Okay, thanks, I'll try longer simulations. Majid
________________________________ From: Justin A. Lemkul <jalem...@vt.edu> To: Gromacs Users' List <gmx-users@gromacs.org> Sent: Fri, April 22, 2011 5:18:50 PM Subject: Re: [gmx-users] DNA not wrapping around CNT in MD simulation 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. > 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. > Movie of output is here: > http://phas.ubc.ca/~majid/Project/msteps/cntdna2000ps.mpg 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. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow > and input em.mdp, and md.mdp files are here: > EM: http://phas.ubc.ca/~majid/Project/msteps/lbfgs.mdp > <http://phas.ubc.ca/~majid/Project/msteps/lbfgs.mdp>MD: >http://phas.ubc.ca/~majid/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 > > <http://phas.ubc.ca/~majid/Project/msteps/md.mdp>I have no clue what is wrong >with the simulation, and any help is much appreciated. > Likely nothing is "wrong," you just aren't simulating long enough. -Justin > Thanks, > Majid > ------------------------------------------------------------------------ > *From:* Justin A. Lemkul <jalem...@vt.edu> > *To:* Gromacs Users' List <gmx-users@gromacs.org> > *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 <jalem...@vt.edu <mailto:jalem...@vt.edu>> > > *To:* Discussion list for GROMACS users <gmx-users@gromacs.org ><mailto:gmx-users@gromacs.org>> > > *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 <mark.abra...@anu.edu.au ><mailto:mark.abra...@anu.edu.au> <mailto:mark.abra...@anu.edu.au ><mailto:mark.abra...@anu.edu.au>>> > > > *To:* Discussion list for GROMACS users <gmx-users@gromacs.org ><mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org ><mailto:gmx-users@gromacs.org>>> > > > *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> <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > ======================================== > > -- gmx-users mailing list gmx-users@gromacs.org ><mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org ><mailto:gmx-users@gromacs.org>> >> 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 gmx-users-requ...@gromacs.org ><mailto:gmx-users-requ...@gromacs.org> <mailto:gmx-users-requ...@gromacs.org ><mailto:gmx-users-requ...@gromacs.org>>. >> 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 gmx-users@gromacs.org ><mailto:gmx-users@gromacs.org> > 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 gmx-users-requ...@gromacs.org ><mailto:gmx-users-requ...@gromacs.org>. > 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 gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists