Hi David,
I have a cube box filled with 100 polymer molecules without any solvent
molecules. I would like to equilibrate the structures and see how all
conformations fold in implicit solvent. As I run the simulations, it
changes the overall dimension or volume of the box. That is what we are not
interested in.
I found another problem while running with ntb = 1 option on in mini.in and
md.in. The box dimensions changed as,
Initial dimensions (min,max)= [(-150, -150,-150),(150, 150,150)]
after running md, the first frame has the following dimensions and there
are additional lines that look like bonding between molecules.
Initial dimensions (min,max)= [(-150, -150,-150),(300, 300,300)]
However, all simulations go well with ntb = 0 and igb = 1 inputs.
Here is my tleap script. I extract the dimension from pdb file using vmd
program.
mybox = loadpdb box104.pdb
set mybox box {300, 300, 300}
set default nocenter on
saveamberparm peg_rna box104.prmtop box104.inpcrd
and these are mini.in and md.in scripts;
> mini.in
&cntrl
imin = 1,
maxcyc = 500,
ncyc = 250,
ntb = 1,
ntr = 0,
cut = 10.0
/
> md.in
&cntrl
imin = 0, ntb = 1,
igb = 0, ntpr = 100, ntwx = 100,
ntt = 3, gamma_ln = 1.0,
tempi = 300.0, temp0 = 300.0
nstlim = 100000, dt = 0.001,
cut = 10.0
/
On Mon, May 16, 2016 at 1:00 PM, <amber-request.ambermd.org> wrote:
> Send AMBER mailing list submissions to
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>
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> AMBER Mailing List Digest
>
> Today's Topics:
>
> 1. MMPBSA for homo-dimer system with ligands (Kat G)
> 2. problem installing AmberTools16 pytraj on Mac (Marc van der Kamp)
> 3. No leaprc.ff14SB anymore in AmberTools16 - reason?
> (Marc van der Kamp)
> 4. Re: No leaprc.ff14SB anymore in AmberTools16 - reason? (Nhai)
> 5. Re: No leaprc.ff14SB anymore in AmberTools16 - reason?
> (Hannes Loeffler)
> 6. Re: No leaprc.ff14SB anymore in AmberTools16 - reason?
> (Marc van der Kamp)
> 7. Re: problem installing AmberTools16 pytraj on Mac
> (Hannes Loeffler)
> 8. Re: problem installing AmberTools16 pytraj on Mac
> (Marc van der Kamp)
> 9. Re: No leaprc.ff14SB anymore in AmberTools16 - reason?
> (Hannes Loeffler)
> 10. Re: Fix dimension of the box throughout the MD simulations
> (Iqbal, Muhammad Sajid)
> 11. Re: Fix dimension of the box throughout the MD simulations
> (David A Case)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 16 May 2016 00:03:35 -0500
> From: Kat G <katwin86.gmail.com>
> Subject: [AMBER] MMPBSA for homo-dimer system with ligands
> To: amber.ambermd.org
> Message-ID:
> <
> CAAoPRXUbXH3ChgGfRj0Nj2MJCKgb2fx3cu2WLT8Xt7KNwZOWLA.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi all,
>
> I am interested in MMPBSA calculation for the interaction of protein and
> ligand. My system is a homo-dimer, and each monomer interacts with the same
> ligand. The question is how should I define "receptor" and "ligand" in this
> case.
>
> The first trial, I treated "receptor" as dimer protein and "ligand" as 2
> ligands. For the second one, "receptor" is a dimer and 1 ligand, and
> "ligand" is the other ligand. Both of these cases give rather big negative
> delG_binding values, the second one seems to be a half of the first. But
> they are all driven by delG_solvation (big negative number), not delG_gas
> (small positive number). Protein-ligand interaction is observed strongly
> during MD and experimental data.
>
> I suppose that my definition "for receptor" and "ligand" would cause the
> trouble to the MMPBSA calculations. Could anyone give me an advice.
>
> Thanks
> k
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 16 May 2016 16:23:11 +0100
> From: Marc van der Kamp <marcvanderkamp.gmail.com>
> Subject: [AMBER] problem installing AmberTools16 pytraj on Mac
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CAGCFhhfTOZJJdDb8N0QrHOjQiPt4NoO7v_c5QL75BULO1DUBzg.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi all,
>
> I just tried to install AmberTools16 on a new Mac Book pro, running OS X El
> Capitan (10.11.4).
