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From: Ern Ong (Ern.Ong_at_student.adfa.edu.au)
Date: Wed Feb 13 2019 - 03:52:42 CST
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Dear VMD users,
I am using VMD for WIN32, version 1.9.3 (November 20, 2016). I am facing a problem whereby I cannot merge psf and pdb files using psfgen. I generated a carbon nanotube (>9,999 atoms) using the nanotube builder but I want to merge it with my other psf+pdb files. It seems to me that the key problem is the number of atoms generated for the carbon nanotube. If the number of CNT atoms is <10,000 atoms, psfgen works fine. The following is the excerpt of the generated pdb file for a CNT with >9,999 atoms. The numbering changes from 9999 to 2710... and this repeats what being numbered previously.
ATOM 9998 C CNT X9998 13.250 -2.816 304.550 0.00 0.00 TUB C
ATOM 9999 C CNT X9999 13.379 -2.119 305.778 0.00 0.00 TUB C
ATOM 10000 C CNT X2710 13.527 -0.709 305.778 0.00 0.00 TUB C
ATOM 10001 C CNT X2711 13.546 0.000 307.006 0.00 0.00 TUB C
ATOM 10002 C CNT X2712 13.471 1.416 307.006 0.00 0.00 TUB C
Can anyone help me to solve this problem?
Thank you.
Regards,
Ernest
-----Original Message-----
From: owner-vmd-l-digest_at_ks.uiuc.edu <owner-vmd-l-digest_at_ks.uiuc.edu>
Sent: Tuesday, 12 February 2019 3:36 AM
To: vmd-l-digest_at_ks.uiuc.edu
Subject: vmd-l digest V1 #3871
vmd-l digest Monday, February 11 2019 Volume 01 : Number 3871
In this issue:
Re: vmd-l: measure distance atom from plane
vmd-l: minimal distance between atoms in all frame
vmd-l: MSD of membrane lipids
----------------------------------------------------------------------
Date: Tue, 5 Feb 2019 19:50:15 +0800
From: Ashar Malik <asharjm_at_gmail.com>
Subject: Re: vmd-l: measure distance atom from plane
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Yes.
You will need:
- equation of the plane (representing the surface)
- the coordinates of the atom (which you should have since you have an
atom)
- some basic maths (from a high-school coordinate geometry section --
both to make the equation above and work out the plane's distance from the
point[atom])
making the equation representing the surface and working out the remaining maths should be relatively straightforward in VMD.
On Tue, Feb 5, 2019 at 7:36 PM alberto <voodoo.bender_at_gmail.com> wrote:
> Hi,
> I would measure distance of atom from surface.
> is it possible with tk console and VMD?
>
> regards
>
> Alberto
>
- --
Best,
/A
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<div dir=3D"ltr">Yes.=C2=A0<div><br></div><div>You will need:</div><div><ul=
><li>equation of the plane (representing the surface)</li><li>the
>coordinat=
es of the atom (which you should have since you have an atom)</li><li>some = basic maths (from a high-school coordinate geometry section -- both to make= the equation above and work out the plane's distance from the point[at= om])</li></ul><div>making the equation representing the surface and working= out the remaining maths should be relatively straightforward in VMD.=C2=A0= </div></div></div><br><div class=3D"gmail_quote"><div dir=3D"ltr" class=3D"= gmail_attr">On Tue, Feb 5, 2019 at 7:36 PM alberto <<a href=3D"mailto:vo= odoo.bender_at_gmail.com" target=3D"_blank">voodoo.bender_at_gmail.com</a>> wr= ote:<br></div><blockquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px= 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir=3D= "ltr"><div class=3D"gmail_default" style=3D"font-family:"courier new&q= uot;,monospace;font-size:small">Hi, <br></div><div class=3D"gmail_default" = style=3D"font-family:"courier new",monospace;font-size:small">I w= ould measure distance
of atom from surface.</div><div class=3D"gmail_defaul= t" style=3D"font-family:"courier new",monospace;font-size:small">=
is it possible with tk console and VMD?</div><div class=3D"gmail_default" s= tyle=3D"font-family:"courier new",monospace;font-size:small"><br>=
</div><div class=3D"gmail_default" style=3D"font-family:"courier new&q= uot;,monospace;font-size:small">regards <br></div><div class=3D"gmail_defau= lt" style=3D"font-family:"courier new",monospace;font-size:small"=
><br></div><div class=3D"gmail_default"
>style=3D"font-family:"courier =
new",monospace;font-size:small">Alberto<br></div></div>
</blockquote></div><br clear=3D"all"><div><br></div>-- <br><div dir=3D"ltr"= class=3D"gmail-m_6426431534075286421gmail_signature">Best,<div>/A</div></d=
iv>
- --0000000000001b21e70581243721--
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Date: Tue, 5 Feb 2019 19:04:43 +0100
From: alberto <voodoo.bender_at_gmail.com>
Subject: vmd-l: minimal distance between atoms in all frame
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Hi,
I found your script in vmd mailing list
I would a script to monitoring distance between atoms of silicon of slab and other atom for all frame.
