Dear all,
I am using g_msd to calculate diffusion coefficient of the centre of mass of
single polymer chain with the following command:
g_msd_mpi -f 1.trr -s eqm.tpr -n run.ndx -rmcomm -beginfit 50000 -endfit 400000
However, it often get killed for number of beads larger than 37, as shown
below:
Reading file eqm.tpr, VERSION 4.0.3 (single precision)
Reading file eqm.tpr, VERSION 4.0.3 (single precision)
Select a group to calculate mean squared displacement for:
Group 0 ( System) has 13042 elements
Group 1 ( PEO) has 37 elements
Group 2 ( WF) has 1301 elements
Group 3 ( W) has 11704 elements
Group 4 ( WF_W) has 13005 elements
Select a group: 1
Selected 1: 'PEO'
Now select a group for center of mass removal:
Group 0 ( System) has 13042 elements
Group 1 ( PEO) has 37 elements
Group 2 ( WF) has 1301 elements
Group 3 ( W) has 11704 elements
Group 4 ( WF_W) has 13005 elements
Select a group: 1
Selected 1: 'PEO'
trn version: GMX_trn_file (single precision)
Reading frame 24000 time 240000.000 Killed.
Is it also a bug in the program or have I done something wrong on the command?
Thank you!
Best Regards
Yutian Yang
________________________________________
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Subject: gmx-users Digest, Vol 109, Issue 112
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Today's Topics:
1. metadynamics (Sathish Kumar)
2. charmm in gromacs cut-offs (tarak karmakar)
3. R: [gmx-users] metadynamics (Spitaleri Andrea)
4. proceed from output of MD (Ewaru)
5. Add CS ions to system (Shima Arasteh)
6. Re: Re: REMD analysis (bharat gupta)
7. Re: proceed from output of MD (Ewaru)
8. Re: charmm in gromacs cut-offs (Justin Lemkul)
----------------------------------------------------------------------
Message: 1
Date: Sat, 18 May 2013 15:56:15 +0530
From: Sathish Kumar <sathishk...@gmail.com>
Subject: [gmx-users] metadynamics
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID:
<CAFi=hw++kxmchytdb+jczp78ptzc5jxfwc9q_r5rtvsyx_r...@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Sir,
i want to learn about metadynamics, how to run metadynamics in
gromacs.please suggest me in this regard.
Thank you.
--
regards
M.SathishKumar
------------------------------
Message: 2
Date: Sat, 18 May 2013 17:28:13 +0530
From: tarak karmakar <tarak20...@gmail.com>
Subject: [gmx-users] charmm in gromacs cut-offs
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID:
<cagzmoouo2wba0osnsodwb6pbcqs1e2cksa102ua+xeit+6p...@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Dear All,
It seems the problem in the cut-off schemes while using charmm force
field in gromacs persists even in the latest gromacs-4.6.1 version.
Recently I have posted regarding this problem came in gromacs-4.5.5
version. If anybody has already tested this issue in the latest version,
please leave a comment in the mailing list.
The cut-off parameters I have used are as follows
rlist = 1.2
rlistlong = 1.4
; 7.3.10 Electrostatics
coulombtype = PME
rcoulomb = 1.2
; 7.3.11 VdW
vdwtype = switch
rvdw = 1.2
rvdw-switch = 1.0
NOTE 3 [file md_sim_ann.mdp]:
The switch/shift interaction settings are just for compatibility; you
will get better performance from applying potential modifiers to your
interactions!
NOTE 4 [file md_sim_ann.mdp]:
For energy conservation with switch/shift potentials, rlist should be 0.1
to 0.3 nm larger than rvdw.
NOTE 5 [file md_sim_ann.mdp]:
The sum of the two largest charge group radii (0.079732) is larger than
rlist (1.200000) - rvdw (1.200000)
This part is reported as bug in gromacs -4.5.5 and required to be verified
by users through their feedback
http://redmine.gromacs.org/issues/1164
In this link it is showing affected version grom-4.6.1 !!
Thanks and regards,
Tarak
------------------------------
Message: 3
Date: Sat, 18 May 2013 15:50:01 +0200
From: Spitaleri Andrea <spitaleri.and...@hsr.it>
Subject: R: [gmx-users] metadynamics
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID:
<685d68d01e4fc74ab398a2f494f4aa1f27dabda...@srexchmb01.sanraf.dom>
Content-Type: text/plain; charset="us-ascii"
Hi,
have look to:
http://www.plumed-code.org/
and
Andrea Spitaleri PhD
Dulbecco Telethon Institute
Center of Genomics, BioInformatics and BioStatistics
Basilica San Raffaele, 3P 34R
Via Olgettina 58
20132 Milano (Italy)
http://sites.google.com/site/andreaspitaleri/
www.biomolnmr.org
Tel: 0039-0226434348
Fax: 0039-0226434153
--------------------------------------------------------------------------
LA TUA CURA E' SCRITTA NEL TUO DNA. AL SAN RAFFAELE LA STIAMO REALIZZANDO.
