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Today's Topics:
1. Rtp for polymer. (varsha gautham)
2. Re: Rtp for polymer. (Mark Abraham)
3. Re: Rtp for polymer. (Andrea Muntean)
4. Gromacs and ssh problem (Bernhard Knapp)
5. RE: micelle disaggregated in serial, but not parallel, runs
using sd integrator (Berk Hess)
6. Re: micelle disaggregated in serial, but not parallel, runs
using sd integrator (Ran Friedman)
----------------------------------------------------------------------
Message: 1
Date: Thu, 5 Feb 2009 11:02:30 +0530
From: varsha gautham <varsha.gautha...@gmail.com>
Subject: [gmx-users] Rtp for polymer.
To: gmx-users@gromacs.org
Message-ID:
<756f9c230902042132r773b5180t8ca395651d35c...@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Hello justin,
Am sorry to say that its not useful.But what i mean is that the rtp
constructed manually is building up the polymer and generating topology
files and gro files.
But when i look into the gro file with vmd the connectivity between each
of
the monomer is not built.That is my polymer consists of 10 monomer units
with ben and primary amine unit as a block polymer.
How can i include the connectivity information between these two in a rtp
file?I can include that in session called bonds. But how to do that??And i
want some help
regarding the workflow that is how gromacs interpreting each of the rtp,
atp
,ffnb.itp,ffbon.itp??I want to know that in a sequential order.are there
any
materials available other than manual..If so please let me know
Thanks in advance.
-krithika
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Message: 2
Date: Thu, 05 Feb 2009 17:06:04 +1100
From: Mark Abraham <mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] Rtp for polymer.
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <498a81cc.50...@anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
varsha gautham wrote:
Hello justin,
Am sorry to say that its not useful.But what i mean is that the rtp
constructed manually is building up the polymer and generating topology
files and gro files.
But when i look into the gro file with vmd the connectivity between each
of the monomer is not built.
VMD merely guesses the connectivity - there's none specified in a .gro
file, which is purely a set of coordinates. A .top file defines a
topology. If your input structure doesn't conform to VMD's heuristics,
then it won't show a bond.
You can't judge the success of your .rtp construct without looking at
the *topology* pdb2gmx produced.
That is my polymer consists of 10 monomer
units with ben and primary amine unit as a block polymer.
How can i include the connectivity information between these two in a
rtp file?I can include that in session called bonds. But how to do
that??And i want some help
regarding the workflow that is how gromacs interpreting each of the rtp,
atp ,ffnb.itp,ffbon.itp??I want to know that in a sequential order.are
there any materials available other than manual..If so please let me know
Try http://wiki.gromacs.org/index.php/.top_file and links thereon.
Mark
------------------------------
Message: 3
Date: Thu, 5 Feb 2009 09:39:38 +0100
From: Andrea Muntean <andreamunt...@gmail.com>
Subject: Re: [gmx-users] Rtp for polymer.
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID:
<b7d3859e0902050039r516bcce9w7adf5769236c1...@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
I connect the monomers by adding a bond in the rtp entry, in which the
first atom of the next residue is given with + (you can also connect
with the previous residue with - in front of the last atom). Sorry to
explain this in a very confuse way. Better look at the example bellow
(for polystyrene):
[PS]
[atoms]
CH2 CH2 0 0
CH CH1 0 0
CB C 0 0
CG1 CR1 0 0
CG2 CR1 0 0
CG3 CR1 0 0
CG4 CR1 0 0
CG5 CR1 0 0
[bonds]
;-CH CH2 gb_ (you put the appropriate bond from the ff*_bon.itp
file)
CH2 CH gb_
CH CB gb_
CB CG1 gb_
CG1 CG2 gb_
CG2 CG3 gb_
CG3 CG4 gb_
CG4 CG5 gb_
CG5 CB gb_
CH +CH2 gb_
[angles]
...
[impropers]
...
[dihedrals]
...
(angles, impropers and dihedrals were defined accordingly, but not listed
here)
I hope that will help.