I would obtain for every frame the minimal distance between silicon atom and nitrogen atom
for single couple I use
set bl [measure bond {IDA IDB} frame all]
regards
Alberto
silica2_dipodal_monodactyl_MeO_Me_pyridine_298K...
<https://drive.google.com/file/d/1rTUz0YcLPLOBucAb5fgTXcKNh0WKVgZB/view?usp=drive_web>
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<div dir=3D"ltr"><div dir=3D"ltr"><div class=3D"gmail_default" style=3D"fon= t-family:courier new,monospace;font-size:small">Hi, <br></div><div class=3D= "gmail_default" style=3D"font-family:courier new,monospace;font-size:small"=
>I found your script in vmd mailing list</div><div
>class=3D"gmail_default" =
style=3D"font-family:courier new,monospace;font-size:small">I would a scrip= t to monitoring distance between atoms of silicon of slab and other atom fo= r all frame.</div><div class=3D"gmail_default" style=3D"font-family:courier= new,monospace;font-size:small"><br></div><div class=3D"gmail_default" styl= e=3D"font-family:courier new,monospace;font-size:small">I would obtain for = every frame the minimal distance between silicon atom and nitrogen atom</di=
v><div class=3D"gmail_default" style=3D"font-family:courier
v>new,monospace;f=
ont-size:small"><br></div><div class=3D"gmail_default" style=3D"font-family= :courier new,monospace;font-size:small">for single couple I use <br></div><= div class=3D"gmail_default" style=3D"font-family:courier new,monospace;font=
- -size:small"><br></div><div class=3D"gmail_default" style=3D"font-family:co= urier new,monospace;font-size:small">set bl [measure bond {IDA IDB} frame a= ll]</div><div class=3D"gmail_default" style=3D"font-family:courier new,mono= space;font-size:small"><br></div><div class=3D"gmail_default" style=3D"font=
- -family:courier new,monospace;font-size:small">regards</div><div class=3D"g= mail_default" style=3D"font-family:courier new,monospace;font-size:small"><=
br></div><div class=3D"gmail_default" style=3D"font-family:courier
br>new,mono=
space;font-size:small">Alberto<br></div><div class=3D"gmail_default" style= =3D"font-family:courier new,monospace;font-size:small"><br></div><div class= =3D"gmail_default" style=3D"font-family:courier new,monospace;font-size:sma= ll"><br></div><div class=3D"gmail_default" style=3D"font-family:courier new= ,monospace;font-size:small"><br></div><div class=3D"gmail_default" style=3D= "font-family:courier new,monospace;font-size:small"><div class=3D"gmail_chi= p gmail_drive_chip" style=3D"width:396px;height:18px;max-height:18px;backgr=
ound-color:#f5f5f5;padding:5px;color:#222;font-family:arial;font-style:norm=
al;font-weight:bold;font-size:13px;border:1px solid #ddd;line-height:1"><a = href=3D"https://drive.google.com/file/d/1rTUz0YcLPLOBucAb5fgTXcKNh0WKVgZB/v=
iew?usp=3Ddrive_web" target=3D"_blank" style=3D"display:inline-block;overfl=
ow:hidden;text-overflow:ellipsis;white-space:nowrap;text-decoration:none;pa=
dding:1px 0px;border:medium none;width:100%"><img style=3D"vertical-align: = bottom; border: none;" src=3D"https://ssl.gstatic.com/docs/doclist/images/i=
con_10_generic_list.png">=C2=A0<span dir=3D"ltr" style=3D"color:#15c;text-d= ecoration:none;vertical-align:bottom">silica2_dipodal_monodactyl_MeO_Me_pyr=
idine_298K...</span></a></div></div></div></div>
- --000000000000481aca05812972d1--
------------------------------
Date: Mon, 11 Feb 2019 16:35:46 +0000
From: "Villalain Boullon, Jose" <jvillalain_at_umh.es>
Subject: vmd-l: MSD of membrane lipids
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Dear all,
I have been trying to obtain the two-dimensional mean squared displacement = (MSD)-based diffusion coefficient of a lipid in a membrane using the VMD Di= ffusion Coefficient Tool (https://github.com/tonigi/vmd_diffusion_coefficie=
nt/tree/master/doc#).