AIUTA LA RICERCA, DAI IL TUO 5XMILLE - CF: 07636600962
info:www.5xmi...@hsr.it - www.5xmille.org
Disclaimer added by CodeTwo Exchange Rules 2007
http://www.codetwo.com
________________________________________
Da: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] per conto di
Sathish Kumar [sathishk...@gmail.com]
Inviato: sabato 18 maggio 2013 12.26
A: Discussion list for GROMACS users
Oggetto: [gmx-users] metadynamics
Sir,
i want to learn about metadynamics, how to run metadynamics in
gromacs.please suggest me in this regard.
Thank you.
--
regards
M.SathishKumar
--
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------------------------------
Message: 4
Date: Sat, 18 May 2013 06:51:00 -0700 (PDT)
From: Ewaru <edina_w...@yahoo.com>
Subject: [gmx-users] proceed from output of MD
To: gmx-users@gromacs.org
Message-ID: <1368885060047-5008364.p...@n6.nabble.com>
Content-Type: text/plain; charset=us-ascii
Hi,
I have run a 20ns MD simulation on my protein structure and about to proceed
with Autodock. I am wondering if I have missed anything. The output of the
file is gro, so I converted it to a pdb file. Then, when I process it with
Autodock Tools, all I get is the water molecules surrounding my protein in a
box. How can I get rid of the box?
Please advice.
Thanking you in advance.
Best regards
--
View this message in context:
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------------------------------
Message: 5
Date: Sat, 18 May 2013 07:02:47 -0700 (PDT)
From: Shima Arasteh <shima_arasteh2...@yahoo.com>
Subject: [gmx-users] Add CS ions to system
To: "gmx-users@gromacs.org" <gmx-users@gromacs.org>
Message-ID:
<1368885767.74664.yahoomail...@web162404.mail.bf1.yahoo.com>
Content-Type: text/plain; charset=iso-8859-1
Hi all,
I want to add CS ions to my system by genion but it seems impossible when go
through the EM.
The molecule section in my top file is:
Protein_chain_A???? 1
Protein_chain_B???? 1
POPC??? ??? 238
SOL???????? 20406
NA?????????????? 681
CL?????????????? 702
CS?????????????? 19
The commands to neutralize and adding CsCl are as follow:
Adding ions:
#grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr
#genion -s ions.tpr -o system_solv_ions.gro -p topol.top -conc 1 -neutral
Adding 19 pairs of CsCl:
#grompp -f ions.mdp -c system_solv_ions.gro -p topol.top -o ions_CsCl.tpr
#genion -s ions_CsCl.tpr -o system_solv_ions_CsCl.gro -p topol.top -pname CS
-np 19 -nname CL -nn 19
EM:
And fatal error as I get is:
#grompp -f minim.mdp -c system_solv_ions_CsCl.gro -p topol.top -o minim.tpr
Fatal error:
No such moleculetype CS
But I see the CS ion in residuetypes.dat which exist in my directory :
CS??? Ion
?
So what's the reason? If it is related to the version of applied GROMACS? I am
working with 4.5.5 GROMACS and CHARMM 36 FF.
Thanks. Would you give me any suggestions?
Sincerely,
Shima
------------------------------
Message: 6
Date: Sun, 19 May 2013 00:17:21 +0900
From: bharat gupta <bharat.85.m...@gmail.com>
Subject: Re: [gmx-users] Re: REMD analysis
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID:
<caah+zsxcyrxgz9dn8up4me884cxvp6weortqb95-_8r8oya...@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Dear Sir,
My main objective of carrying out REMD is to study peptide folding and if
possible to get some insight in protein design and folding. I read some
articles related to my work and they always show temp (replica_index)
graphs for 2-3 replicas , saying that the sufficient sampling had been
achieved. In my case I checked the replica_temp for first three replicas (
https://www.dropbox.com/s/gkbu0g0e1r37l57/replica_temp0.png) (
https://www.dropbox.com/s/sffq8rwghjublu0/replica_temp1.png)
https://www.dropbox.com/s/ulccw8xabj66ktm/replica_temp2.png)
Almost all the three graphs are similar and the last 15ns shows that there
is no enough exchange (if I have analyzed correctly) ?? In this case the
acceptance ratio was fine and PE overlap was also good, but problem lies
with efficient sampling ?? What shall I do in such a case ??
On Sat, May 18, 2013 at 12:27 AM, Mark Abraham <mark.j.abra...@gmail.com>wrote:
> On Fri, May 17, 2013 at 4:26 PM, bharat gupta <bharat.85.m...@gmail.com
> >wrote:
>
> > Dear Sir,
> >
> > The the default bin width is 0.1 which I used for plotting the graphs.
> >
>
> That's nice. You need to decide what you need to do about it if you want
> graphs that look like those you see reported :-)
>
>
> > Another question is about your last reply to my thread "exchange
> acceptance
> > is a poor proxy for sampling efficiency". Sorry to ask this, but how to
> > check whether the sampling efficiency is optimal or not (what should be
> > optimal sampling efficiency) ??
