[gmx-users] gromacs.org_gmx-users Digest, Vol 149, Issue 40

munubas at yahoo.com munubas at yahoo.com
Tue Sep 13 13:02:59 CEST 2016 

Hi allMy OS is Redhat enterprise 5.4. Manually installed Cmake nd FFTW latest version.used following commands to install Gromacs Latest vesion.
            tar xfz gromacs­5.1.3.tar.gz            cd gromacs­5.1.3            mkdir build            cd build    As I installed FFTW manually, the below cmake command is ineffective. 
and finally it is difficult to install by indicating configuration error.  Please help me to install in the above OS what exactly to do for the same.

B Govardhan
            cmake .. ­DGMX_BUILD_OWN_FFTW=ON ­DREGRESSIONTEST_DOWNLOAD=ON            make            make check            sudo make install            source /usr/local/gromacs/bin/GMXRC
      From: "gromacs.org_gmx-users-request at maillist.sys.kth.se" <gromacs.org_gmx-users-request at maillist.sys.kth.se>
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 Sent: Tuesday, 13 September 2016, 15:30
 Subject: gromacs.org_gmx-users Digest, Vol 149, Issue 40
   
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Today's Topics:

  1. Re: How to use/obtain TIP4P-D water model? (Jo?o Henriques)
  2. Re: The role of Jacobian factor in free energy simulations
      (BOSISIO Stefano)


----------------------------------------------------------------------

Message: 1
Date: Tue, 13 Sep 2016 09:22:58 +0200
From: Jo?o Henriques <joao.henriques.32353 at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Subject: Re: [gmx-users] How to use/obtain TIP4P-D water model?
Message-ID:
    <CALC+HGQjBiGzDW+xjQVeZfKDDyoLdSUT218aOD3R30+nARAwkg at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

Dear Andrew,

[1] From Stefano Piana's own words:

"The parameters of the model are reported in Table 1 of the paper (charge
on the hydrogen 0.58, C6=900 kcal/mol/A^6 C12=904657 kcal/mol/A^12). The
geometry is the same as the TIP4P/2005 water model of Vega and Miguel. To
run simulation with TIP4P-D in GROMACS, you may use the TIP4P/2005 water
model as a starting point and modify the charges and LJ parameters."

- - -

[2] In more technical "GROMACS terms", this is the procedure:

You need to add the new oxygen atom type for TIP4P-D along with its C6 and
C12 parameters into your "ffnonbonded.itp". Notice that you need to convert
Piana's parameters into the right units for GROMACS. Then, you need to
create an individual topology for TIP4P-D. I used the topology of the
TIP4P/2005 model from Abascal et al. as the base and changed the partial
charges and atom types. If you can't find the TIP4P/2005 topology, use the
"TIP4P.itp" which is included in most force field directories, but be aware
that the virtual sites parameters differ slightly. Make sure the atom types
check with the new entries under "ffnonbonded.itp". To end, add an entry
for the new water model under "watermodels.dat", so that you get presented
with the option to select that water model when you run "pdb2gmx".

One extra note, you need to solvate the system using an appropriate
pre-equilibrated water box that fits with this model.

- - -

[3] I have never used GROMACS 2016, so a lot of this stuff may change or
not. I am not familiar with the changes. Maybe one of the experts on this
list can help you with that. What I can do is provide you with my own
custom AMBER ff99SB-ILDN modified for use with TIP4P-D, but it is intended
to be used for GROMACS 4.6.7.

Best regards,
Jo?o




On Tue, Sep 13, 2016 at 4:15 AM, Andrew Guy <andrew.guy at burnet.edu.au>
wrote:

> Hi all,
>
> I am trying to follow the approach used by Henriques and Skep? (2016) to
> model a short disordered protein region (
> http://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b00429).
>
> In their paper, they use GROMACS with a new water model, TIP4P-D. I am
> unsure how to go about adding and using this water model in GROMACS.
>
> I suspect I have to add a new water model in my gromacs/share/top folder,
> or perhaps in the relevant subfolder for the force field I am using.
> However, I only have the parameters for TIP4P-D that are listed in the
> primary reference - http://pubs.acs.org/doi/suppl/10.1021/jp508971m - and
> don't know how to translate these to a format suitable for GROMACS. I have
> also tried reading through the GROMACS manual, but couldn't seem to find
> anything.
>
> Many thanks,
>
> Andrew
>
> (p.s. I am using GROMACS 2016)
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------------------------------

Message: 2
Date: Tue, 13 Sep 2016 07:50:35 +0000
From: BOSISIO Stefano <s1374284 at sms.ed.ac.uk>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Subject: Re: [gmx-users] The role of Jacobian factor in free energy
    simulations
Message-ID: <4BC27F51-DA79-4BE7-850F-6BE7D7525B6A at sms.ed.ac.uk>
Content-Type: text/plain; charset="us-ascii"

Thanks Hannes for the suggestion
I will write on the other mailing list

Best regards,
Stefano



> On 13 Sep 2016, at 07:06, Hannes Loeffler <Hannes.Loeffler at stfc.ac.uk> wrote:
> 
> Hi Stefano,
> 
> you might be better off either inspecting the code yourself or
> contacting the developers directly (the Gromacs developer list may be
> open to this).
> 
> Cheers,
> Hannes.
> 
> 
> On Mon, 12 Sep 2016 18:52:42 +0000
> BOSISIO Stefano <s1374284 at sms.ed.ac.uk> wrote:
> 
>> Dear Gromacs staff,
>> 
>> I am trying to understand some internal issues between my code and
>> Gromacs in alchemical free energy calculations.
>> 
>> Considering a simple alchemical free energy calculation (e.g ethane
>> to methanol) with a constraint applied to all the hydrogen bonds
>> does Gromacs calculate a Jacobian correction ? (Boresch Stefan, and
>> Martin Karplus "The Jacobian factor in free energy simulations." The
>> Journal of chemical physics105.12 (1996): 5145-5154  ) Alternatively,
>> does Gromacs apply any correction to the computed free energy changes
>> if constraints were applied to a solute?
>> 
>> 
>> Thank you
>> 
>> Best regards,
>> 
>> Stefano
> 
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