However, I have several trajectories (65 trajectories, 300 ns) and I have n= ot found the way to concatenate the results for each one of them and obtain= the MSD.
Could you please point me how to do it or a link where I could obtain the M= SD throughout all the trajectories?.
Thanks a lot.
Jos=E9.
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<body lang=3D"ES" link=3D"#0563C1" vlink=3D"#954F72"> <div class=3D"WordSection1"> <p class=3D"MsoNormal"><span lang=3D"EN-GB" style=3D"font-family:"Aria= l",sans-serif;color:black;background:white">Dear all,<o:p></o:p></span=
></p>
<p class=3D"MsoNormal"><span lang=3D"EN-GB" style=3D"font-family:"Aria= l",sans-serif;color:black;background:white"><o:p> </o:p></span></=
p>
<p class=3D"MsoNormal"><span lang=3D"EN-GB" style=3D"font-family:"Aria= l",sans-serif;color:black;background:white">I have been trying to </span><span lang=3D"EN-GB" style=3D"font-family:"Arial",sans-ser=
if;color:#24292E;background:white">obtain the two-dimensional mean squared = displacement (MSD)-based diffusion coefficient of a lipid in a membrane usi= ng the VMD Diffusion Coefficient Tool (https://github.com/tonigi/vmd_diffus=
ion_coefficient/tree/master/doc#).<o:p></o:p></span></p>
<p class=3D"MsoNormal"><span lang=3D"EN-GB" style=3D"font-family:"Aria= l",sans-serif;color:#24292E;background:white"><o:p> </o:p></span>=
</p>
<p class=3D"MsoNormal"><span lang=3D"EN-GB" style=3D"font-family:"Aria= l",sans-serif;color:#24292E;background:white">However, I have several = trajectories (65 trajectories, 300 ns) and I have not found the way to conc= atenate the results for each one of them and obtain the MSD.<o:p></o:p></span></p> <p class=3D"MsoNormal"><span lang=3D"EN-GB" style=3D"font-family:"Aria= l",sans-serif;color:#24292E;background:white"><o:p> </o:p></span>=
</p>
<p class=3D"MsoNormal"><span lang=3D"EN-GB" style=3D"font-family:"Aria= l",sans-serif;color:#24292E;background:white">Could you please point m= e how to do it or a link where I could obtain the MSD throughout all the tr= ajectories?.<o:p></o:p></span></p>
<p class=3D"MsoNormal"><span lang=3D"EN-GB" style=3D"font-family:"Aria= l",sans-serif;color:#24292E;background:white"><o:p> </o:p></span>=
</p>
<p class=3D"MsoNormal"><span lang=3D"EN-GB" style=3D"font-family:"Aria= l",sans-serif;color:#24292E;background:white">Thanks a lot.<o:p></o:p>= </span></p> <p class=3D"MsoNormal"><span lang=3D"EN-GB" style=3D"font-family:"Aria= l",sans-serif;color:#24292E;background:white">Jos=E9.<o:p></o:p></span=
></p>
<p class=3D"MsoNormal"><span lang=3D"EN-GB" style=3D"font-family:"Aria= l",sans-serif;color:#24292E;background:white"><o:p> </o:p></span>=
</p>
<p class=3D"MsoNormal"><span lang=3D"EN-GB" style=3D"font-family:"Aria= l",sans-serif;color:#24292E;background:white"><o:p> </o:p></span>=
</p>
<p class=3D"MsoNormal"><span lang=3D"EN-GB" style=3D"font-family:"Aria= l",sans-serif;color:#24292E;background:white"><o:p> </o:p></span>=
</p>
<p class=3D"MsoNormal"><span lang=3D"EN-GB" style=3D"font-family:"Aria= l",sans-serif;color:#24292E;background:white"><o:p> </o:p></span>=
</p>
<p class=3D"MsoNormal"><span lang=3D"EN-GB" style=3D"font-family:"Aria= l",sans-serif;color:#24292E;background:white"><o:p> </o:p></span>=
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p>
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