned on,
in which case you are pulling against the center of mass of
the whole system. If you have solvent, thermodynamically
the pulling will have no effect, since the protein can move
along, if you pull slow enough. If you pull too fast (which is
very likely), you will get horrendous artifacts.

Berk


Date: Thu, 25 Jun 2009 11:02:41 +0200
From: ilona.bal...@bioquant.uni-heidelberg.de
To: g...@hotmail.com
Subject: RE: [gmx-users] pullx.xvg  Meaning of output?


Hi Berk,

I am trying to unfold a protein by stretching/pulling it from both
sides in Z (and -Z) direction. To this end, I am trying to figure out
the best parameters. If I understand you correctly, it should not make
any difference to the pulling itself, i.e. the forces the protein
experiences, whether a reference group is chosen or not.
Unfortunately, my simulations show something different: I did exactly
the same pulling simulation twice, using a backbone atom as reference
group in the first case and no reference group in the second case. The
differences I found are as follows:
When I use no reference group, the molecule center moves less along
the Z axis than in case of a defined reference group. The reason I do
bother about that fact is that  I do not want my molecule to leave the
box on one end due to pulling effects even though the box is more than
3 nm longer than the unfolded protein.
Also, pullf.xvg shows quite similar values for the simulation without
reference group whereas forces differ more if a reference group is
used. (see attached files). Why is that so?

Best wishes, Ilona





Quoting Berk Hess :

>
> Hi,
>
> Everything depends on what you want to accomplish, which you
> do not write.
> I don't see why you would want to look at single atoms.
> Since you pull on COM's, only the COM coordinates are relevant.
> If you want to look at single atoms, simply store them in the xtc file.
>
> If you have only two groups, there is no physical difference between
> the reference group and  the first pull group. They are simply two
> groups between which the distance is calculated and the forces act.
> If you used an absolute reference, 0Z is the absolute reference   
coordinate,

> not the coordinate of a group.
>
> Berk
>
>> Date: Tue, 23 Jun 2009 14:39:48 +0200
>> From: ilona.bal...@bioquant.uni-heidelberg.de
>> To: gmx-users@gromacs.org
>> Subject: RE: [gmx-users] pullx.xvg  Meaning of output?
>>
>>
>> Dear Berk,
>>
>> Thanks for the quick reply. That leads me to my next questions:
>> *I used the whole N and C residues for pulling. Is there any way of
>> reconstructing the values for the single atoms? Or do you recommend
>> only to pull N and C in the first place?
>> *What does the reference group actually do? Can I simply leave it out?
>> Does it influence pulling?  What would be a good reference group? A
>> random backbone atom from the middle of the protein?
>>
>> I'm looking forward to your reply. Thank you very much in advance.
>>
>> Best wishes, Ilona
>>
>>
>> Quoting Berk Hess :
>>
>> >
>> > Hi,
>> >
>> > This is actually not (yet) documented.
>> > 0Z is the Z-coordinate of group 0.
>> > 1dZ is the the Z-coordinate of group 1 minus the one of group 0.
>> >
>> > Berk
>> >
>> >> Date: Tue, 23 Jun 2009 12:54:37 +0200
>> >> From: ilona.bal...@bioquant.uni-heidelberg.de
>> >> To: gmx-users@gromacs.org
>> >> Subject: [gmx-users] pullx.xvg  Meaning of output?
>> >>
>> >> Hi!
>> >>
>> >> I am trying to understand the output of my pulling simulation:
>> >> I get a pullx.xvg file which shows 0Z, 1dZ, 2dZ after pulling in Z and
>> >> -Z direction. I really cannot figure out the meaning of 1dZ and 2dZ.
>> >> Since the website is down I cannot check on previous issues, so sorry
>> >> for asking the same question again as I already asked last week but
>> >> which remained unanswered.
>> >>
>> >> I would appreciate any advice.
>> >>
>> >> Thanks a lot. Ilona
>> >> ___
>> >> gmx-users mailing listgmx-users@gromacs.org
>> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >> Please search the archive at http://ww

[gmx-users] Re: Re: Re: Re: problems with some calculated trajectories

[Bernhard Knapp]

The whole complex consists of 5 chains (MHC-alpha, MHC-beta, epitope, 
T-cell receptor alpa, T-cell receptor beta).

What you can see in
http://www.meduniwien.ac.at/msi/biosim/bk/4afterNoJump1767.jpg
http://www.meduniwien.ac.at/msi/biosim/bk/4afterNoJump1768.jpg
is exactly the same angle. The two MHC chains "jump" away from each 
other and from the T-cell receptor. I have already simulated some of 
these complexes before with slightly different amino acid sequences but 
with an overall similar structure and this "jumping" never occured.


I did the following conversion:

trjconv -f 1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.trr -o 
1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.noJump.xtc -s 
1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.tpr -n index.ndx -pbc nojump 
-novel -fit progressive -skip 10


and the rmds calculation with
g_rms -f 1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.noJump.xtc -s 
1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.tpr -o 
rmsd.TcrCdrs.noJump.fitpMHC.xvg -n index.cdrsAndStrands.ndx -ng 7



but also if I calculate the rmsd directly from the trr-file the jumps 
are inside and the same as from the xtc file without  "-pbc nojump"
g_rms -f 1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.trr -s 
1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.tpr -o 
rmsd.TcrCdrs.fitpMHC.FromOriginalTRR.xvg -n index.cdrsAndStrands.ndx -ng 7



cheers
Bernhard




Today's Topics:

  1. Re: Re: Re: problems with some calculated trajectories
 (Tsjerk Wassenaar)
  2. Re: Re: Re: problems with some calculated trajectories
 (Mark Abraham)
  3. RE: Re: Re: problems with some calculated trajectories (Berk Hess)

 


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Re: [gmx-users] Problem in energy minimization for a empty membrane system

[Mark Abraham]

Bing Bing wrote:

Hi! Thanks a alot for all the suggestions i've got from Justin and Mark.
I found out that i actually deleted the box information from the 
starting structure PDB. Once i put it back, It worked. However,

it stopped with this message.

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)


That can be normal.


writing lowest energy coordinates.

Back Off! I just backed up em.trr to ./#em.trr.19#

Back Off! I just backed up em.gro to ./#em.gro.11#

Steepest Descents converged to machine precision in 76 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  = -2.24796600790506e+05
Maximum force =  1.14539522791599e+03 on atom 6619
Norm of force =  1.62353061702859e+04

Is it mean that the minimization is done and is already converged?
Here the result for the final Step 75.


Energies (kJ/mol)
   Bond  AngleProper Dih. Ryckaert-Bell.  Improper Dih.
1.23491e+039.85552e+034.48086e+034.81663e+031.33894e+03

  LJ-14 Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.
4.09985e+038.28955e+03   -1.68827e+04   -1.04035e+05   -1.38691e+05
 Position Rest.  PotentialKinetic En.   Total EnergyTemperature
6.95754e+02   -2.24797e+050.0e+00   -2.24797e+050.0e+00

 Pressure (bar)
0.0e+00


These all seem plausible. The proof is in MD running in a stable fashion.

Mark
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[gmx-users] Problem in energy minimization for a empty membrane system

[Bing Bing]

Hi! Thanks a alot for all the suggestions i've got from Justin and Mark.
I found out that i actually deleted the box information from the starting
structure PDB. Once i put it back, It worked. However,
it stopped with this message.

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Back Off! I just backed up em.trr to ./#em.trr.19#

Back Off! I just backed up em.gro to ./#em.gro.11#

Steepest Descents converged to machine precision in 76 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  = -2.24796600790506e+05
Maximum force =  1.14539522791599e+03 on atom 6619
Norm of force =  1.62353061702859e+04

Is it mean that the minimization is done and is already converged?
Here the result for the final Step 75.

Energies (kJ/mol)
   Bond  AngleProper Dih. Ryckaert-Bell.  Improper Dih.
1.23491e+039.85552e+034.48086e+034.81663e+031.33894e+03
  LJ-14 Coulomb-14LJ (SR)   Coulomb (SR)   Coul. recip.
4.09985e+038.28955e+03   -1.68827e+04   -1.04035e+05   -1.38691e+05
 Position Rest.  PotentialKinetic En.   Total EnergyTemperature
6.95754e+02   -2.24797e+050.0e+00   -2.24797e+050.0e+00
 Pressure (bar)
0.0e+00

The position restraint is working fine as well

Thank you so much.

Regards,
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RE: [gmx-users] Re: Re: problems with some calculated trajectories

[Berk Hess]

> Date: Thu, 25 Jun 2009 18:39:53 +1000
> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Re: Re: problems with some calculated trajectories
> 
> Bernhard Knapp wrote:
> > 1) trjconv with the "-pbc nojump" option does not help - it removes most 
> 
> If I understand correctly, -pbc nojump will help when the relevant atoms 
> are part of the same [moleculetype]. One fragment in each of your two 
> examples is apparently the same four-strand sheet with helix wrapped 
> around it. This suggests to me that you might have several chains, each 
> as a different [moleculetype] and your observations are actually what 
> you should expect. If so, -pbc cluster is the kind of thing you should 
> be using.
> 

You did not understand correctly :)
-pbc nojump removes periodic jumps of atoms, it does not now about molecules.
The effect is that no periodic jumps occur from the reference structure
(either tpr or first frame). This means, for instance, that protein complexes
will stay intact and that water will diffuse out of the box in visualization.

Berk

> In any case, a description of the composition of your system and copies 
> of a series of commands that reproduces your result would always have 
> been appropriate :-)
> 
> Mark
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Re: [gmx-users] Re: Re: problems with some calculated trajectories

[Mark Abraham]

Bernhard Knapp wrote:
1) trjconv with the "-pbc nojump" option does not help - it removes most 


If I understand correctly, -pbc nojump will help when the relevant atoms 
are part of the same [moleculetype]. One fragment in each of your two 
examples is apparently the same four-strand sheet with helix wrapped 
around it. This suggests to me that you might have several chains, each 
as a different [moleculetype] and your observations are actually what 
you should expect. If so, -pbc cluster is the kind of thing you should 
be using.


In any case, a description of the composition of your system and copies 
of a series of commands that reproduces your result would always have 
been appropriate :-)


Mark
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Re: [gmx-users] Re: Re: problems with some calculated trajectories

[Tsjerk Wassenaar]

Hi Bernhard,

The images, are they taken from exactly the same angle? If so, there's
some change in orientation that is just impossible in such a short
time. You didn't happen to fit your structure to a reference prior to
removal of jumps, did you? Fitting messes up PBC and garbles results
from -pbc nojump. If these are not from the original trajectory (mdrun
output), have a look what happens there. Otherwise, trace back all
your steps. Maybe paste here what you've done exactly...

Cheers,

Tsjerk

On Thu, Jun 25, 2009 at 10:10 AM, Bernhard
Knapp wrote:
> 1) trjconv with the "-pbc nojump" option does not help - it removes most of
> the jumps but one big remains- the rmsd for the trajectory is
> http://www.meduniwien.ac.at/msi/biosim/bk/4.jpg
> before the converting with -pbc and
> http://www.meduniwien.ac.at/msi/biosim/bk/4noJump.jpg
> after conversion.
>
> interestingly under linux vmd could load the trajectories which look like
> that:
> http://www.meduniwien.ac.at/msi/biosim/bk/4afterNoJump1767.jpg
> and
> http://www.meduniwien.ac.at/msi/biosim/bk/4afterNoJump1768.jpg
>
> 2) Here an illustration for other trajectories with the same problem:
> http://www.meduniwien.ac.at/msi/biosim/bk/1.jpg
> http://www.meduniwien.ac.at/msi/biosim/bk/2.jpg
> http://www.meduniwien.ac.at/msi/biosim/bk/jumppoint.jpg
>
>
> 3) gmxcheck returns no error, just this:
>
> trn version: GMX_trn_file (single precision)
> Reading frame   0 time    0.000
> # Atoms  167731
> Reading frame   2 time 6.000
>
> Item    #frames Timestep (ps)
> Step 20261    3
> Time 20261    3
> Lambda   20261    3
> Coords   20261    3
> Velocities    2027    30
> Forces    2027    30
> Box  20261    3
>
>
> any further ideas what I could do with those trajectories or what I shall do
> to avoid such problems in future (integration step, water shell size, ... ?)
>
> cheers
> Bernhard
>
>
>
>
>
>
> --
>
> Message: 4
> Date: Mon, 22 Jun 2009 16:37:44 +0200
> From: Erik Marklund 
> Subject: Re: [gmx-users] problems with some calculated trajectories
> To: Discussion list for GROMACS users 
> Message-ID: <4a3f9738.7070...@xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi,
>
> Could it be a periodicity issue? Have you tried using trjconv -pbc nojump ?
>
> /Erik
>
> --
>
> Message: 2
> Date: Mon, 22 Jun 2009 17:19:43 +0200
> From: Martin H?fling 
> Subject: Re: [gmx-users] problems with some calculated trajectories
> To: Discussion list for GROMACS users 
> Message-ID: <806bd6cf-4903-465f-a2b6-8d0ffa984...@lmu.de>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> Hey Bernhard, here some thoughts of mine:
>
> In principle, vmd should be able to read the trajectories if pdb2gmx
> tells you that the trajectory is ok. If this is not the case, you can
> use gmx_rescue64 to extract the undamaged parts.
>
> Reasons for damaged trajectories, even when gromacs runs through fine...
> ... for me - filesystem issues were causing this. In particular this
> happened for me with NFS shares and on Lustre filesystems. My NFS
> problems got solved with an upgrade of the NFS packages on our
> machines (at least 1 1/2 yrs ago).
>
> Best
>   Martin
>
>
>
> --
>
> Message: 3
> Date: Mon, 22 Jun 2009 18:06:13 +0200
> From: Martin H?fling 
> Subject: Re: [gmx-users] problems with some calculated trajectories
> To: Discussion list for GROMACS users 
> Message-ID: 
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes
>
>
> Am 22.06.2009 um 17:19 schrieb Martin Höfling:
>
>
>
> Hey Bernhard, here some thoughts of mine:
>
> In principle, vmd should be able to read the trajectories if pdb2gmx
> tells you that the trajectory is ok. If this is not the case, you
> can use gmx_rescue64 to extract the undamaged parts.
>
>
>
> ^
> ^^
> = gmxcheck :-)
>
> Best
>   Martin
>
> --
>
> Message: 4
> Date: Mon, 22 Jun 2009 13:29:10 -0400
> From: "Justin A. Lemkul" 
> Subject: Re: [gmx-users]  -bash:
>   /home_soft/soft_chem/soft_install/gromac/bin/GMXRC.bash:No such 
> file
>   or directory
> To: Discussion list for GROMACS users 
> Message-ID: <4a3fbf66.4010...@vt.edu>
> Content-Type: text/plain; charset=GB2312
>
>
>
> ___
> gmx-users mailing list    gmx-us...@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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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
_

[gmx-users] Re: Re: problems with some calculated trajectories

[Bernhard Knapp]

1) trjconv with the "-pbc nojump" option does not help - it removes most 
of the jumps but one big remains- the rmsd for the trajectory is

http://www.meduniwien.ac.at/msi/biosim/bk/4.jpg
before the converting with -pbc and
http://www.meduniwien.ac.at/msi/biosim/bk/4noJump.jpg
after conversion.

interestingly under linux vmd could load the trajectories which look 
like that:

http://www.meduniwien.ac.at/msi/biosim/bk/4afterNoJump1767.jpg
and
http://www.meduniwien.ac.at/msi/biosim/bk/4afterNoJump1768.jpg

2) Here an illustration for other trajectories with the same problem:
http://www.meduniwien.ac.at/msi/biosim/bk/1.jpg
http://www.meduniwien.ac.at/msi/biosim/bk/2.jpg
http://www.meduniwien.ac.at/msi/biosim/bk/jumppoint.jpg


3) gmxcheck returns no error, just this:

trn version: GMX_trn_file (single precision)
Reading frame   0 time0.000  
# Atoms  167731
Reading frame   2 time 6.000  


Item#frames Timestep (ps)
Step 202613
Time 202613
Lambda   202613
Coords   202613
Velocities202730
Forces202730
Box  202613


any further ideas what I could do with those trajectories or what I 
shall do to avoid such problems in future (integration step, water shell 
size, ... ?)


cheers
Bernhard






--

Message: 4
Date: Mon, 22 Jun 2009 16:37:44 +0200
From: Erik Marklund 
Subject: Re: [gmx-users] problems with some calculated trajectories
To: Discussion list for GROMACS users 
Message-ID: <4a3f9738.7070...@xray.bmc.uu.se>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi,

Could it be a periodicity issue? Have you tried using trjconv -pbc nojump ?

