[gmx-users] g_sas

Sat Aug 16 20:53:20 CEST 2014

Hi Eric,
By vacuum accessible surface area, I assume that you mean the area defined
the surface of the interstitial volume. In my understanding, using g_sas
will give you the solvent accessible area (non buried area) averaged over
all the molecules and the trajectory. This is different from the
interstitial surface area. Someone please correct me if I am wrong.

Justin is correct when he says that the program displays time frames as it
analyses the trajectory. From your description, I feel that g_sas is stuck
on the first frame itself since it is calculating over all the liquid
molecules. And there is no way to figure out how much of that frame has
been analysed. What is your system made of?

I am not sure what you mean when you say trajectory like information. g_sas
prints out information for every time step.

Regards,

On Saturday, August 16, 2014, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/16/14, 1:40 PM, Eric Smoll wrote:
>
>> Rajat,
>>
>> Thank you for the rapid response. It is very helpful.
>>
>> "1) Yes. Use a probe radius of 0 nm.
>> 2) No. There is no verbose option in g_sas AFAIK. As an aside, you may
>> want
>> to reconsider -xvg none
>>
>
> #2 is incorrect; all Gromacs programs print out which frame they are
> working on to the terminal.
>
>  3) No difference in my experience."
>>
>> Let me get this straight. You are saying that analyzing a .trr outputs an
>> average, not trajectory-like information. You are saying, for your
>> specific
>> system, you see little difference in the surface formed from analyzing a
>> trajectory and analyzing a snapshot. That may be for a protein but I am
>> studying a molecular liquid.
>>
>>
> The type of output depends on what you ask for in your command line.  The
> use of -o will give you a time series of all the frames in your trajectory.
>
>  "4) g_sas uses vdwradii.dat, which may not have the vdw radius for a
>> particular atom type. Eg: Phosphorus is not present by default in
>> vdwradii.dat (for phosphorylated proteins). You may add this manually to a
>> local copy of vdwradii.dat"
>>
>> Thank you. Exactly, the information I was looking for!
>>
>> "Sorry, I misread your mail. You cannot compute the vacuum accessible
>> surface area for a liquid because the molecules are in constant motion."
>>
>> So are you saying that *I cannot use g_sas to compute the vacuum
>> accessible
>> surface area for a liquid at all* or *I cannot use g_sas to compute the
>> vacuum accessible surface area with a trajectory*?
>>
>> Surely we can define a vacuum accessible surface for any timestep of this
>> trajectory, correct? I agree that molecules at the surface are constantly
>> changing making the definition of a surface ill-defined over a trajectory
>> but I am looking for some way to obtain a time-averaged atom-composition
>> of
>> the liquid surface. If g_sas can be used for temporal snaphot .gro file,
>> perhaps I can extract a variety of timesteps and carry out the calculation
>> manually.
>>
>>
> This should not be necessary; you can provide the trajectory and g_sas
> should do this for you.  Whether or not that output is meaningful to you is
> up to you; I have never dealt in vacuum-accessible SA.
>
> -Justin
>
>  Thanks again Rajat,
>>
>> Best,
>> Eric
>>
>>
>>  Message: 7
>>> Date: Sat, 16 Aug 2014 21:17:36 +0530
>>> From: rajat desikan <rajatdesikan at gmail.com>
>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>> Subject: Re: [gmx-users] g_sas
>>> Message-ID:
>>>          <
>>> CA+d_LwtqQ+0GPhTQ+8WQhoLrfQbwY6Ycz6Q-i4YAg7HwmzHe-A at mail.gmail.com>
>>> Content-Type: text/plain; charset=UTF-8
