Re: [gmx-users] Configurations stored in REMD trajectories

[César Ávila]

Thanks :D

2011/12/30 Mark Abraham 

> On 31/12/2011 7:03 AM, César Ávila wrote:
>
>> Dear all,
>> perhaps someone can help me with this doubt. When a REMD simulation is
>> run, which configuration is stored for any given replica, the one before
>> the exchange or the one that we get after the exchange (i.e. the exchange
>> partner configuration)?
>>
>
> Replica exchange occurs after all output - it's essentially the last thing
> that happens in the main loop.
>
> Mark
> --
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[gmx-users] Configurations stored in REMD trajectories

[César Ávila]

Dear all,
perhaps someone can help me with this doubt. When a REMD simulation is run,
which configuration is stored for any given replica, the one before the
exchange or the one that we get after the exchange (i.e. the exchange
partner configuration)?
Best regards
Cesar
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Re: [gmx-users] CMAP for alanine dipeptide in Charmm27 ff

[César Ávila]

Done

2011/10/10 Mark Abraham 

>  On 11/10/2011 4:51 AM, César Ávila wrote:
>
> v4.5.4
> As I commented above, I had to manually add an entrance for the cmap terms
> in the topology file as pdb2gmx would not generate them for the alanine
> dipeptide. There seems to be no problem for larger peptides.
> Cheers
> Cesar
>
>
> That sounds like a bug. Please describe your symptoms in a new issue here -
> http://redmine.gromacs.org
>
> Mark
>
>
>  2011/10/10 Jianguo Li 
>
>>  which gromacs version are you using? cMAP is implemented in v4.5  or
>> later
>>  Jianguo
>>
>>   --
>> *From:* César Ávila 
>> *To:* Discussion list for GROMACS users 
>> *Sent:* Sunday, 9 October 2011 12:07 AM
>> *Subject:* [gmx-users] CMAP for alanine dipeptide in Charmm27 ff
>>
>> I would like to run REMD simulations on the alanine dipeptide using the
>> Charmm27ff + CMAP. Still, after processing the pdb with pdb2gmx, I do not
>> see any entrance referring to the cmap term in the topology file. Does this
>> mean that Cmap won't be calculated?
>>
>>
>>  --
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>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>
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>
>
>
>
>
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Re: [gmx-users] CMAP for alanine dipeptide in Charmm27 ff

[César Ávila]

v4.5.4
As I commented above, I had to manually add an entrance for the cmap terms
in the topology file as pdb2gmx would not generate them for the alanine
dipeptide. There seems to be no problem for larger peptides.
Cheers
Cesar

2011/10/10 Jianguo Li 

> which gromacs version are you using? cMAP is implemented in v4.5  or later
> Jianguo
>
> --
> *From:* César Ávila 
> *To:* Discussion list for GROMACS users 
> *Sent:* Sunday, 9 October 2011 12:07 AM
> *Subject:* [gmx-users] CMAP for alanine dipeptide in Charmm27 ff
>
> I would like to run REMD simulations on the alanine dipeptide using the
> Charmm27ff + CMAP. Still, after processing the pdb with pdb2gmx, I do not
> see any entrance referring to the cmap term in the topology file. Does this
> mean that Cmap won't be calculated?
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>
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[gmx-users] Re: CMAP for alanine dipeptide in Charmm27 ff

[César Ávila]

It looks like pdb2gmx does not generate an entrance for cmap terms. I added
it manually to the topology file.

2011/10/8 César Ávila 

> I would like to run REMD simulations on the alanine dipeptide using the
> Charmm27ff + CMAP. Still, after processing the pdb with pdb2gmx, I do not
> see any entrance referring to the cmap term in the topology file. Does this
> mean that Cmap won't be calculated?
>
>
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[gmx-users] CMAP for alanine dipeptide in Charmm27 ff

[César Ávila]

I would like to run REMD simulations on the alanine dipeptide using the
Charmm27ff + CMAP. Still, after processing the pdb with pdb2gmx, I do not
see any entrance referring to the cmap term in the topology file. Does this
mean that Cmap won't be calculated?
-- 
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http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] Replex in REMD