>
> I've installed and selected gcc4.9 (and also installed flex, py27-numpy &
> py27-matplotlib) through MacPorts.
>
> All is well (i.e. most things are compiled) until I get to pytraj, where
> "make install" eventually fails with the following:
> gcc: error: unrecognized command line option '-Wshorten-64-to-32'
>
> At this point, I don't yet need pytraj, but it would be nice to have a
> complete install.
> Any insight in how to fix this would be welcome.
>
> Thanks,
> Marc
>
> More detail:
>
> creating build/temp.macosx-10.11-intel-2.7/pytraj
>
> gcc -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g
> -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX
> -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv
> -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe
> -I/Users/chmwvdk/amber16/AmberTools/src/cpptraj/src
> -I/Users/chmwvdk/amber16/AmberTools/src/pytraj/pytraj/
>
> -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7
> -c pytraj/c_dict.cpp -o build/temp.macosx-10.11-intel-2.7/pytraj/c_dict.o
> -O0 -ggdb
>
> gcc: error: unrecognized command line option '-Wshorten-64-to-32'
>
> error: command 'gcc' failed with exit status 1
>
> make[2]: *** [pytraj] Error 1
>
> make[1]: *** [serial] Error 2
>
> make: *** [install] Error 2
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 16 May 2016 16:27:38 +0100
> From: Marc van der Kamp <marcvanderkamp.gmail.com>
> Subject: [AMBER] No leaprc.ff14SB anymore in AmberTools16 - reason?
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAGCFhhciNxWFHjVSotAn20jk=
> WiQAj7ooJfvR-q42stuDA-fdw.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> I'm just wondering why there is no $AMBERHOME/dat/leap/cmd/leaprc.ff14SB
> anymore in AmberTools16?
>
> I understand that now leaprc.protein.ff14SB exists, and one could combine
> this with other leaprc files to achieve the same (although not 100% how to
> get exactly the same) as with
> source leaprc.ff14SB
>
> but for backwards compatibility, it wouldn't hurt to still have
> leaprc.ff14SB, IMO.
>
> I notice that $AMBERHOME/dat/leap/cmd/leaprc.ff14SB.redq still exists, for
> example (which is essentially the same, apart from the .lib files it loads
> - i.e. those with the reduced charges)
>
> Thanks,
> Marc
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 16 May 2016 11:30:49 -0400
> From: Nhai <nhai.qn.gmail.com>
> Subject: Re: [AMBER] No leaprc.ff14SB anymore in AmberTools16 -
> reason?
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <FFD48F6B-E97F-4926-A3EE-398C2E7A8D90.gmail.com>
> Content-Type: text/plain; charset=us-ascii
>
> Hi, you can try
>
> source oldff/leaprc.ff14SB
>
> Hai
>
> > On May 16, 2016, at 11:27 AM, Marc van der Kamp <
> marcvanderkamp.gmail.com> wrote:
> >
> > Hi,
> >
> > I'm just wondering why there is no $AMBERHOME/dat/leap/cmd/leaprc.ff14SB
> > anymore in AmberTools16?
> >
> > I understand that now leaprc.protein.ff14SB exists, and one could combine
> > this with other leaprc files to achieve the same (although not 100% how
> to
> > get exactly the same) as with
> > source leaprc.ff14SB
> >
> > but for backwards compatibility, it wouldn't hurt to still have
> > leaprc.ff14SB, IMO.
> >
> > I notice that $AMBERHOME/dat/leap/cmd/leaprc.ff14SB.redq still exists,
> for
> > example (which is essentially the same, apart from the .lib files it
> loads
> > - i.e. those with the reduced charges)
> >
> > Thanks,
> > Marc
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 16 May 2016 16:33:04 +0100
> From: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
> Subject: Re: [AMBER] No leaprc.ff14SB anymore in AmberTools16 -
> reason?
> To: <amber.ambermd.org>
> Message-ID: <20160516163304.7342b8f9.zgb83773vig.dl.ac.uk>
> Content-Type: text/plain; charset="US-ASCII"
>
> Marc,
>
> look into $AMBERHOME/dat/leap/cmd/oldff/
>
> Cheers,
> Hannes.
>
>
> On Mon, 16 May 2016 16:27:38 +0100
> Marc van der Kamp <marcvanderkamp.gmail.com> wrote:
>
> > Hi,
> >
> > I'm just wondering why there is no
> > $AMBERHOME/dat/leap/cmd/leaprc.ff14SB anymore in AmberTools16?
