[gmx-users] g_sas
Eric Smoll
ericsmoll at gmail.com
Sun Aug 17 03:09:05 CEST 2014
Hello Rajat and Justin,
I am deeply grateful for the responses. Thank you.
Rajat,
You said: "By vacuum accessible surface area, I assume that you mean the
area defined
the surface of the interstitial volume."
I am looking for the vacuum accessible surface area at a vacuum-liquid
interface. I am very sorry for the confusion. Instead of carrying on with a
conversation on the nature of the g_sas simulation output, perhaps I should
just try to get a surface calculation working and examine it myself.
Rajat and Justin,
The file "vdwradii.dat" only appears in a few places in the manual and it
is unclear if g_sas actually uses it. I made a local copy of
share/gromacs/top, edited vdwradii.dat with the following format
{3-LETTER-RESIDUE-NAME .TOP/.GRO-FILE-ATOM-NAME RADIUS-IN-NM} and
updated the GMXLIB environment variable to point to this edited directory
with "export path/to/new/top". I created a .tpr file with grompp and made a
call with g_sas as I described before. I get the same 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
As I mentioned before, 640 matches the number of molecules I have in the
simulation. I have no idea why the g_sas is not referencing the sigma
values in my ffnonbonded file or my vdwradii.dat. I have used vim regular
expression capabilities to ensure that every atom in my .gro/.top files is
represented in the vdwradii.dat file. More guidance would be much
appreciated.
Thanks again for your help Justin and Rajat,
Best,
Eric
On Sat, Aug 16, 2014 at 12:53 PM, rajat desikan <rajatdesikan at gmail.com>
wrote:
> 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
> >>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >>>>> posting!
> >>>>>
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> >>>>>
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> or
> >>>>> send a mail to gmx-users-request at gromacs.org.
> >>>>>
> >>>>>
> >>>>
> >>>>
> >>>> --
> >>>> 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
> --
> Gromacs Users mailing list
>
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