[César Ávila]

Dear all,
I am running REMD simulations in gromacs. Taking advantage of vsites I have
set the timestep to 5 fs. In the mdp file I have adjusted the energy and
frames to be written every 1000 steps (5 ps). While running the simulations
I have also selected the exchange trials to be done every 1000 steps (5 ps).
I would like to decrease the number of steps between exchange trials, while
storing energy and configurations every 5 ps. Is it ok to do so, or will  I
have some problem in the future while trying to analyse the data?
Thanks in advance
Cesar
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Re: [gmx-users] secondary structure propensities of residues

[César Ávila]

I am using the latest vesion of DSSP (the one available at DSSP homepage)

2011/8/11 Mark Abraham 

>  On 10/08/2011 6:03 AM, César Ávila wrote:
>
> Hi,
> I downloaded release-4-5-patches from git. It compiles and installs
> successfully. Nevertheless I am getting a segmentation fault.
>
>
> Are you using a version of DSSP that is compatible with GROMACS, pre
> previous discussion of DSSP changes?
>
> Mark
>
>
> With gdb I am getting the following messages
>
>
> gdb --args do_dssp -f ../0_trajout.xtc -s ../input/replica_0.tpr -ssdump
> data.dat -b 17 -e 18 -dt 10
> GNU gdb (GDB) 7.2-ubuntu
> Copyright (C) 2010 Free Software Foundation, Inc.
> License GPLv3+: GNU GPL version 3 or later <
> http://gnu.org/licenses/gpl.html>
> This is free software: you are free to change and redistribute it.
> There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
> and "show warranty" for details.
> This GDB was configured as "x86_64-linux-gnu".
> Para las instrucciones de informe de errores, vea:
> <http://www.gnu.org/software/gdb/bugs/>...
> Leyendo símbolos desde /usr/local/gromacs/bin/do_dssp...(no se encontraron
> símbolos de depuración)hecho.
> (gdb) run
> Starting program: /usr/local/gromacs/bin/do_dssp -f ../0_trajout.xtc -s
> ../input/replica_0.tpr -ssdump data.dat -b 17 -e 18 -dt 10
> [Depuración de hilo usando libthread_db enabled]
>  :-)  G  R  O  M  A  C  S  (-:
>
>Gromacs Runs One Microsecond At Cannonball Speeds
>
>   :-)  VERSION 4.5.4-dev-20110803-e49fb5a  (-:
>
> Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
>   Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
> Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
>Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
> Michael Shirts, Alfons Sijbers, Peter Tieleman,
>
>Berk Hess, David van der Spoel, and Erik Lindahl.
>
>Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2010, The GROMACS development team at
> Uppsala University & The Royal Institute of Technology, Sweden.
> check out http://www.gromacs.org for more information.
>
>  This program is free software; you can redistribute it and/or
>   modify it under the terms of the GNU General Public License
>  as published by the Free Software Foundation; either version 2
>  of the License, or (at your option) any later version.
>
> :-)  /usr/local/gromacs/bin/do_dssp  (-:
>
> Option Filename  Type Description
> 
>   -f ../0_trajout.xtc  InputTrajectory: xtc trr trj gro g96 pdb cpt
>   -s ../input/replica_0.tpr  InputStructure+mass(db): tpr tpb tpa
> gro
>g96 pdb
>   -n  index.ndx  Input, Opt.  Index file
> -ssdumpdata.dat  Output, Opt! Generic data file
> -map ss.map  Input, Lib.  File that maps matrix data to colors
>   -o ss.xpm  Output   X PixMap compatible matrix file
>  -sc scount.xvg  Output   xvgr/xmgr file
>   -a   area.xpm  Output, Opt. X PixMap compatible matrix file
>  -tatotarea.xvg  Output, Opt. xvgr/xmgr file
>  -aa   averarea.xvg  Output, Opt. xvgr/xmgr file
>
> Option   Type   Value   Description
> --
> -[no]h   bool   no  Print help info and quit
> -[no]version bool   no  Print version info and quit
> -niceint19  Set the nicelevel
> -b   time   17  First frame (ps) to read from trajectory
> -e   time   18  Last frame (ps) to read from trajectory
> -dt  time   10  Only use frame when t MOD dt = first time (ps)
> -tu  enum   ps  Time unit: fs, ps, ns, us, ms or s
> -[no]w   bool   no  View output .xvg, .xpm, .eps and .pdb files
> -xvg enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
> -sss string HEBTSecondary structures for structure count
>
> Reading file ../input/replica_0.tpr, VERSION 4.5.3 (single precision)
> Reading file ../input/replica_0.tpr, VERSION 4.5.3 (single precision)
>
> Program received signal SIGSEGV, Segmentation fault.
> 0x76ae043c in gmx_strcasecmp () from
> /usr/local/gromacs/lib/libgmx.so.6
> (gdb) bt
> #0  0x76ae043c in gmx_strcasecmp () from
> /usr/local/gromacs/lib/libgmx.so.6
> #1  0x76ade68f in search_str () from
> /usr/local/gromacs