> >
> > I understand that now leaprc.protein.ff14SB exists, and one could
> > combine this with other leaprc files to achieve the same (although
> > not 100% how to get exactly the same) as with
> > source leaprc.ff14SB
> >
> > but for backwards compatibility, it wouldn't hurt to still have
> > leaprc.ff14SB, IMO.
> >
> > I notice that $AMBERHOME/dat/leap/cmd/leaprc.ff14SB.redq still
> > exists, for example (which is essentially the same, apart from
> > the .lib files it loads
> > - i.e. those with the reduced charges)
> >
> > Thanks,
> > Marc
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 16 May 2016 16:37:11 +0100
> From: Marc van der Kamp <marcvanderkamp.gmail.com>
> Subject: Re: [AMBER] No leaprc.ff14SB anymore in AmberTools16 -
> reason?
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CAGCFhheMHjsUo4KaYzyeVRoY3NRkMrPiSS656Fyc-OKGrmK9ZQ.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Thanks Hai and Hannes.
> source oldff/leaprc.ff14SB
> does indeed work.
> Obviously, this will mean that 'old' tleap input scripts need changing.
>
> --Marc
>
> On 16 May 2016 at 16:33, Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
> wrote:
>
> > Marc,
> >
> > look into $AMBERHOME/dat/leap/cmd/oldff/
> >
> > Cheers,
> > Hannes.
> >
> >
> > On Mon, 16 May 2016 16:27:38 +0100
> > Marc van der Kamp <marcvanderkamp.gmail.com> wrote:
> >
> > > Hi,
> > >
> > > I'm just wondering why there is no
> > > $AMBERHOME/dat/leap/cmd/leaprc.ff14SB anymore in AmberTools16?
> > >
> > > I understand that now leaprc.protein.ff14SB exists, and one could
> > > combine this with other leaprc files to achieve the same (although
> > > not 100% how to get exactly the same) as with
> > > source leaprc.ff14SB
> > >
> > > but for backwards compatibility, it wouldn't hurt to still have
> > > leaprc.ff14SB, IMO.
> > >
> > > I notice that $AMBERHOME/dat/leap/cmd/leaprc.ff14SB.redq still
> > > exists, for example (which is essentially the same, apart from
> > > the .lib files it loads
> > > - i.e. those with the reduced charges)
> > >
> > > Thanks,
> > > Marc
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> ------------------------------
>
> Message: 7
> Date: Mon, 16 May 2016 16:37:14 +0100
> From: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
> Subject: Re: [AMBER] problem installing AmberTools16 pytraj on Mac
> To: <amber.ambermd.org>
> Message-ID: <20160516163714.706e8bf2.zgb83773vig.dl.ac.uk>
> Content-Type: text/plain; charset="US-ASCII"
>
> http://archive.ambermd.org/201605/0147.html
>
> On Mon, 16 May 2016 16:23:11 +0100
> Marc van der Kamp <marcvanderkamp.gmail.com> wrote:
>
> > Hi all,
> >
> > I just tried to install AmberTools16 on a new Mac Book pro, running
> > OS X El Capitan (10.11.4).
> >
> > I've installed and selected gcc4.9 (and also installed flex,
> > py27-numpy & py27-matplotlib) through MacPorts.
> >
> > All is well (i.e. most things are compiled) until I get to pytraj,
> > where "make install" eventually fails with the following:
> > gcc: error: unrecognized command line option '-Wshorten-64-to-32'
> >
> > At this point, I don't yet need pytraj, but it would be nice to have a
> > complete install.
> > Any insight in how to fix this would be welcome.
> >
> > Thanks,
> > Marc
> >
> > More detail:
> >
> > creating build/temp.macosx-10.11-intel-2.7/pytraj
> >
> > gcc -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64
> > -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE
> > -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32
> > -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE
> > -arch i386 -arch x86_64 -pipe
> > -I/Users/chmwvdk/amber16/AmberTools/src/cpptraj/src
> > -I/Users/chmwvdk/amber16/AmberTools/src/pytraj/pytraj/
> >
> -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7
> > -c pytraj/c_dict.cpp -o
> > build/temp.macosx-10.11-intel-2.7/pytraj/c_dict.o -O0 -ggdb
> >
> > gcc: error: unrecognized command line option '-Wshorten-64-to-32'
> >
> > error: command 'gcc' failed with exit status 1
> >
> > make[2]: *** [pytraj] Error 1
> >
> > make[1]: *** [serial] Error 2
> >
> > make: *** [install] Error 2
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> ------------------------------
>
> Message: 8
> Date: Mon, 16 May 2016 16:39:32 +0100
> From: Marc van der Kamp <marcvanderkamp.gmail.com>
> Subject: Re: [AMBER] problem installing AmberTools16 pytraj on Mac
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAGCFhhf=
> 0Tow_zdCot_fYQAeTr9ZS4PEPccAxF7D0nGmY94jAQ.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Apologies - I missed that!