/Erik




--

Message: 2
Date: Mon, 22 Jun 2009 17:19:43 +0200
From: Martin H?fling 
Subject: Re: [gmx-users] problems with some calculated trajectories
To: Discussion list for GROMACS users 
Message-ID: <806bd6cf-4903-465f-a2b6-8d0ffa984...@lmu.de>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes

Hey Bernhard, here some thoughts of mine:

In principle, vmd should be able to read the trajectories if pdb2gmx  
tells you that the trajectory is ok. If this is not the case, you can  
use gmx_rescue64 to extract the undamaged parts.


Reasons for damaged trajectories, even when gromacs runs through fine...
... for me - filesystem issues were causing this. In particular this  
happened for me with NFS shares and on Lustre filesystems. My NFS  
problems got solved with an upgrade of the NFS packages on our  
machines (at least 1 1/2 yrs ago).


Best
Martin



--

Message: 3
Date: Mon, 22 Jun 2009 18:06:13 +0200
From: Martin H?fling 
Subject: Re: [gmx-users] problems with some calculated trajectories
To: Discussion list for GROMACS users 
Message-ID: 
Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes


Am 22.06.2009 um 17:19 schrieb Martin Höfling:

 


Hey Bernhard, here some thoughts of mine:

In principle, vmd should be able to read the trajectories if pdb2gmx  
tells you that the trajectory is ok. If this is not the case, you  
can use gmx_rescue64 to extract the undamaged parts.
   

^ 
^^

= gmxcheck :-)

Best
Martin

--

Message: 4
Date: Mon, 22 Jun 2009 13:29:10 -0400
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users]-bash:
/home_soft/soft_chem/soft_install/gromac/bin/GMXRC.bash:No such 
file
or directory
To: Discussion list for GROMACS users 
Message-ID: <4a3fbf66.4010...@vt.edu>
Content-Type: text/plain; charset=GB2312

 



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Re: [gmx-users] Problem wih Fe-S cluster

[Tsjerk Wassenaar]

Hi Subarna,

If you just want to retain the structure of the cluster it doesn't
matter too much. It may be good to average values from different
structures, though. HOWEVER, an FeS cluster is a catalytic site, which
probably has fancy electronic properties, which may well affect the
behaviour of the surrounding protein. If you are interested in the
protein dynamics, you want to describe it properly. Doing so requires
proper parameterization, ergo performing quantum mechanical
calculations with validation against experimental data, ergo doing a
lot of work. This is not something for a lazy Sunday afternoon!

Cheers,

Tsjerk

On Thu, Jun 25, 2009 at 7:55 AM, subarna
thakur wrote:
> Hi everyone
>
> I am facing a problem with derivation of parameters of Fe-S cluster in a
> protein.Can anybody please tell me for deriving a parameters do I have to
> consider the co-ordinates of a typical fe-s cluster as there in Protein Data
> Base (PDB) or the co-ordinates of the Fe-S cluster present  in my protein of
> interest.
>
>
>
> Subarna
>
> 
> ICC World Twenty20 England '09 exclusively on YAHOO! CRICKET
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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] Can N(CH2)3 be set a charge group?

[Berk Hess]

Hi,

I don't think that is a good idea.
I put the following advise in grompp
 "Since atoms only see each other when the centers of geometry of the charge 
groups they belong to are within the cut-off distance, too large charge groups 
can lead to serious cut-off artifacts.\n"
"For efficiency and accuracy, charge group should consist of a few 
atoms.\n"
"For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, 
etc.",'

We should also put this somewhere in the manual.

Berk

From: xiaowu...@hotmail.com
To: gmx-users@gromacs.org
Date: Thu, 25 Jun 2009 15:28:08 +0800
Subject: [gmx-users] Can N(CH2)3 be set a charge group?








Dear gmx users,

  Can N(CH2)3 be set a charge group? Is it too large to set? Any reply would be 
thanked very much.

 

Sincerely

Chaofu Wu

把MSN装进手机，更多聊天乐趣等你挖掘！ 立刻下载！
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[gmx-users] Can N(CH2)3 be set a charge group?

[wuxiao]

Dear gmx users,

  Can N(CH2)3 be set a charge group? Is it too large to set? Any reply would be 
thanked very much.

 

Sincerely

Chaofu Wu

_
打工，挣钱，买房子，快来MClub一起”金屋藏娇”！
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