[gmx-users] Calculating distance between solute and solid surface

[Ahmed Mohammed]

Hello GMX users,

I'm simulating a polymer in water on a solid surface. I'm trying to
calculate the dynamic distance between polymer monomers and the surface
(top layer of the surface). My reference is the surface and I used this
command

gmx distance -f NVT.xtc -s NVT.tpr -selrpos atom -seltype mol_com -oav
dist.xvg -tu ns

The problem is, this does not give a resonable results in comparsion
with trajectory visulization

Anyone has done same thing before that could hepe me in this?

Thank you

Ahmed
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Re: [gmx-users] Calculating Distance

[Tsjerk Wassenaar]

Hi Sanket,

You can use 'gmx traj' to write the COM over time.

Cheers,

Tsjerk

On Wed, May 18, 2016 at 7:09 AM, Sanket Ghawali 
wrote:

> Thank you Justin. I am sorry, I didn't make my query specific.
>
> g_dist calculates distance between COMS of 2 groups with reference to time.
> I want to monitor the change in the COM of the peptide with respect to the
> initial position (COM) of the peptide at 0ns and not between COM of 2
> different groups with reference to time.
>
> Please help me with "how to fix the reference position for distance
> calculation"
>
> Greatly appreciate your help and do let me know if I need to explain the
> query further
>
> With regards,
>
> Sanket.
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-- 
Tsjerk A. Wassenaar, Ph.D.
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Re: [gmx-users] Calculating Distance

[Sanket Ghawali]

Thank you Justin. I am sorry, I didn't make my query specific.

g_dist calculates distance between COMS of 2 groups with reference to time.
I want to monitor the change in the COM of the peptide with respect to the
initial position (COM) of the peptide at 0ns and not between COM of 2
different groups with reference to time.

Please help me with "how to fix the reference position for distance
calculation"

Greatly appreciate your help and do let me know if I need to explain the
query further

With regards,

Sanket.
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Re: [gmx-users] Calculating Distance

[Christopher Neale]

In case anybody else finds the gmx distance input as confusing as I did... if 
you want to get the distance between the center of mass of the peptide and the 
center of mass of the SDS, you would first create Protein and SDS groups in an 
index file (say they are groups 1 and 2), then send that to "gmx distance" and 
you would type "com of group 1 plus com of group 2" interactively or script the 
piping of this text into "gmx distance"


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul 
<jalem...@vt.edu>
Sent: 16 May 2016 07:51:51
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Calculating Distance

On 5/16/16 3:20 AM, Sanket Ghawali wrote:
> Dear, gmx-users,
>
> Hello everyone,
> I'm simulating a peptide in an SDS micelle. The simulation was
> performed for 100ns
> When I visualize the trajectory in VMD, the peptide moves to the SDS
> interface where initially it was placed in the center,  the results
> are as expected. I would like to calculate the distance the peptide
> has traveled or moved from the center to the interface
>
>
> Any suggestions on how to go about doing this?
>

Calculating distances is what the gmx distance program is for.  Simply obtain
the COM distance between the micelle and peptide (or any subset of atoms that
makes sense).

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Calculating Distance

[Justin Lemkul]

On 5/16/16 3:20 AM, Sanket Ghawali wrote:

Dear, gmx-users,

Hello everyone,
I'm simulating a peptide in an SDS micelle. The simulation was
performed for 100ns
When I visualize the trajectory in VMD, the peptide moves to the SDS
interface where initially it was placed in the center,  the results
are as expected. I would like to calculate the distance the peptide
has traveled or moved from the center to the interface


Any suggestions on how to go about doing this?



Calculating distances is what the gmx distance program is for.  Simply obtain 
the COM distance between the micelle and peptide (or any subset of atoms that 
makes sense).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Calculating Distance

[masoud keramati]

choose a atom, then calculate the transition vector of it with use of the
initial and final coordinate.


On Mon, May 16, 2016 at 11:50 AM, Sanket Ghawali 
wrote:

> Dear, gmx-users,
>
> Hello everyone,
> I'm simulating a peptide in an SDS micelle. The simulation was
> performed for 100ns
> When I visualize the trajectory in VMD, the peptide moves to the SDS
> interface where initially it was placed in the center,  the results
> are as expected. I would like to calculate the distance the peptide
> has traveled or moved from the center to the interface
>
>
> Any suggestions on how to go about doing this?
>
> Thanks,
>
> Sanket
> --
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> * Please search the archive at
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> posting!
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> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] Calculating Distance

[Sanket Ghawali]

Dear, gmx-users,

Hello everyone,
I'm simulating a peptide in an SDS micelle. The simulation was
performed for 100ns
When I visualize the trajectory in VMD, the peptide moves to the SDS
interface where initially it was placed in the center,  the results
are as expected. I would like to calculate the distance the peptide
has traveled or moved from the center to the interface


Any suggestions on how to go about doing this?

Thanks,

Sanket
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