<p style="border:0; padding:0; margin:0; font-family:'Gulim'; font-size:10pt; cursor: text;"><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;"></p><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;"></p><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;"></p><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;"></p><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;"></p><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;"></p><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;"></p><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;"></p><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;"></p><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;"></p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;"><font face="Times New Roman" size="3">Dear Justin and all,</font></p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;"><font face="Times New Roman" size="3"></font></p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;"><span style="font-family: 'Times New Roman'; font-size: medium;">I am stoked by what g_select can do (after reading the gmx-users list) and there is no one-size-fits-all.</span></p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;"><span style="font-family: 'Times New Roman'; font-size: medium;">However, as I wanted to look for more resources on g_select, I was met with no further information, for example: </span></p><pre style="color: rgb(34, 34, 34); line-height: 24px; text-align: justify;"><span style="font-family: 'Times New Roman'; font-size: medium;">g_select_mpi -select 'help position' OR g_select_mpi -select 'help all'</span></pre><pre style="color: rgb(34, 34, 34); line-height: 24px; text-align: justify;"><font face="Times New Roman" size="3">The commands below did not return anything but "No trajectory or topology provided, nothing to do!".</font></pre><blockquote style="font-family: Gulim; font-size: 12px; border-left-style: solid; border-left-width: 2px; margin: 0pt 0pt 0pt 0.8em; padding-left: 1em;"><div style="font-family:arial,돋움;line-height:1.5"><br><!-- original content --><div style="margin-top:5px;"><pre>On 12/27/14 2:05 AM, Kester Wong wrote:
> Dear gmx-users,
>
>
>
> Q1) I would like to plot the radius profile of a water droplet on graphene, as a
> function of z-direction, as per below:
>
> http://journals.aps.org/prl/article/10.1103/PhysRevLett.109.176101/figures/2/large
>
>
> Which GROAMCS utility should I use, and how do I go about plotting the profile?
>
It will require several steps. Not something I've ever done, but I would think
g_traj for coordinate extraction, then post-processing to calculate the diameter
or radius, would be the first step. Presumably you would have to do this for
various slices (assuming you're looking at cross-sections in the x-y plane for
varying values of z), so g_select to define atoms within that slice will be
needed before even running g_traj. Then you construct the profile from this
information.
</pre></div></div></blockquote><font><br><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;"><span style="font-family: 'Times New Roman'; font-size: medium;">Firstly, I am only able to use g_select to define the bottom bin for water droplet; could you please advise on indexing the bins from the bottom water layer?</span></p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;"><span style="font-family: 'Times New Roman'; font-size: medium; color: rgb(56, 56, 56); line-height: 1.571428em;">g_select_mpi -f traj_comp.xtc -s topol.tpr -n system.ndx -b 9000 -e 10000 -select 'resname SOL and res_com z < 10' -on output-system.ndx</span></p><div><br></div><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;"><font face="Times New Roman" size="3">How does one select SOL between z > 10 and z < 15, so on and so forth? </font></p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;"><font face="Times New Roman" size="3">I have looked at this for reference: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-June/072150.html</font></p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><p style="border: 0px; padding: 0px; margin: 0px; cursor: text;"><font face="Times New Roman" size="3">I am aware that after g_select, I will also have to do the following</font></p><p style="margin-bottom: 0px; margin-top: 0px;"><font face="Times New Roman" size="3" style="line-height: 1.5;">- Perform center of mass calc to identify the relative position of the droplet: g_traj -f traj_comp.xtc -s topol.tpr -n system.ndx -com -fp -b 9000 -e 10000 -ox coord.xvg<br>- Suppose there are more than one frame within the 9-10ns period, a shell script will be needed to loop through the frames for the (R,z) extraction?<br><br>One must then use a shell script to conduct further analysis using the produced index files, something like your script below?<br>https://www.mail-archive.com/gmx-users@gromacs.org/msg52656.html<br></font><br><font face="Times New Roman" size="3"><span style="line-height: 1.5;">Thanks for your advise and I wish you a </span><span style="line-height: 24px;">jolly</span><span style="line-height: 1.5;"> 2015!</span></font></p><p style="line-height: 1.5; margin-bottom: 0px; margin-top: 0px;"><font face="Times New Roman" size="3">Regards,</font></p><font face="Times New Roman" size="3">Kester</font><br><br><br><span style="font-size: 12px; font-family: Gulim; line-height: 18px; white-space: pre;"><br></span></font><blockquote style="font-family: Gulim; font-size: 12px; border-left-style: solid; border-left-width: 2px; margin: 0pt 0pt 0pt 0.8em; padding-left: 1em;"><div style="font-family:arial,돋움;line-height:1.5"><div style="margin-top:5px;"><pre><br></pre><pre><br></pre><pre><br></pre><pre>>
> Q2) Another question that I have is, suppose I have equilibrated (NVT) a water
> droplet for 10ns, and would like to plot the H-bond density (along the
> z-direction),
>
> I type the following command:
>
> g_density_mpi -f traj_comp.xtc -n system.ndx -s topol.tpr -b 9000 -e 10000 -sl
> 1000 -dens number -o number-density-OH.xvg
>
>
> I was only able to select:
>
> System
>
> Graphene (my substrate)
>
> Water
>
>
> How can I create a system.ndx such that it allows me to choose the OH (instead
> of water)?
>
make_ndx or g_select create index files. If you're defining "hydrogen bond
density" as "number of hydrogen bonds per slice," along with the above, you need
g_select and then you need g_hbond. g_density is not the right program here.</pre></div></div></blockquote><blockquote style="font-family: Gulim; font-size: 12px; border-left-style: solid; border-left-width: 2px; margin: 0pt 0pt 0pt 0.8em; padding-left: 1em;"><div style="font-family:arial,돋움;line-height:1.5"><div style="margin-top:5px;"><pre><span style="font-family: arial, 돋움; line-height: 1.5;">></span></pre><pre>> Q3) Regarding Q2, the g_density_mpi utility read the frames contained within the
> time frame of 9 - 10 ns, but does it average the frames to give a time-averaged
> density.xvg?
>
Yes. But again, g_density is probably not what you want here; see the help
description.
-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
jalemkul@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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