<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:'times new roman', 'new york', times, serif;font-size:12pt"><div>Okay, thanks, I'll try longer simulations.</div><div><br></div><div>Majid</div><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><br><div style="font-family:arial, helvetica, sans-serif;font-size:10pt"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br><b><span style="font-weight: bold;">To:</span></b> Gromacs Users' List <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Fri, April 22, 2011 5:18:50 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] DNA not wrapping around CNT in MD simulation<br></font><br>
<br><br>majid hasan wrote:<br>> Okay, thanks, I removed restraints from water.<br>> <br>> In the final simulation, I increased the simulation time from 20ps to 2000ps to see if they wrap around. However in .trr output, CNT and DNA remain stable, jiggles around and jump across the box in a weird manner (might have something to do with periodic boundary conditions?) but don't seem to be attracted towards each other. <br><br>2 ns is still what would be considered an extremely short simulation. Large-scale behavior may take tens or hundreds of ns. I have no experience with DNA-CNT interactions, but for protein-protein interactions (even for small peptides), such time scales are certainly necessary.<br><br>> Movie of output is here:<br><span>> <a target="_blank" href="http://phas.ubc.ca/~majid/Project/msteps/cntdna2000ps.mpg">http://phas.ubc.ca/~majid/Project/msteps/cntdna2000ps.mpg</a></span><br><br>I don't see anything odd about
this at all. If you're having periodicity issues, trjconv is the tool to take care of that.<br><br><span><a target="_blank" href="http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow">http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow</a></span><br><br>> and input em.mdp, and md.mdp files are here:<br><span>> EM: <a target="_blank" href="http://phas.ubc.ca/~majid/Project/msteps/lbfgs.mdp">http://phas.ubc.ca/~majid/Project/msteps/lbfgs.mdp</a></span><br>> <<a href="http://phas.ubc.ca/~majid/Project/msteps/lbfgs.mdp" target="_blank">http://phas.ubc.ca/~majid/Project/msteps/lbfgs.mdp</a><span>>MD: <a target="_blank" href="http://phas.ubc.ca/~majid/Project/msteps/md.mdp">http://phas.ubc.ca/~majid/Project/msteps/md.mdp</a></span><br>> <br>> Commands that I have been using to build input coordinates, and topologies are
below:<br>> <br>> For dna: pdb2gmx -f dna.pdb -o dna.gro -p dna.top -ff select (Selected amber99sb, and TIP3P water model)<br>> For cnt: g_x2top -f cnt.gro -o cnt.top -ff select -pbc (selected amber99sb)<br>> For mixing : genbox -cp cnt.gro -ci dna.gro -o cntdna.gro -nmol 1 -try 20 <br>> For solvation: genbox -cp cntdna.gro -cs spc.gro -o cntdnasol.gro<br>> <br>> <<a href="http://phas.ubc.ca/~majid/Project/msteps/md.mdp" target="_blank">http://phas.ubc.ca/~majid/Project/msteps/md.mdp</a>>I have no clue what is wrong with the simulation, and any help is much appreciated. <br><br>Likely nothing is "wrong," you just aren't simulating long enough.<br><br>-Justin<br><br>> Thanks,<br>> Majid<br>> ------------------------------------------------------------------------<br>> *From:*
Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>> *To:* Gromacs Users' List <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> *Sent:* Fri, April 22, 2011 10:59:22 AM<br>> *Subject:* Re: [gmx-users] DNA not wrapping around CNT in MD simulation<br>> <br>> <br>> <br>> majid hasan wrote:<br>> > Yes, ideally I didn't want to, but I read somewhere on mailing list that one shouldn't use define = -DFLEXIBLE while running dynamics. So I thought I will use restrained water...<br>> ><br>> > I'll move back to -DFLEXIBLE though, if I got a successful mdrun for restrained water.<br>> ><br>> <br>> Constraints and restraints are separate ideas.<br>> <br><span>> <a target="_blank"
href="http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints">http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints</a></span><br>> <br>> If you *restrain* the water, the molecules won't move. If you *constrain* (i.e., using rigid water and not -DFLEXIBLE, which for MD you shouldn't be doing) you fix the geometry of a molecule while still allowing it to actually move.<br>> <br>> -Justin<br>> <br>> > Thanks,<br>> > Majid<br>> ><br>> > ------------------------------------------------------------------------<br>> > *From:* Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a> <mailto:<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>>><br>> > *To:* Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>>><br>> > *Sent:* Fri, April 22, 2011 10:44:45 AM<br>> > *Subject:* Re: [gmx-users] DNA not wrapping around CNT in MD simulation<br>> ><br>> ><br>> ><br>> > majid hasan wrote:<br>> > > I just checked and DNA position should not be restrained because I didn't use define = -DPOSRES in .mdp file. I am going to run it for a longer time now, and use position restraints for water<br>> > ><br>> ><br>> > What purpose does restraining the water have? You'll be trying to observe diffusion of your DNA or CNT through an immobile solvent.<br>> ><br>> > -Justin<br>> ><br>> > > Thank