Re: [gmx-users] secondary structure propensities of residues

[César Ávila]

Hi,
I downloaded release-4-5-patches from git. It compiles and installs
successfully. Nevertheless I am getting a segmentation fault.
With gdb I am getting the following messages


gdb --args do_dssp -f ../0_trajout.xtc -s ../input/replica_0.tpr -ssdump
data.dat -b 17 -e 18 -dt 10
GNU gdb (GDB) 7.2-ubuntu
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later 
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-linux-gnu".
Para las instrucciones de informe de errores, vea:
...
Leyendo símbolos desde /usr/local/gromacs/bin/do_dssp...(no se encontraron
símbolos de depuración)hecho.
(gdb) run
Starting program: /usr/local/gromacs/bin/do_dssp -f ../0_trajout.xtc -s
../input/replica_0.tpr -ssdump data.dat -b 17 -e 18 -dt 10
[Depuración de hilo usando libthread_db enabled]
 :-)  G  R  O  M  A  C  S  (-:

   Gromacs Runs One Microsecond At Cannonball Speeds

  :-)  VERSION 4.5.4-dev-20110803-e49fb5a  (-:

Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
  Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
   Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,

   Berk Hess, David van der Spoel, and Erik Lindahl.

   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.

:-)  /usr/local/gromacs/bin/do_dssp  (-:

Option Filename  Type Description

  -f ../0_trajout.xtc  InputTrajectory: xtc trr trj gro g96 pdb cpt
  -s ../input/replica_0.tpr  InputStructure+mass(db): tpr tpb tpa
gro
   g96 pdb
  -n  index.ndx  Input, Opt.  Index file
-ssdumpdata.dat  Output, Opt! Generic data file
-map ss.map  Input, Lib.  File that maps matrix data to colors
  -o ss.xpm  Output   X PixMap compatible matrix file
 -sc scount.xvg  Output   xvgr/xmgr file
  -a   area.xpm  Output, Opt. X PixMap compatible matrix file
 -tatotarea.xvg  Output, Opt. xvgr/xmgr file
 -aa   averarea.xvg  Output, Opt. xvgr/xmgr file

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-[no]version bool   no  Print version info and quit
-niceint19  Set the nicelevel
-b   time   17  First frame (ps) to read from trajectory
-e   time   18  Last frame (ps) to read from trajectory
-dt  time   10  Only use frame when t MOD dt = first time (ps)
-tu  enum   ps  Time unit: fs, ps, ns, us, ms or s
-[no]w   bool   no  View output .xvg, .xpm, .eps and .pdb files
-xvg enum   xmgrace  xvg plot formatting: xmgrace, xmgr or none
-sss string HEBTSecondary structures for structure count

Reading file ../input/replica_0.tpr, VERSION 4.5.3 (single precision)
Reading file ../input/replica_0.tpr, VERSION 4.5.3 (single precision)