> Marc
>
> On 16 May 2016 at 16:37, Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
> wrote:
>
> > http://archive.ambermd.org/201605/0147.html
> >
> > On Mon, 16 May 2016 16:23:11 +0100
> > Marc van der Kamp <marcvanderkamp.gmail.com> wrote:
> >
> > > Hi all,
> > >
> > > I just tried to install AmberTools16 on a new Mac Book pro, running
> > > OS X El Capitan (10.11.4).
> > >
> > > I've installed and selected gcc4.9 (and also installed flex,
> > > py27-numpy & py27-matplotlib) through MacPorts.
> > >
> > > All is well (i.e. most things are compiled) until I get to pytraj,
> > > where "make install" eventually fails with the following:
> > > gcc: error: unrecognized command line option '-Wshorten-64-to-32'
> > >
> > > At this point, I don't yet need pytraj, but it would be nice to have a
> > > complete install.
> > > Any insight in how to fix this would be welcome.
> > >
> > > Thanks,
> > > Marc
> > >
> > > More detail:
> > >
> > > creating build/temp.macosx-10.11-intel-2.7/pytraj
> > >
> > > gcc -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64
> > > -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE
> > > -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32
> > > -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE
> > > -arch i386 -arch x86_64 -pipe
> > > -I/Users/chmwvdk/amber16/AmberTools/src/cpptraj/src
> > > -I/Users/chmwvdk/amber16/AmberTools/src/pytraj/pytraj/
> > >
> >
> -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7
> > > -c pytraj/c_dict.cpp -o
> > > build/temp.macosx-10.11-intel-2.7/pytraj/c_dict.o -O0 -ggdb
> > >
> > > gcc: error: unrecognized command line option '-Wshorten-64-to-32'
> > >
> > > error: command 'gcc' failed with exit status 1
> > >
> > > make[2]: *** [pytraj] Error 1
> > >
> > > make[1]: *** [serial] Error 2
> > >
> > > make: *** [install] Error 2
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> ------------------------------
>
> Message: 9
> Date: Mon, 16 May 2016 16:42:55 +0100
> From: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
> Subject: Re: [AMBER] No leaprc.ff14SB anymore in AmberTools16 -
> reason?
> To: <amber.ambermd.org>
> Message-ID: <20160516164255.0c260195.zgb83773vig.dl.ac.uk>
> Content-Type: text/plain; charset="US-ASCII"
>
> tleap is just a shell script so you may want to include the
> old directories there:
>
> $AMBERHOME/bin/teLeap \
> -I$AMBERHOME/dat/leap/prep \
> -I$AMBERHOME/dat/leap/prep/oldff \
> -I$AMBERHOME/dat/leap/lib \
> -I$AMBERHOME/dat/leap/lib/oldff \
> -I$AMBERHOME/dat/leap/parm \
> -I$AMBERHOME/dat/leap/cmd \
> -I$AMBERHOME/dat/leap/cmd/oldff \
> $*
>
>
> On Mon, 16 May 2016 16:37:11 +0100
> Marc van der Kamp <marcvanderkamp.gmail.com> wrote:
>
> > Thanks Hai and Hannes.
> > source oldff/leaprc.ff14SB
> > does indeed work.
> > Obviously, this will mean that 'old' tleap input scripts need
> > changing.
> >
> > --Marc
> >
> > On 16 May 2016 at 16:33, Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
> > wrote:
> >
> > > Marc,
> > >
> > > look into $AMBERHOME/dat/leap/cmd/oldff/
> > >
> > > Cheers,
> > > Hannes.
> > >
> > >
> > > On Mon, 16 May 2016 16:27:38 +0100
> > > Marc van der Kamp <marcvanderkamp.gmail.com> wrote:
> > >
> > > > Hi,
> > > >
> > > > I'm just wondering why there is no
> > > > $AMBERHOME/dat/leap/cmd/leaprc.ff14SB anymore in AmberTools16?
