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<DIV>Dear Anton and users,</DIV>
<DIV>When we simulate molecules under force, is it possible to set a distance limit such as a spring?, once the limit between two ends (atoms) is reached, the spring will broken and two ends(atoms) will separate and move in opposite direction.</DIV>
<DIV>( sorry, I am in mechanical area and please forgive me to raise the stupid inquiry)</DIV>
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<DIV>In VMD, I only can view the structures of molecules, but could not see the broken and opposite movement.</DIV>
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<DIV>Thanks!</DIV>
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<DIV> <BR><BR><B><I>Anton Feenstra <feenstra@chem.vu.nl></I></B> wrote:</DIV>
<BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">Albert Sun wrote:<BR>> Thanks, Anton and users,<BR>> <BR>> I understand this should reply on time scale and size, also forces applied, but<BR>> I tried a few examples and could not see how those atoms are broken and separated.<BR><BR>You can try e.g. g_rdf to get an overall picture of molecule packings,<BR>or you could inspect 'visually' using a trajectory viewer (e.g. ngmx or<BR>vmd), or look at snapshots (e.g. load a pdb file in rasmol).<BR><BR>By the way, atoms are not likely to break... Also, molecules will not<BR>break in MD, but they may separate... ;-)<BR><BR><BR>-- <BR>Groetjes,<BR><BR>Anton<BR>_____________ _______________________________________________________<BR>| | |<BR>| _ _ ___,| K. Anton Feenstra |<BR>| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |<BR>|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |<BR>| \_/ \_/ | |
| Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |<BR>| | Feenstra@chem.vu.nl - www.chem.vu.nl/~feenstra/ |<BR>| | "If You See Me Getting High, Knock Me Down" |<BR>| | (Red Hot Chili Peppers) |<BR>|_____________|_______________________________________________________|<BR><BR><BR>_______________________________________________<BR>gmx-users mailing list<BR>gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>Please don't post (un)subscribe requests to the list. Use the <BR>www interface or send it to gmx-users-request@gromacs.org.</BLOCKQUOTE></DIV><p><hr SIZE=1>
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