Program received signal SIGSEGV, Segmentation fault.
0x76ae043c in gmx_strcasecmp () from
/usr/local/gromacs/lib/libgmx.so.6
(gdb) bt
#0  0x76ae043c in gmx_strcasecmp () from
/usr/local/gromacs/lib/libgmx.so.6
#1  0x76ade68f in search_str () from
/usr/local/gromacs/lib/libgmx.so.6
#2  0x77b508d4 in bPhobics () from
/usr/local/gromacs/lib/libgmxana.so.6
#3  0x0040309a in main ()


2011/3/9 Mark Abraham 

> On 10/03/2011 1:36 AM, Justin A. Lemkul wrote:
>
>>
>>
>> ZHAO Lina wrote:
>>
>>> Hi,
>>>
>>> How do get the percentage of the secondary structure propensities of
>>> residues?
>>>
>>> seems dssp none such effect?
>>>
>>>
>> The scout.xvg file contains everything you need (in a broad sense) -
>> number of residues in a given secondary structure over time.  If you need a
>> per-residue breakdown, there is no Gromacs tool that does that, but the .xpm
>> file contains that information, so you can write your own script and extract
>> it.
>>
>
> Actually I modified do_dssp in late January to do that. The OP will need to
> do

[gmx-users] git release-4-5-patches behind proxy

[César Ávila]

I want to calculate secondary structure propensities of residues.

Following Mark's message on thread
Re: [gmx-users] secondary structure propensities of residues


I would like to get the release-4.5-patches from git (in order to get
do_dssp.c). Nevertheless I found problems while trying to fetch it from git
repository due to the proxy. (I followed the advices on
http://www.gromacs.org/Developer_Zone/Git/Git_Tutorial#Git_behind_a_proxy

$ git clone git://git.gromacs.org/gromacs.git
Initialized empty Git repository in ~/gromacs/.git/
2011/08/09 10:37:46 socat[17264] E CONNECT git.gromacs.org:9418: Forbidden
fatal: The remote end hung up unexpectedly

I tried the alternative suggested by Roland

git clone  http://repo.or.cz/r/gromacs.git
Initialized empty Git repository in ~/gromacs/.git/

The gromacs directory is created and populated. After this I ran

$git branch
* master

$git checkout --track -b release-4-5-patches origin/release-4-5-patches
fatal: git checkout: updating paths is incompatible with switching branches.
Did you intend to checkout 'origin/release-4-5-patches' which can not be
resolved as commit?

Is this a problem of the server I am using or is it just a misuse of git?

Thanks








2011/3/22 Roland Schulz 

> you can clone from http://repo.or.cz/r/gromacs.git if you have problems
> with a proxy.
>
> On Mon, Mar 21, 2011 at 10:54 PM, Alif M Latif wrote:
>
>>Dear Gromacs Developers,
>>
>> Just dropping by to say THANK YOU for v4.5.4, surely is updated version of
>> 4.5.3 with all the bugfixes yes?. I'm having problem getting past my
>> university's proxy server to use git. Now hopefully I can continue my
>> research and solve git problems later..Your hard work is greatly
>> appreciated!
>>
>> MUHAMMAD ALIF MOHAMMAD LATIF
>> Laboratory of Theoretical and Computational Chemistry
>> Department of Chemistry
>> Faculty of Science
>> Universiti Putra Malaysia
>> 43400 UPM Serdang, Selangor
>> MALAYSIA
>>
>>
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
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>>
>
>
>
> --
> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
> 865-241-1537, ORNL PO BOX 2008 MS6309
>
> --
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Re: [gmx-users] do we still have a do_dssp and dssp compatibility issue? thread: do_dssp failed to execute

[César Ávila]

I was dealing with the same situation. I am using the latest version of DSSP
(April 2011). Neither gromacs 4.5.3 or 4.5.4 would work.
After applying Pradip's patch, do_dssp worked for me.

I would say that the change in flags is related to the fact that "In 2011
Maarten Hekkelman has written new software" (as stated on DSSP homepage).

Thanks :D.