Andrea
2009/2/5 varsha gautham <varsha.gautha...@gmail.com>:
Hello justin,
Am sorry to say that its not useful.But what i mean is that the rtp
constructed manually is building up the polymer and generating topology
files and gro files.
But when i look into the gro file with vmd the connectivity between each
of
the monomer is not built.That is my polymer consists of 10 monomer units
with ben and primary amine unit as a block polymer.
How can i include the connectivity information between these two in a rtp
file?I can include that in session called bonds. But how to do that??And
i
want some help
regarding the workflow that is how gromacs interpreting each of the rtp,
atp
,ffnb.itp,ffbon.itp??I want to know that in a sequential order.are there
any
materials available other than manual..If so please let me know
Thanks in advance.
-krithika
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------------------------------
Message: 4
Date: Thu, 05 Feb 2009 10:07:07 +0100
From: Bernhard Knapp <bernhard.kn...@meduniwien.ac.at>
Subject: [gmx-users] Gromacs and ssh problem
To: gmx-users@gromacs.org
Message-ID: <498aac3b.3050...@meduniwien.ac.at>
Content-Type: text/plain; charset=us-ascii; format=flowed
Hi
I installed Gromacs successfully on Fedora 8 nodes. Afterwards I ran a
successful small simulation. Thereafter I moved the node to our
server-room did the following:
- set ip adress, subnetmask and gateway
- changed the ssh port in /etc/ssh/sshd_config since we use port
forwarding on our router and /usr/sbin/semanage port -a -t
inetd_child_port_t -p tcp 5101
- changed the firewall settings to additionally allow the new port
- changed the hostname via hostname command
Then I started exactly the same simulation (same command, same data) as
before (before the network configuration) and Gromacs comes up with:
ssh: quoVadis01: Name or service not known
--------------------------------------------------------------------------
A daemon (pid 5039) died unexpectedly with status 255 while attempting
to launch so we are aborting.
There may be more information reported by the environment (see above).
This may be because the daemon was unable to find all the needed shared
libraries on the remote node. You may set your LD_LIBRARY_PATH to have the
location of the shared libraries on the remote nodes and this will
automatically be forwarded to the remote nodes.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that the job aborted, but has no info as to the process
that caused that situation.
--------------------------------------------------------------------------
mpirun: clean termination accomplished
How is possible that some network configurations screw up Gromacs? The
simulation is running in parallel on the 4 local cores of the maschine
no network interaction is necessary at all. Can anybody tell me where
the problem is. The error message above is obviously incorrect since it
was already working and the library paths are ok ...
cheers
Bernhard
------------------------------
Message: 5
Date: Thu, 5 Feb 2009 10:25:09 +0100
From: Berk Hess <g...@hotmail.com>
Subject: RE: [gmx-users] micelle disaggregated in serial, but not
parallel, runs using sd integrator
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <blu134-w513d4ad5766aecd691f1ac8e...@phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
I don't know why I did not add checks for ld-seed before.
Now grompp gives a note when continutation=yes and ld-seed!=-1.
tpbconv will now generate a new ld-seed when reading a trajectory
(but you should not use tpbconv, use a checkpoint file instead).
But yesterday I forgot to tell that there is a bug in the checkpointing
of mdrun in 4.0 - 4.0.3. Without domain decomposition the initial box
size would always be stored in the checkpoint file, which causes problems
with NPT simulations. NPT simulations with domain decomposition and
all NVT simulations were fine.
Gromacs 4.0.4 will all bugs fixed and extra checks should be released
today.
Berk
Date: Wed, 4 Feb 2009 19:30:47 -0500
From: chris.ne...@utoronto.ca
To: gmx-users@gromacs.org
Subject: [gmx-users] micelle disaggregated in serial, but not parallel,
runs using sd integrator
It appears as if you were correct Berk. I will report on the results of
my 24h test tomorrow, but I also set up another system
that used ld_seed=1993 and ran in 20 ps segments instead of the 200 ps
segments that I was previously using. This system shows
signs of disaggregation on the 200 ps time-scale as opposed to the 2 ns
time-scale that I observed for 200 ps segments.
I don't know how you figured that one out, but I am very grateful.
Now that I see the trajectories, it does make sense that any net movement
applied to an individual molecule by the noise will
lead to directed movement over many separate segments.
I think this is probably worth a note in the grompp output for sd runs
when a user sets ld_seed to something other than -1 and
utilizes the -t option (or some other indication that this is intended as
a continuation).
Chris.
-- original message --
Thank you Berk,
I will repeat my runs using the checkpoint file and report my findings
back to this list. Thank you for this advice.
Chris.
-- original message --
Hi,
In this manner you use the same random seed and thus noise for all parts.
In most cases this will not lead to serious artifacts with SD,
but you can never be sure.
When checkpoints are used, you do not repeat random numbers.
This also gives a difference between serial and parallel in 4.0.
With serial you get exactly the same noise per atom, in parallel not,
since atoms migrate from one node to another (with domain decompostion).
If you do not use checkpoints, use ld_seed=-1 and do not use tpbconv.
Berk
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Message: 6
Date: Thu, 05 Feb 2009 10:43:22 +0100
From: Ran Friedman <r.fried...@bioc.uzh.ch>
Subject: Re: [gmx-users] micelle disaggregated in serial, but not
parallel, runs using sd integrator
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <498ab4ba.2080...@bioc.uzh.ch>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
Maybe it's a good idea to have ld-seed=-1 as a default if that's not
already the case.
Ran.
Berk Hess wrote:
Hi,
I don't know why I did not add checks for ld-seed before.
Now grompp gives a note when continutation=yes and ld-seed!=-1.
tpbconv will now generate a new ld-seed when reading a trajectory
(but you should not use tpbconv, use a checkpoint file instead).
But yesterday I forgot to tell that there is a bug in the checkpointing
of mdrun in 4.0 - 4.0.3. Without domain decomposition the initial box
size would always be stored in the checkpoint file, which causes problems
with NPT simulations. NPT simulations with domain decomposition and
all NVT simulations were fine.
Gromacs 4.0.4 will all bugs fixed and extra checks should be released
today.
Berk
> Date: Wed, 4 Feb 2009 19:30:47 -0500
> From: chris.ne...@utoronto.ca
> To: gmx-users@gromacs.org
> Subject: [gmx-users] micelle disaggregated in serial, but not
parallel, runs using sd integrator
>
> It appears as if you were correct Berk. I will report on the results
of my 24h test tomorrow, but I also set up another system
> that used ld_seed=1993 and ran in 20 ps segments instead of the 200
ps segments that I was previously using. This system shows
> signs of disaggregation on the 200 ps time-scale as opposed to the 2
ns time-scale that I observed for 200 ps segments.
>
> I don't know how you figured that one out, but I am very grateful.
>
> Now that I see the trajectories, it does make sense that any net
movement applied to an individual molecule by the noise will
> lead to directed movement over many separate segments.
>
> I think this is probably worth a note in the grompp output for sd
runs when a user sets ld_seed to something other than -1 and
> utilizes the -t option (or some other indication that this is
intended as a continuation).
>
> Chris.
>
> -- original message --
>
> Thank you Berk,
>
> I will repeat my runs using the checkpoint file and report my
findings back to this list. Thank you for this advice.
>
> Chris.
>
> -- original message --
>
> Hi,
>
> In this manner you use the same random seed and thus noise for all
parts.
> In most cases this will not lead to serious artifacts with SD,
> but you can never be sure.
> When checkpoints are used, you do not repeat random numbers.
> This also gives a difference between serial and parallel in 4.0.
> With serial you get exactly the same noise per atom, in parallel not,
> since atoms migrate from one node to another (with domain
> decompostion).
>
> If you do not use checkpoints, use ld_seed=-1 and do not use tpbconv.
>
> Berk
>
>
> _______________________________________________
> 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!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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