> >
>
> Ah, now here's the real question :-) Spacing the replicas for optimal
> *flow* is a difficult problem, even for toy peptides, see e.g. papers by
> Nadler and Hansmann. Merely accepting exchanges does not imply flow. The
> belief is that getting flow enhances sampling, but the latter is hard to
> demonstrate without showing that "simulation time to converged sampling"
> actually reduces. I'm not aware of anybody who's actually done that - but
> it would certainly be an advantage if your application is interested in
> data at a range of temperatures.
>
> Mark
>
> On Fri, May 17, 2013 at 11:10 PM, Mark Abraham <mark.j.abra...@gmail.com
> > >wrote:
> >
> > > Histograms 101: The smaller your bin width, the more variations you
> see.
> > > The more samples you have, the fewer variations you see. A histogram
> that
> > > does not mention either of this is a work of fiction.
> > >
> > > The number of degrees of freedom in the potential energy distribution
> is
> > > also a factor in whether the distribution will look smooth for a given
> > bin
> > > width and number of samples.
> > >
> > > Mark
> > >
> > > On Fri, May 17, 2013 at 3:51 PM, bharat gupta <
> bharat.85.m...@gmail.com
> > > >wrote:
> > >
> > > > Dear Sir,
> > > >
> > > > I tried plotting the PE overlap using the following way :-
> > > >
> > > > 1. extract PE of each replica using g_energy
> > > > 2. get the PE distribution using g_analyze -f potential_0.xvg -dist
> > > > pot0.xvg
> > > > 3. used xmgrace to plot all the PE distribution graphs together.
> > > >
> > > > The same thing I did for temperature distribution for each replica.
> > > >
> > > > Here's the file for both PE overlap (
> > > > https://www.dropbox.com/s/895f1bi0hkuy884/pe_dist.png)
> > > > temp distribution (
> > > https://www.dropbox.com/s/ed66uop16blgqwa/temp_dist.png
> > > > )
> > > > Is this the correct way ??
> > > >
> > > >
> > > > But the plot doesnot look like this (
> > > > https://www.dropbox.com/s/fsuabkl7zrydnib/sample%20PE%20overlap.jpg
> ).
> > > Do i
> > > > have to normalize the data and then plot in order to get a smooth
> plot
> > > like
> > > > this one??
> > > >
> > > > --------
> > > > Bharat
> > > > --
> > > > gmx-users mailing list gmx-users@gromacs.org
> > > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > > * Please search the archive at
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> > > >
> > > --
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> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> > >
> > --
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------------------------------
Message: 7
Date: Sat, 18 May 2013 08:31:30 -0700 (PDT)
From: Ewaru <edina_w...@yahoo.com>
Subject: [gmx-users] Re: proceed from output of MD
To: gmx-users@gromacs.org
Message-ID: <1368891090035-5008368.p...@n6.nabble.com>
Content-Type: text/plain; charset=us-ascii
Hey,
I have figured that out! My bad! :D
Thank you.
Best regards
--
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------------------------------
Message: 8
Date: Sat, 18 May 2013 14:46:38 -0400
From: Justin Lemkul <jalem...@vt.edu>
Subject: Re: [gmx-users] charmm in gromacs cut-offs
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <5197cc8e.9080...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 5/18/13 7:58 AM, tarak karmakar wrote:
> Dear All,
>
> It seems the problem in the cut-off schemes while using charmm force
> field in gromacs persists even in the latest gromacs-4.6.1 version.
> Recently I have posted regarding this problem came in gromacs-4.5.5
> version. If anybody has already tested this issue in the latest version,
> please leave a comment in the mailing list.
>
> The cut-off parameters I have used are as follows
>
> rlist = 1.2
> rlistlong = 1.4
>
> ; 7.3.10 Electrostatics
> coulombtype = PME
> rcoulomb = 1.2
>
> ; 7.3.11 VdW
> vdwtype = switch
> rvdw = 1.2
> rvdw-switch = 1.0
>
> NOTE 3 [file md_sim_ann.mdp]:
> The switch/shift interaction settings are just for compatibility; you
> will get better performance from applying potential modifiers to your
> interactions!
>
> NOTE 4 [file md_sim_ann.mdp]:
> For energy conservation with switch/shift potentials, rlist should be 0.1
> to 0.3 nm larger than rvdw.
>
> NOTE 5 [file md_sim_ann.mdp]:
> The sum of the two largest charge group radii (0.079732) is larger than
> rlist (1.200000) - rvdw (1.200000)
>
> This part is reported as bug in gromacs -4.5.5 and required to be verified
> by users through their feedback
>
> http://redmine.gromacs.org/issues/1164
>
> In this link it is showing affected version grom-4.6.1 !!
>
There are a lot of conditionals that are evaluated and probably (as Mark has
indicated) some of them are conflicting. What you have posted above seems
correct from my interpretation of everything I have read about using CHARMM.
Since all you are getting are notes (rather than errors), you shouldn't have any
problems.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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