>>>
>>> Hi Eric,
>>> Sorry, I misread your mail. You cannot compute the vacuum accessible
>>> surface area for a liquid because the molecules are in constant motion.
>>>
>>> Regards,
>>>
>>>
>>> On Sat, Aug 16, 2014 at 9:15 PM, rajat desikan <rajatdesikan at gmail.com>
>>> wrote:
>>>
>>>  Hi Eric,
>>>> 1) Yes. Use a probe radius of 0 nm.
>>>> 2) No. There is no verbose option in g_sas AFAIK. As an aside, you may
>>>> want to reconsider -xvg none
>>>> 3) No difference in my experience.
>>>> 4) g_sas uses vdwradii.dat, which may not have the vdw radius for a
>>>> particular atom type. Eg: Phosphorus is not present by default in
>>>> vdwradii.dat (for phosphorylated proteins). You may add this manually to
>>>>
>>> a
>>>
>>>> local copy of vdwradii.dat
>>>>
>>>> Regards,
>>>>
>>>>
>>>> On Sat, Aug 16, 2014 at 9:01 PM, Eric Smoll <ericsmoll at gmail.com>
>>>> wrote:
>>>>
>>>>  Hello,
>>>>>
>>>>> I am interested in using g_sas in gromacs 4.6.5. I have a few
>>>>> questions:
>>>>>
>>>>> 1.) Is it advisable to use this tool to compute the vacuum accessible
>>>>> surface area for a liquid?
>>>>>
>>>>> 2.) I ran a test using .gro / .trr / .tpr output from a production run
>>>>>
>>>> in
>>>
>>>> my workflow as shown follows: { g_sas -f A.gro -s A.tpr -o TEST1.xvg
>>>>>
>>>> -xvg
>>>
>>>> none -b 2000 -e 4000 -probe 0.15 -pbc -minarea 0.2 -ndots 24 -i
>>>>>
>>>> TEST1.itp;
>>>
>>>> g_sas -f A.trr -s A.tpr -o TEST2.xvg -xvg none -b 2000 -e 4000 -probe
>>>>>
>>>> 0.15
>>>
>>>> -pbc -minarea 0.2 -ndots 24 -i TEST2.itp }. The .trr / .tpr run produces
>>>>> no
>>>>> output while processing so it is unclear when it will end. Is there
>>>>>
>>>> anyway
>>>
>>>> to enable output that will report on the progress of the calculation?
>>>>>
>>>>> 3.) What are the difference in output when processing a .gro vs a .trr?
>>>>> Does trajectory input produce trajectory output or some sort of
>>>>> average?
>>>>>
>>>>> 4.) When running on the .gro / .tpr combination I received the
>>>>> following
>>>>> error:
>>>>>
>>>>> WARNING: Masses and atomic (Van der Waals) radii will be guessed
>>>>>           based on residue and atom names, since they could not be
>>>>>           definitively assigned from the information in your input
>>>>>           files. These guessed numbers might deviate from the mass
>>>>>           and radius of the atom type. Please check the output
>>>>>           files if necessary.
>>>>>
>>>>> WARNING: could not find a Van der Waals radius for 640 atoms
>>>>> 29440 out of 34560 atoms were classified as hydrophobic
>>>>>
>>>>> Note that I am using 640 molecules in my liquid simulation. I have not
>>>>> received this error for any other step in my molecular dynamics
>>>>>
>>>> workflow.
>>>
>>>> It concerns me. Is this an indication that my coordinate and parameter
>>>>> files are somehow incomplete? How do I go about troubleshooting this
>>>>> and
>>>>> specifying the missing parameters?
>>>>>
>>>>> Best,
>>>>> Eric
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
>>>>> * Please search the archive at
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>>>>> posting!
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>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Rajat Desikan (Ph.D Scholar)
>>>> Prof. K. Ganapathy Ayappa's Lab (no 13),
>>>> Dept. of Chemical Engineering,
>>>> Indian Institute of Science, Bangalore
>>>>
>>>>
>>>
>>>
>>> --
>>> Rajat Desikan (Ph.D Scholar)
>>> Prof. K. Ganapathy Ayappa's Lab (no 13),
>>> Dept. of Chemical Engineering,
>>> Indian Institute of Science, Bangalore
>>>
>>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore