<br>
The starting structure is a homology model. <br>
(If you need some more details then please tell me)<br>
<br>
force field : GROMOS96 43a1 <br>
<br>
I have not at all added or removed any ion manually. <br>
<br>
amount of water : using genboc -cs ( spc216.gro ) water is added.<br>
Here the details are as follows <br>
<br>
<span style="font-style: italic;">Reading solute configuration</span><br style="font-style: italic;">
<span style="font-style: italic;">ecol</span><br style="font-style: italic;">
<span style="font-style: italic;">Containing 1791 atoms in 175 residues</span><br style="font-style: italic;">
<span style="font-style: italic;">Initialising van der waals distances...</span><br style="font-style: italic;">
<span style="font-style: italic;">Reading solvent configuration</span><br style="font-style: italic;">
<span style="font-style: italic;">"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"</span><br style="font-style: italic;">
<span style="font-style: italic;">solvent configuration contains 648 atoms in 216 residues</span><br style="font-style: italic;">
<br style="font-style: italic;">
<span style="font-style: italic;">Initialising van der waals distances...</span><br style="font-style: italic;">
<span style="font-style: italic;">Will generate new solvent configuration of 4x4x5 boxes</span><br style="font-style: italic;">
<span style="font-style: italic;">Generating configuration</span><br style="font-style: italic;">
<span style="font-style: italic;">Sorting configuration</span><br style="font-style: italic;">
<span style="font-style: italic;">Found 1 molecule type:</span><br style="font-style: italic;">
<span style="font-style: italic;"> SOL ( 3 atoms): 17280 residues</span><br style="font-style: italic;">
<span style="font-style: italic;">Calculating Overlap...</span><br style="font-style: italic;">
<span style="font-style: italic;">box_margin = 0.315</span><br style="font-style: italic;">
<span style="font-style: italic;">Removed 13368 atoms that were outside the box</span><br style="font-style: italic;">
<span style="font-style: italic;">Neighborsearching with a cut-off of 0.48</span><br style="font-style: italic;">
<span style="font-style: italic;">Table routines are used for coulomb: FALSE</span><br style="font-style: italic;">
<span style="font-style: italic;">Table routines are used for vdw: FALSE</span><br style="font-style: italic;">
<span style="font-style: italic;">Cut-off's: NS: 0.48 Coulomb: 0.48 LJ: 0.48</span><br style="font-style: italic;">
<span style="font-style: italic;">System total charge: 0.000</span><br style="font-style: italic;">
<span style="font-style: italic;">Neighborsearching with a cut-off of 0.48</span><br style="font-style: italic;">
<span style="font-style: italic;">Grid: 28 x 23 x 36 cells</span><br style="font-style: italic;">
<span style="font-style: italic;">Succesfully made neighbourlist</span><br style="font-style: italic;">
<span style="font-style: italic;">nri = 75512, nrj = 2292910</span><br style="font-style: italic;">
<span style="font-style: italic;">Checking Protein-Solvent overlap: tested 36365 pairs, removed 2592 atoms.</span><br style="font-style: italic;">
<span style="font-style: italic;">Checking Solvent-Solvent overlap: tested 377819 pairs, removed 4773 atoms.</span><br style="font-style: italic;">
<span style="font-style: italic;">Added 10369 molecules</span><br style="font-style: italic;">
<span style="font-style: italic;">Generated solvent containing 31107 atoms in 10369 residues</span><br style="font-style: italic;">
<span style="font-style: italic;">Writing generated configuration to ecolinusG_b4em.gro</span><br style="font-style: italic;">
<span style="font-style: italic;">ecol</span><br style="font-style: italic;">
<br style="font-style: italic;">
<span style="font-style: italic;">Output configuration contains 32898 atoms in 10544 residues</span><br style="font-style: italic;">
<span style="font-style: italic;">Volume
: 341.479 (nm^3)</span><br style="font-style: italic;">
<span style="font-style: italic;">Density
: 1005.02 (g/l)</span><br style="font-style: italic;">
<span style="font-style: italic;">Number of SOL molecules: 10369</span><br>
<br><br>
<br>
<br>
<br>
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<br>
<br><div><span class="gmail_quote">On 8/21/06, <b class="gmail_sendername">David van der Spoel</b> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dhananjay wrote:<br>> Hello all,<br>><br>> I am running mdrun for a system of protein having 182 residues. (Before<br>> going for MD, mdrun for EM and PR has been done as per the<br>> instructions given in the online manual.)
<br>> After 3ns job is over, I calculated RMSD and it is about 0.6 nm. This<br>> is too high.<br>><br>> In the mailing list, most of the search suggests that RMSD may be high<br>> depends on the system.<br>
> One of the mails suggests to calculate RMSD domainwise. Hence I have<br>> calculated it domainwise as the system consists of two domains. I found<br>> that one of the domains has RMSD about 0.35 nm but the other domain is
<br>> still showing around 0.6 nm<br><br>please give more details,<br>amount of water,<br>force field,<br>ions<br>where does that starting structure come from<br>etc.<br><br>><br>> Is there something wrong in assigning the parameter ?
<br>><br>> Please give me suggestions.........<br>><br>> Thanking you in advance.<br>><br>> The full mdrun paramitors are as follows:<br>><br>> title = xyz<br>>
cpp
= /usr/bin/cpp<br>> constraints = all-bonds<br>> integrator = md<br>>
dt = 0.001 ;
ps !<br>>
nsteps = 20000000
; total 20 ns<br>> nstcomm = 1<br>> nstxout = 500<br>> nstvout = 1000<br>> nstfout = 0<br>> nstlist = 10<br>> nstlog = 10<br>
> nstenergy = 10<br>> ns_type = grid<br>>
rlist
= 0.9 ; nm<br>> coulombtype = PME<br>>
rcoulomb = 0.9 ;
nm<br>> rvdw = 1.4<br>> fourierspacing = 0.12<br>> fourier_nx = 0<br>> fourier_ny = 0<br>> fourier_nz = 0<br>> pme_order = 4
<br>> ewald_rtol = 1e-5<br>> optimize_fft = yes<br>> ; Berendsen temperature coupling is on in three groups<br>> Tcoupl = berendsen<br>>
tau_t
= 0.1 0.1<br>> tc_grps = protein sol<br>>
ref_t
= 300 300<br>> ; Pressure coupling is on<br>> Pcoupl = berendsen<br>> pcoupltype = isotropic<br>> tau_p = 0.5<br>> compressibility = 4.5e-5<br>> ref_p =
1.0<br>> ; Generate velocites is on at 300 K.<br>> gen_vel = yes<br>> gen_temp = 300.0<br>> gen_seed = 173529<br>><br>><br>> --<br>> Dhananjay<br>><br>><br>
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<br>--<br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.
<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755<br><a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org
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</a><br></blockquote></div><br><br clear="all"><br>-- <br>Dhananjay <br>