> > > >
> > > > I understand that now leaprc.protein.ff14SB exists, and one could
> > > > combine this with other leaprc files to achieve the same (although
> > > > not 100% how to get exactly the same) as with
> > > > source leaprc.ff14SB
> > > >
> > > > but for backwards compatibility, it wouldn't hurt to still have
> > > > leaprc.ff14SB, IMO.
> > > >
> > > > I notice that $AMBERHOME/dat/leap/cmd/leaprc.ff14SB.redq still
> > > > exists, for example (which is essentially the same, apart from
> > > > the .lib files it loads
> > > > - i.e. those with the reduced charges)
> > > >
> > > > Thanks,
> > > > Marc
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> ------------------------------
>
> Message: 10
> Date: Mon, 16 May 2016 09:56:15 -0600
> From: "Iqbal, Muhammad Sajid" <iqbal.uleth.ca>
> Subject: Re: [AMBER] Fix dimension of the box throughout the MD
> simulations
> To: amber.ambermd.org
> Message-ID:
> <
> CALXFyFtjBr3WYB0Avx2-jW0P-8vO0EYfCC_7eJiQ91DiGNdOcQ.mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Amber community,
>
> I have conducted the simulations following the tutorial B1 - Section 5 with
> ntb = 1 and igb = 0. I also specify the box dimensions using the following
> command.
>
> set mybox box {300.092, 300.141, 300.087}
>
> However, the box dimensions are still changing. Could you please, provide
> any way.
>
> Please let me know, if need top/crd and input files.
>
> thank you
>
> Dear amber community,
>
> I performed MD simulations on a box of dimension 300 x 300 x 300. I defined
> the dimensions using the following command.
>
> setbox mybox vdw
>
> I noticed that, as MD simulations proceed, the box dimension are changing.
> My first frame has the following dimension, generated by vmd.
>
>
> min1 = (1.2740000486373901, 1.4450000524520874, 1.0440000295639038)
> max1 = (302.4549865722656, 302.99700927734375, 302.3590087890625)
> total = ( 301.181, 301.552, 301.315 )
>
>
> and the final frame has the following dimensions after completing 125000
> steps.
>
> min2 = Vector(1.371000051498413, -6.394000053405762, -1.9179999828338623)
> max2 = Vector(305.86700439453125, 305.4129943847656, 306.697998046875)
> total= ( 304.496, 311.807, 308.616 )
>
> If I perform additional 10times steps, the dimension keeping changing to a
> very large number. Could any one please guide me how I can keep the
> dimensions fix to 300x300x300 throughout the simulations.
>
> Here is my MD script.
>
> imin = 0, ntb = 0,
> igb = 1, ntpr = 100, ntwx = 100, ntwr = 8000
> ntt = 3, gamma_ln = 1.0,
> tempi = 300.0, temp0 = 300.0
> nstlim = 125000, dt = 0.001,
> cut = 999
>
>
> ------------------------------
>
> Message: 11
> Date: Mon, 16 May 2016 14:50:49 -0400
> From: David A Case <david.case.rutgers.edu>
> Subject: Re: [AMBER] Fix dimension of the box throughout the MD
> simulations
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20160516185049.GA65334.scarletmail.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Mon, May 16, 2016, Iqbal, Muhammad Sajid wrote:
> >
> > I have conducted the simulations following the tutorial B1 - Section 5
> with
> > ntb = 1 and igb = 0. I also specify the box dimensions using the
> following
> > command.
> >
> > set mybox box {300.092, 300.141, 300.087}
>
> First, note that this is very different from how the tutorial sets the box
> size, which is done inside the "solvateOct" command. So you are doing
> something very unusual, yet you have not given us information about how
> you built the system (did you use *both* solvateOct and set ... box?)
>
> Second, the only mdin input you have specified used ntb=0. You say above
> that you are now setting ntb=1, but there might be other problems with the
> input that you are not seeing, and which we cannot know about either.
>
> Try running a sample simulation without the "set mybox box" command above,
> and verify that the box dimension is not changing. If that works, but
> what you want to do does not work, please post both your leap.in scripts
> and
> your md.in scripts...these are short, yet may provide valuable clues. I'm
> still guessing (based on very little evidence, to be sure) that there is
> some
> mismatch between how you built the system in LEaP, and how you are trying
> to run it with MD.
>
> It would probably be helpful to indicate why you wish to use the above
> command, i.e. what sort of simulation you have in mind.
>
> ...dac
>
>
>
>
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>
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> End of AMBER Digest, Vol 1578, Issue 1
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Received on Mon May 16 2016 - 22:30:04 PDT
