Thanks, I am going through literature at the moment. Any suggestions about tutorials, I don't find much related to it on gromacs?
Thanks again, Majid ________________________________ From: Mark Abraham <[email protected]> To: Discussion list for GROMACS users <[email protected]> Sent: Fri, April 22, 2011 5:45:22 PM Subject: Re: [gmx-users] DNA not wrapping around CNT in MD simulation On 4/23/2011 9:21 AM, majid hasan wrote: Okay, thanks, I removed restraints from water. > > > 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. > > >Movie of output is here: >http://phas.ubc.ca/%7Emajid/Project/msteps/cntdna2000ps.mpg >and input em.mdp, and md.mdp files are here: >EM: http://phas.ubc.ca/%7Emajid/Project/msteps/lbfgs.mdp >MD: http://phas.ubc.ca/%7Emajid/Project/msteps/md.mdp > > >Commands that I have been using to build input coordinates, and > >topologies are below: > > > For dna: pdb2gmx -f dna.pdb -o dna.gro -p dna.top -ff >select (Selected amber99sb, and TIP3P water model) > >For cnt: g_x2top -f cnt.gro -o cnt.top -ff select -pbc > >(selected amber99sb) > >For mixing : genbox -cp cnt.gro -ci dna.gro -o cntdna.gro >-nmol 1 -try 20 > > >For solvation: genbox -cp cntdna.gro -cs spc.gro -o >cntdnasol.gro > > >I have no clue what is wrong with the simulation, and any help is >much >appreciated. > > You're still not following a sound equilibration protocol. The velocities you generate at the start are only roughly correct, and your density is probably a bit off. Check out some tutorials, and published work on similar systems. You also need to consider how far apart these species are. If the driving force is electrostatic, the forces drop off as 1/r^2, so you can wait a long time for those to act over a few nanometers, while re-organizing the solvent between them. In real biochemical systems, one doesn't normally observe a single pair of interacting species mate up smoothly. There's a whole pile of things that have to happen, and each successful binding probably results from very many failed attempts. Having many such pairs over longer periods of times means that statistically the events do happen, but that's no good to you if you can only simulate a single pair in a short period. Mark Thanks, >Majid > > ________________________________ From: Justin A. Lemkul <[email protected]> >To: Gromacs Users' List <[email protected]> >Sent: Fri, April 22, 2011 10:59:22 AM >Subject: Re: [gmx-users] DNA not wrapping around CNT in MD >simulation > > > >majid hasan wrote: >> 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... >> >> I'll move back to -DFLEXIBLE though, if I got a successful mdrun >>for restrained water. >> > >Constraints and restraints are separate ideas. > >http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints > >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. > >-Justin > >> Thanks, >> Majid >> >> >>------------------------------------------------------------------------ >> *From:* Justin A. Lemkul <[email protected]> >> *To:* Discussion list for GROMACS users <[email protected]> >> *Sent:* Fri, April 22, 2011 10:44:45 AM >> *Subject:* Re: [gmx-users] DNA not wrapping around CNT in MD >>simulation >> >> >> >> majid hasan wrote: >> > 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 >> > >> >> What purpose does restraining the water have? You'll be trying >> to >>observe diffusion of your DNA or CNT through an immobile solvent. >> >> -Justin >> >> > Thank You, >> > Majid. >> > >> > >>------------------------------------------------------------------------ >> > *From:* Mark Abraham <[email protected] >><mailto:[email protected]>> >> > *To:* Discussion list for GROMACS users <[email protected] >><mailto:[email protected]>> >> > *Sent:* Fri, April 22, 2011 1:51:47 AM >> > *Subject:* Re: [gmx-users] DNA not wrapping around CNT in MD >>simulation >> > >> > On 4/22/2011 6:48 PM, Mark Abraham wrote: >> >> On 4/22/2011 4:54 PM, majid hasan wrote: >> >>> Dear All, >> >>> >> >>> 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. >> >>> >> >>> movie of .trr file is here: >> >>> >>> >> http://phas.ubc.ca/%7Emajid/Project/cntdna.mpg >> >>> >> >>> My .mdp files are placed here (both .mdp files are same >> except >>for the value of integrator): >>> >> http://phas.ubc.ca/%7Emajid/Project/lbfgs.mdp (used for EM) >>> >> http://phas.ubc.ca/%7Emajid/Project/md.mdp (used for MD) >> >>> >> >>> >> >>> >> >>> I created cnt, and dna using following commands: >> >>> For dna: pdb2gmx -f dna.pdb -o dna.gro -p dna.top -ff >> select >>(Selected amber99sb, and TIP3P water model) >> >>> For cnt: g_x2top -f cnt.gro -o cnt.top -ff select -pbc >>(selected amber99sb) >> >>> 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 >> >>> 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? >> >> >> >> #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. >> >> >> >>> It seems that something is wrong with non-bonded >> interactions, >>but I don't understand what? >> >> >> >> 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. >> > >> > 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. >> > >> > Mark >> > >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu<http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list [email protected] >><mailto:[email protected]> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >>http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www >>interface or send it to [email protected] >><mailto:[email protected]>. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >-- ======================================== > >Justin A. Lemkul >Ph.D. Candidate >ICTAS Doctoral Scholar >MILES-IGERT Trainee >Department of Biochemistry >Virginia Tech >Blacksburg, VA >jalemkul[at]vt.edu | (540) 231-9080 >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > >======================================== >-- gmx-users mailing list [email protected] >http://lists.gromacs.org/mailman/listinfo/gmx-users >Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/Search >before posting! >Please don't post (un)subscribe requests to the list. Use the www >interface or send it to [email protected]. >Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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