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. Thanks, Majid ________________________________ From: Justin A. Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <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> > *To:* Discussion list for GROMACS users <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 | (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