2011/8/6 Pradip Biswas 

> I encountered the exact same error with Gromacs-4.5  as posted by Sunita
> Patel back in October 2010 and could not find any solution in the
> gmx_thread. The error was:
>
> Failed to execute command: /home/path-to-dssp -na dd3sOJn3 ddZl9dcf >
> /dev/null 2> /dev/null
>
> I found that the do_dssp fails to fork dssp as the latter does not
> recognize the flag "-na" defined in do_dssp. The dssp code that I downloaded
> recently, recognizes the only flags "-i", "-o", "-v", "-d" and "-h".
>
> So, I just tweaked the "-na" flag in the do_dssp source code as follows and
> the do_dssp and dssp combination worked fine for me.
>
> original:
> sprintf(dssp,"%s %s %s %s > /dev/null %s",
>   dptr,bDoAccSurf?"":"-na",pdbfile,tmpfile,bVerbose?"":"2> /dev/null");
>
> replaced by:
> sprintf(dssp,"%s %s %s %s > /dev/null %s",
>   dptr,bDoAccSurf?"":"-i",pdbfile,"-o",tmpfile,bVerbose?"":"2> /dev/null");
>
> -pb
>
>
>
> --
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Re: [gmx-users] Thermostat for REMD simulations in implicit solvent

[César Ávila]

I also noticed this error on my setup, so I changed tau-t to 0.1, which is
commonly found on others setup.
tau-t = 0.0109 seems too low.

2010/11/26 Per Larsson 

> Hi!
>
> Have never tried remd with implicit solvent, but note that the unit of
> tau-t in the mdp-file is ps, not ps-1. This means you should set tau-t =
> 0.0109 rather than 91.
>
> Try this and see if the problem goes away!
>
> /Per
>
> 26 nov 2010 kl. 15:55 skrev César Ávila :
>
> > Dear all,
> > I am trying to set up a REMD simulation for a peptide (CHARMM ff) in
> implicit solvent (OBC GB).
> > Following Bjelkmar et al* I am using stochastics dynamics integration
> with an inverse friction constant of 91 ps-1, 5 fs timestep,
> > virtual-sites for hydrogens, all-vs-all nonbonded (no cutoff).  The full
> .mdp file is attached at the end of this mail. The problem I am
> > facing is that after a while, the temperatures of all replicas start
> dropping even below the lowest target temperature.
> > Would you suggest changing some parameter or the whole thermostat to
> prevent this from happening?
> >
> > @ s0 legend "Temperature"
> > 0.00  310.811523
> > 5.00  435.627045
> >10.00  417.161713
> >15.00  414.248901
> >20.00  399.390686
> >25.00  375.087219
> >30.00  338.131256
> >35.00  339.961151
> >40.00  319.424561
> >45.00  290.442322
> >50.00  289.587921
> >55.00  248.746246
> >60.00  253.192047
> >65.00  242.619476
> >70.00  256.051941
> >75.00  237.648468
> >80.00  231.938690
> >85.00  217.029953
> >90.00  211.447983
> >95.00  210.393890
> >   100.00  208.518417
> >   105.00  196.718445
> >   110.00  219.245682
> >   115.00  202.957993
> >   120.00  193.128159
> >   125.00  198.278198
> >   130.00  175.304108
> >   135.00  164.925613
> >   140.00  195.024490
> >   145.00  201.153046
> >   150.00  211.160797
> >   155.00  189.525085
> >   160.00  191.156006
> >   165.00  186.545242
> >   170.00  186.885422
> >   175.00  182.838486
> >   180.00  174.960098
> >   185.00  175.244049
> >   190.00  179.517975
> >   195.00  165.785416
> >   200.00  189.871048
> >   205.00  179.510178
> >   210.00  152.527710
> >   215.00  160.109955
> >   220.00  163.564148
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > * "Implementation of the CHARMM ff in GROMACS" (2010) JCTC, 6, 459-466
> >
> >
> > ; Run parameters
> > integrator  =  sd
> > dt  =  0.005; ps !
> > nsteps  =  2
> > nstcomm = 1
> > comm_mode   = angular   ; non-periodic system
> >
> > ; Bond parameters
> > constraints = all-bonds
> > constraint_algorithm= lincs
> > lincs-iter  = 1
> > lincs-order = 6
> >
> > ; required cutoffs for implicit
> > nstlist =  0
> > ns_type =  grid
> > rlist   =  0
> > rcoulomb=  0
> > rvdw=  0
> > epsilon_rf  =  0
> > rgbradii=  0
> >
> > ; cutoffs required for qq and vdw
> > coulombtype =  cut-off
> > vdwtype =  cut-off
> >
> > ; temperature coupling
> > tcoupl  = v-rescale
> > tc-grps = system
> > tau-t   = 91
> > ref-t   = 300
> >
> > ; Pressure coupling is off
> > Pcoupl  = no
> >
> > ; Periodic boundary conditions are off for implicit
> > pbc = no
> >
> > ; Settings for implicit solvent
> > implicit_solvent= GBSA
> > gb_algorithm= OBC
> > gb_epsilon_solvent  = 78.3
> > sa_surface_tension  = 2.25936
> >
> > ;Output control
> > nstxout = 1000
> > nstfout = 0
> > nstvout = 0
> > nstxtcout   = 0
> > nstlog  = 1000
> > nstcalcenergy   = -1
> > nstenergy   = 1000
> >
> > ; GENERATE VELOCITIES FOR STARTUP RUN
> > gen_vel = yes
> > gen_temp = 300
> > gen_seed = 1993
> >
> >
> >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http:

