Allright, I will check the configurations of out and inputs to find out the reason of warning. Please let me know something: Should I expect to see changes in area per lipids in each shrinking or it would happen after 25th repeat suddenly?
Thanks . Sincerely, Shima ________________________________ From: Justin Lemkul <jalem...@vt.edu> To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Tuesday, August 21, 2012 2:57 PM Subject: Re: [gmx-users] EM in kalp15_DPPC On 8/21/12 6:14 AM, Shima Arasteh wrote: > > > > Hi, > > I'm doing the KALP-15 IN DPPC through the Justin's tutorial > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html > The problem I got stuck into, is in "2. Pack the lipids around the protein" > step. > After generating the new position restrain file, I start to energy > minimization to get the correct area per lipid. As below: > > Scale the lipid positions by a factor of 4: > #perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat > > LOOP : > " > Energy minimization with restrained protein > #grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr >-maxwarn 1 Why are you using -maxwarn? It's almost always a bad idea. What error are you trying to circumvent? > #mdrun -deffnm em > scale down the lipids by a factor of 0.95 > #perl inflategro.pl em.gro 0.95 DPPC 0 system_shrink1.gro 5 >area_shrink1.dat > " > > > The EM contains a warning: > Tolerance (Fmax) = 1.00000e+03 > Number of steps = 50000 > Warning: 1-4 interaction between 2321 and 2325 at distance 2.307 which is > larger than the 1-4 table size 2.200 nm > These are ignored for the rest of the simulation > This usually means your system is exploding, > if not, you should increase table-extension in your mdp file > or with user tables increase the table size > > but because of the -maxwarn 1 its output is: > > Steepest Descents converged to Fmax < 1000 in 557 steps > Potential Energy = -9.2383398e+04 > Maximum force = 9.0041455e+02 on atom 65 > Norm of force = 7.1919853e+01 > > First, is it acceptable to ignore that warning? > Generally not. You should check your input and output configurations carefully. Something is wrong. > # perl inflategro.pl em.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat > Determining upper and lower leaflet... > 66 lipids in the upper... > 62 lipids in the lower leaflet > > Centering protein.... > Writing scaled bilayer & centered protein... > > > Calculating Area per lipid... > Protein X-min/max: 122 136 > Protein Y-min/max: 122 135 > X-range: 14 A Y-range: 13 A > Building 14 X 13 2D grid on protein coordinates... > Calculating area occupied by protein.. > full TMD.. > upper TMD.... > lower TMD.... > Area per protein: 2 nm^2 > Area per lipid: 9.29991419025 nm^2 > > Area per protein, upper half: 1.75 nm^2 > Area per lipid, upper leaflet : 9.02188648751515 nm^2 > > Area per protein, lower half: 2 nm^2 > Area per lipid, lower leaflet : 9.59991142219355 nm^2 > > Writing Area per lipid... > Done! > > Here, the area per lipid is too far from 71 Å2! > Then you haven't done enough iterations of shrinking. The outcome from 26 iterations of shrinking is very reproducible. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist 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 * Only plain text messages are allowed! * 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
