Hi,
Have you looked at your entire trajectory? This sounds like it could
be an imaging artifact to me. Because the DNA is two separate
molecules, occasionally one strand gets imaged and the other doesn't.
This has no affect during the simulation since it's just for
visualization, but it is particularly bad if you have restraints that
depend on the DNA molecules because restraints are *not* imaged.
Whenever I simulate multiple solute molecules with PBC and restraints
I always re-image my coordinate files before restarting. You should
try re-imaging your restart with cpptraj's 'autoimage' command (the
one you used as coordinates for the run that blew up) and see if that
helps.
If on the other hand you've viewed your trajectory and the DNA is
actually falling apart gradually (i.e. there is no sudden "jump" from
imaging) that's another story.
-Dan
On Fri, Dec 12, 2014 at 1:49 AM, Aditya Sarkar <aditya.molbio.gmail.com> wrote:
> Dear Amber users,
>
> I am new to the MD simulation. I have faced a strange problem in doing
> simulation of protein-DNA complex. The problem, questions and the setup
> details are given below:
>
> *****PROBLEM********
> ---------------------------------
>
> I have planned to run 100ns simulation and divide the whole run in 50
> restart (each of 2ns). My simulation ran well upto 94ns but at the begining
> of the next restart I found the DNA get horribly denatured. I have attached
> the picture with this mail.
>
> *****QUESTION********
> ---------------------------------
>
> 1. I have checked the prmtop file with rdparm to make sure about the use of
> proper force field. But I have doubt whether my way of selection of force
> field is correct or not? and also regarding the production run script.
>
> 2. I did not get why the DNA get unstable and how can I analyze the cause
> and correct it?
>
>
> *****SETUP********
> ---------------------------
>
> 1. The structure is a crystal structure with all crystal water. DNA residue
> no: 103-138
>
> *2.Force field used: ff99SB-ILDN along with parambsc0*
>
> *[tleap file command: source leaprc.ff99SBildn*
> * loadoff DNA_CI.lib*
> * loadamberparams frcmod.parmbsc0*
>
>
> *I do did energy minimization (with and without position restraint, heating
> (with position restraint), NPT equilibration (gradually relaxing restraint)
> and finally performed production run*
>
> *3.Production run:*
> &cntrl
> imin = 0, irest = 1, ntx = 5,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 8.0, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 1.0, ig = -1, iwrap = 1,
> nstlim = 1000000, dt = 0.002, nmropt =1,
> ntpr = 2500, ntwx = 2500, ntwr = 2500,
> ntwv = 2500, ntwe = 2500
> /
> &wt type='DUMPFREQ', istep1=2000
> /
> &wt type='END'
> /
> LISTOUT=POUT
> DISANG=DIST.rst
> DUMPAVE=rest_values_INPRORUN1
> END
>
> *4. Distance restraint input file*
> 2 ALA O 6 ALA N 3.0
> 3 LEU O 7 ARG N 3.0
> 53 ALA O 57 ALA N 3.0
> 54 LEU O 58 ARG N 3.0
> 50 LEU N 46 ARG O 2.9
> 49 LYS N 45 ALA O 3.2
> 101 LEU N 97 ARG O 3.0
> 100 LYS N 96 ALA O 3.0
> 103 DG5 O6 138 DC3 H41 2.0
> 103 DG5 H1 138 DC3 N3 1.9
> 103 DG5 H22 138 DC3 O2 3.5
> 121 DG5 O6 120 DC3 H41 1.9
> 121 DG5 H1 120 DC3 N3 1.9
> 121 DG5 H22 120 DC3 O2 3.5
>
> *5. Commands used:*
>
> to generate DIST.rst file:
> ****************************
> makeDIST_RST -upb DNA_Protein-endDISTRST -pdb emin_NoRST.pdb -rst DIST.rst
>
>
> For production run:
> **********************
> nohup mpiexec.hydra -n 8 sander.MPI -O -i production1.in -o prodrun1.out -p
> GCN4_CREB_inbox.prmtop -c equil_NPT.rst -r prodrun1.rst -x prodrun1.mdcrd
>
> nohup mpiexec.hydra -n 8 pmemd.MPI -O -i production2.in -o prodrun2.out -p
> GCN4_CREB_inbox.prmtop -c prodrun1.rst -r prodrun2.rst -x prodrun2.mdcrd
>
> *NOTE: I was initially unsure about using "pmemd" that's why I started
> first run with sander and after reading maual and Amber blog, I started
> using "pmemd".
>
>
> Looking forward for your reply.
>
> regards
> Aditya
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Dec 12 2014 - 07:00:02 PST