[gmx-users] Thermostat for REMD simulations in implicit solvent

[César Ávila]

Dear all,
I am trying to set up a REMD simulation for a peptide (CHARMM ff) in
implicit solvent (OBC GB).
Following Bjelkmar et al* I am using stochastics dynamics integration with
an inverse friction constant of 91 ps-1, 5 fs timestep,
virtual-sites for hydrogens, all-vs-all nonbonded (no cutoff).  The full
.mdp file is attached at the end of this mail. The problem I am
facing is that after a while, the temperatures of all replicas start
dropping even below the lowest target temperature.
Would you suggest changing some parameter or the whole thermostat to prevent
this from happening?

@ s0 legend "Temperature"
0.00  310.811523
5.00  435.627045
   10.00  417.161713
   15.00  414.248901
   20.00  399.390686
   25.00  375.087219
   30.00  338.131256
   35.00  339.961151
   40.00  319.424561
   45.00  290.442322
   50.00  289.587921
   55.00  248.746246
   60.00  253.192047
   65.00  242.619476
   70.00  256.051941
   75.00  237.648468
   80.00  231.938690
   85.00  217.029953
   90.00  211.447983
   95.00  210.393890
  100.00  208.518417
  105.00  196.718445
  110.00  219.245682
  115.00  202.957993
  120.00  193.128159
  125.00  198.278198
  130.00  175.304108
  135.00  164.925613
  140.00  195.024490
  145.00  201.153046
  150.00  211.160797
  155.00  189.525085
  160.00  191.156006
  165.00  186.545242
  170.00  186.885422
  175.00  182.838486
  180.00  174.960098
  185.00  175.244049
  190.00  179.517975
  195.00  165.785416
  200.00  189.871048
  205.00  179.510178
  210.00  152.527710
  215.00  160.109955
  220.00  163.564148









* "Implementation of the CHARMM ff in GROMACS" (2010) JCTC, 6, 459-466


; Run parameters
integrator  =  sd
dt  =  0.005; ps !
nsteps  =  2
nstcomm = 1
comm_mode   = angular   ; non-periodic system

; Bond parameters
constraints = all-bonds
constraint_algorithm= lincs
lincs-iter  = 1
lincs-order = 6

; required cutoffs for implicit
nstlist =  0
ns_type =  grid
rlist   =  0
rcoulomb=  0
rvdw=  0
epsilon_rf  =  0
rgbradii=  0

; cutoffs required for qq and vdw
coulombtype =  cut-off
vdwtype =  cut-off

; temperature coupling
tcoupl  = v-rescale
tc-grps = system
tau-t   = 91
ref-t   = 300

; Pressure coupling is off
Pcoupl  = no

; Periodic boundary conditions are off for implicit
pbc = no

; Settings for implicit solvent
implicit_solvent= GBSA
gb_algorithm= OBC
gb_epsilon_solvent  = 78.3
sa_surface_tension  = 2.25936