You,<br>> > > Majid.<br>> > ><br>> > > ------------------------------------------------------------------------<br>> > > *From:* Mark Abraham <<a ymailto="mailto:Mark.Abraham@anu.edu.au" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a> <mailto:<a ymailto="mailto:Mark.Abraham@anu.edu.au" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>> <mailto:<a ymailto="mailto:Mark.Abraham@anu.edu.au" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a> <mailto:<a ymailto="mailto:Mark.Abraham@anu.edu.au" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>>>><br>> > > *To:* Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users@gromacs.org"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>>>><br>> > > *Sent:* Fri, April 22, 2011 1:51:47 AM<br>> > > *Subject:* Re: [gmx-users] DNA not wrapping around CNT in MD simulation<br>> > ><br>> > > On 4/22/2011 6:48 PM, Mark Abraham wrote:<br>> > >> On 4/22/2011 4:54 PM, majid hasan wrote:<br>> > >>> Dear All,<br>> > >>><br>> > >>> I am doing a MD simulation of dna, and cnt in water. I get a stable simulation in which DNA, and CNT wiggles around there positions, but they don't seem to be attracted towards each
other. CNT starts in the middle of the box and just moves a little, and DNA starts at top right corner of the box and remains there throughout the simulation.<br>> > >>><br>> > >>> movie of .trr file is here:<br>> > >>><br><span>>> > >> <a target="_blank" href="http://phas.ubc.ca/%7Emajid/Project/cntdna.mpg">http://phas.ubc.ca/%7Emajid/Project/cntdna.mpg</a></span><br>> > >>><br>> > >>> My .mdp files are placed here (both .mdp files are same except for the value of integrator):<br><span>>> > >> <a target="_blank" href="http://phas.ubc.ca/%7Emajid/Project/lbfgs.mdp">http://phas.ubc.ca/%7Emajid/Project/lbfgs.mdp</a> (used for EM)</span><br><span>>> > >> <a target="_blank" href="http://phas.ubc.ca/%7Emajid/Project/md.mdp">http://phas.ubc.ca/%7Emajid/Project/md.mdp</a>
(used for MD)</span><br>> > >>><br>> > >>><br>> > >>><br>> > >>> I created cnt, and dna using following commands:<br>> > >>> For dna: pdb2gmx -f dna.pdb -o dna.gro -p dna.top -ff select (Selected amber99sb, and TIP3P water model)<br>> > >>> For cnt: g_x2top -f cnt.gro -o cnt.top -ff select -pbc (selected amber99sb)<br>> > >>> For mixing and solvation: genbox -cp cnt.gro -ci dna.gro -o cntdna.gro -nmol 1 -try 20 genbox -cp cntdna.gro -cs spc.gro -o cntdnasol.gro<br>> > >>> In the dna.top file, amber99sb/ions.itp, and a position restraint file was also included along with tip3p.itp. I mentioned it because I am not sure why would it add ions and position restraints on adding water?<br>> > >><br>>
> >> #including molecule .itp files adds nothing to the system - only the potential to have molecule type(s). The system is defined in the [system] directive, and must match the corresponding coordinate file.<br>> > >><br>> > >>> It seems that something is wrong with non-bonded interactions, but I don't understand what?<br>> > >><br>> > >> Why aren't you following a proper equilibration protocol before trying to make observations? You might be using position restraints, have your species too far apart, or simply have not simulated long enough to observe any movement. 200ps is an eye-blink.<br>> > ><br>> > > Actually, you simulated 20ps. Your MD timestep is 0.2fs, which is unreasonably short. 100,000 of them is far too short to see anything happen.<br>> > ><br>>
> > Mark<br>> > ><br>> ><br>> > -- ========================================<br>> ><br>> > Justin A. Lemkul<br>> > Ph.D. Candidate<br>> > ICTAS Doctoral Scholar<br>> > MILES-IGERT Trainee<br>> > Department of Biochemistry<br>> > Virginia Tech<br>> > Blacksburg, VA<br>> > jalemkul[at]<a target="_blank" href="http://vt.edu">vt.edu</a><span> <<a target="_blank" href="http://vt.edu">http://vt.edu</a>> <</span><a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<br><span>>> <a target="_blank" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a></span><br>> ><br>> > ========================================<br>> > -- gmx-users mailing list
<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>>><br><span>>> <a target="_blank" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a></span><br>>> Please search the archive at <br><span>> <a target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!</span><br>> > Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a
ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>> <mailto:<a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>>.<br><span>>> Can't post? Read <a target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a></span><br>> <br>> -- ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>>
Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>> <br>> ========================================<br>> -- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the www interface or send it to
<a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br><br>-- ========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>-- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></div></div><div style="position:fixed"></div>
</div></body></html>