;Output control
nstxout = 1000
nstfout = 0
nstvout = 0
nstxtcout   = 0
nstlog  = 1000
nstcalcenergy   = -1
nstenergy   = 1000

; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = yes
gen_temp = 300
gen_seed = 1993
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[gmx-users] Adding custom residue to Charmm FF in Gromacs

[César Ávila]

Hi,
I would like to add topology and parameter information for a custom residue
to the CHARMM forcefield on GROMACS 4.5.3. Which are the files that I should
edit for this? Should I also perform some units conversion?
Thanks
Cesar
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[gmx-users] Using Charmm FF with implicit solvent on gromacs

[César Ávila]

Dear all,
I would like to know if anyone has experience on running simulations using
the Charmm FF and implicit solvent model on gromacs. I have found that
gromacs has three implementations for GB models

   - Still
   - Hawkins-Cramer-Truhlar (HCT)
   - Onufriev-Bashford-Case (OBC)

The charmm FF has been extensively tested with the GBSW* implementation (in
Charmm program) for which the backbone phi/psi cross-term (CMAP) and the
atomic input radii were specifically optimized (Chan, Im and Brooks, JACS,
2006).

Is there a way to perform the same calculation on gromacs?

* W. Im, M.S. Lee, and C.L. Brooks III  "Generalized Born Model with a
Simple Smoothing Function." J. Comput. Chem. 24:1691-1702 (2003).
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Re: [gmx-users] How can I reconstruct the system in CGMD simulation?

[César Ávila]

For a detailed description of how to set up protein simulation, I recomend
you to read the Martini Tutorial on
http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.html
there you will find  step by step instructions along with some explanations
of what you are actually doing.
In this case you only want to build a water box around your protein. For
that you will use editconf and a vdw distance of 0.19.

Regards
Cesar

2009/12/17 rasoul nasiri 

> yes, I know there will be limitation for modeling of Folding/Unfolding
> proteins with MARtini CGFF if I want to look at complete folding/unfolding
> mechanism of proteins but I want to find out localized regions of the
> protein (e.g. the C- or N-termini) that they have contribution to the
> denaturation mechanism.
> My question is about vdwd in beads of water. Is it OK if I select distances
> of 0.15-0.20nm as vdwd of water beads in CGMD simulation or I have to
> reconstruct the system in smaller vdw distance of the water beads for doing
> my purpose. and Which commands of Gromacs can do it?
>
> Best regards
> Rasoul
>
> On Thu, Dec 17, 2009 at 5:03 PM, César Ávila  wrote:
>
>> I suggest you read the original paper for Martini Protein FF. I think it
>> is not suitable for your purpouse.
>>
>> 2009/12/17 rasoul nasiri 
>>
>>> Hi,
>>>
>>> My purpose is finding of denaturation mechanism of proteins with MArtini
>>> CGFF by Gromacs.
>>> I mean after filling box in which there are beads of protein from water
>>> beads with suitable van der wall distance (larger than 0.105nm), when I want
>>> to start production phase, first switch back to the smaller radius of van
>>> der waals of the water beads, then I will continue CGMD simulation. Is it
>>> possible I reduce this radius? Which commands of Gromacs suit can do it?
>>>
>>> Rasoul
>>>
>>>
>>> On Thu, Dec 17, 2009 at 1:42 PM, Mark Abraham 
>>> wrote:
>>>
>>>> rasoul nasiri wrote:
>>>>
>>>>> greetings GMX users,
>>>>>
>>>>> When I use genbox command for filling solvent in CGMD simulation with
>>>>> Gromacs suit, I must use a larger van der Waals distance to avoid crashes.
>>>>> when I use default value (0.105nm), system will crash. Which distance is
>>>>> suitable for performing CGMD simulation. I used  0.15 or 0.2nm as 
>>>>> distances.
>>>>> Are those OK?
>>>>>
>>>>
>>>> Read up on your forcefield and find out how "large" the particles tend
>>>> to be. It only has to be good enough, not perfect.
>>>>
>>>>
>>>>  I have to switch back to the smaller radius afterward, Is it correct?
>>>>>
>>>>
>>>> Changing what for what purpose?
>>>>
>>>>
>>>>  if yes, How can I do it? I tried with editconf but could not.
>>>>>
>>>>
>>>> I don't know what you mean.
>>>>
>>>> Mark
>>>> --
>>>> gmx-users mailing listgmx-users@gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>>>
>>>
>>>
>>> --
>>>
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>>
>>
>> --
>>
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Re: [gmx-users] How can I reconstruct the system in CGMD simulation?

[César Ávila]

I suggest you read the original paper for Martini Protein FF. I think it is
not suitable for your purpouse.

2009/12/17 rasoul nasiri 

> Hi,
>
> My purpose is finding of denaturation mechanism of proteins with MArtini
> CGFF by Gromacs.
> I mean after filling box in which there are beads of protein from water
> beads with suitable van der wall distance (larger than 0.105nm), when I want
> to start production phase, first switch back to the smaller radius of van
> der waals of the water beads, then I will continue CGMD simulation. Is it
> possible I reduce this radius? Which commands of Gromacs suit can do it?
>
> Rasoul
>
>
> On Thu, Dec 17, 2009 at 1:42 PM, Mark Abraham wrote:
>
>> rasoul nasiri wrote:
>>
>>> greetings GMX users,
>>>
>>> When I use genbox command for filling solvent in CGMD simulation with
>>> Gromacs suit, I must use a larger van der Waals distance to avoid crashes.
>>> when I use default value (0.105nm), system will crash. Which distance is
>>> suitable for performing CGMD simulation. I used  0.15 or 0.2nm as distances.
>>> Are those OK?
>>>
>>
>> Read up on your forcefield and find out how "large" the particles tend to
>> be. It only has to be good enough, not perfect.
>>
>>
>>  I have to switch back to the smaller radius afterward, Is it correct?
>>>
>>
>> Changing what for what purpose?
>>
>>
>>  if yes, How can I do it? I tried with editconf but could not.
>>>
>>
>> I don't know what you mean.
>>
>> Mark
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>
>
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Re: [gmx-users] Reproducing Chain Tilt on DPPC gel phase with Martini FF

[César Ávila]

Dear Xavier,
thanks for your response. Yes, indeed I have tried to contact the authors,
but perhaps they can't receive my mails. I have tried scaling sigma alone to
0.9 or 0.965 (which would correspond to a 10% reduction of radius or volume
respectively). Since some special particles scale epsilon along with sigma,
I also tried this, but with no success.
Cheers,
Cesar


2009/12/10 XAvier Periole 

>
> On Dec 9, 2009, at 11:21 PM, César Ávila wrote:
>
>  Dear all,
>> I would like to simulate a DPPC membrane in gel phase using Martini Force
>> Field. As stated on
>>
>> "Simulation of gel phase formation and melting in lipid bilayers using a
>> coarse grained model", CPL 135 (2005) 223-244
>>
>> the correct 30º angle chain tilt for DPPC might be reproduced by reducing
>> the acyl chain spheres volume by 10%.
>>  So far, I have tried changing sigma and epsilon for C1-C1 pair
>> interaction without success.
>>
> The sphere volume or radius is defined by sigma. Epsilon deals with the
> strength of the interactions; you do not want to modify it.
> Did you try to contact the authors? They might be of better
> help!
>
>>
>> Best regards
>> Cesar Avila
>>
>>
>>
>> --
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[gmx-users] Reproducing Chain Tilt on DPPC gel phase with Martini FF

[César Ávila]

Dear all,
I would like to simulate a DPPC membrane in gel phase using Martini Force
Field. As stated on

"Simulation of gel phase formation and melting in lipid bilayers using a
coarse grained model", CPL 135 (2005) 223-244

the correct 30º angle chain tilt for DPPC might be reproduced by reducing
the acyl chain spheres volume by 10%.
 So far, I have tried changing sigma and epsilon for C1-C1 pair interaction
without success.

Best regards
Cesar Avila
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