Dear Justin,<br><br>I have run into another problem.<br><br>I created the system by including DHB in vwdradii.dat as follows:<br><br>; Very approximate VanderWaals radii<br>; only used for drawing atoms as balls or for calculating atomic overlap.<br>
; longest matches are used<br>; '???' or '*' matches any residue name<br>; 'AAA' matches any protein residue name<br>??? C 0.15<br>??? F 0.12<br>??? H 0.04<br>??? N 0.110<br>??? O 0.105<br>
??? S 0.16<br><b>DHB C 0.5<br>DHB H 0.5<br>DHB O 0.5</b><br>; Water charge sites<br>SOL MW 0<br>SOL LP 0<br>; Masses for vsite construction<br>GLY MN1 0<br>GLY MN2 0<br>ALA MCB1 0<br>ALA MCB2 0<br>
VAL MCG1 0<br>VAL MCG2 0<br>ILE MCG1 0<br>ILE MCG2 0<br>ILE MCD1 0<br>ILE MCD2 0<br>LEU MCD1 0<br>LEU MCD2 0<br>MET MCE1 0<br>MET MCE2 0<br>TRP MTRP1 0<br>TRP MTRP2 0<br>THR MCG1 0<br>THR MCG2 0<br>
LYSH MNZ1 0<br>LYSH MNZ2 0<br><br>After making this change, DHB molecules were not over lapping with each other.<br><br>I tried to energy minimized the system. <br>minim.mdp<br>; minim.mdp - used as input into grompp to generate em.tpr<br>
; Parameters describing what to do, when to stop and what to save<br>integrator = steep ; Algorithm (steep = steepest descent minimization)<br>;emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm<br>
emstep = 0.01 ; Energy step size<br>nsteps = 50000 ; Maximum number of (minimization) steps to perform<br><br>; Parameters describing how to find the neighbors of each atom and how to calculate the interactions<br>
nstlist = 1 ; Frequency to update the neighbor list and long range forces<br>ns_type = grid ; Method to determine neighbor list (simple, grid)<br>rlist = 1.0 ; Cut-off for making neighbor list (short range forces)<br>
coulombtype = PME ; Treatment of long range electrostatic interactions<br>rcoulomb = 1.0 ; Short-range electrostatic cut-off<br>rvdw = 1.0 ; Short-range Van der Waals cut-off<br>pbc = xyz ; Periodic Boundary Conditions (yes/no)<br>
constraints = none<br><br><br> After about 6000 steps the run stops with the message:<br>Stepsize too small, or no change in energy.<br>Converged to machine precision,<br>but not to the requested precision Fmax < 10<br>
<br>Double precision normally gives you higher accuracy.<br><br>Steepest Descents converged to machine precision in 6012 steps,<br>but did not reach the requested Fmax < 10.<br>Potential Energy = 1.0655116e+05<br>Maximum force = 1.6512177e+02 on atom 2076<br>
Norm of force = 6.5337501e+00 <br><br><br><br>The potential energy is high, but I still continued to equilibration.<br>After NVT equilibration, NVT equilbration runs into the following error as soon it starts:<br><br>
<br>Warning: 1-4 interaction between 4512 and 4516 at distance 6.148 which is larger than the 1-4 table size 2.000 nm<br>These are ignored for the rest of the simulation<br>This usually means your system is exploding,<br>
if not, you should increase table-extension in your mdp file<br>or with user tables increase the table size<br>/var/spool/pbs/mom_priv/jobs/<a href="http://1869547.lionxj.rcc.psu.edu.SC">1869547.lionxj.rcc.psu.edu.SC</a>: line 14: 2359 Segmentation fault mdrun -deffnm npt<br>
<br><br><br><br>So, I have three questions:<br><br>1. Is the starting structure bad?<br>2. Did I change the vdwd radii by a lot (0.105 to 0.5)<br>3. What value of table extension should be used for 1-4 interaction ( default value is?) if thats the problem to be fixed.<br>
<br>Please guide.<br><br>Thanks,<br>SN<br><br><br><br><br><div class="gmail_quote">On Tue, Jun 14, 2011 at 11:29 AM, shivangi nangia <span dir="ltr"><<a href="mailto:shivangi.nangia@gmail.com">shivangi.nangia@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Thanks Justin, vdwradii.dat suggestion worked :)<div><div></div><div class="h5"><br><br><br>
<br><div class="gmail_quote">On Mon, Jun 13, 2011 at 11:05 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div><br>
<br>
shivangi nangia wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hello dear gmx-users,<br>
<br>
I am trying to create a system which has 2,5-dihydobenzoic acid (DHB) as the solvent ( with a positively charged protein and few DHB anions) in a box.<br>
<br>
I have created the .itp and .gro file of DHB using PRODRG.<br>
<br>
</blockquote>
<br></div>
Unrelated advice - the topology is probably useless unless you've corrected the charges. See the paper linked from:<br>
<br>
<a href="http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips" target="_blank">http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips</a><div><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
I am able to create the system, but when I try to energy minimize the system I get the message:<br>
<br>
Steepest Descents:<br>
Tolerance (Fmax) = 1.00000e+01<br>
Number of steps = 50000<br>
Step= 14, Dmax= 1.2e-06 nm, Epot= 9.04353e+19 Fmax= inf, atom= 2781<br>
Stepsize too small, or no change in energy.<br>
Converged to machine precision,<br>
but not to the requested precision Fmax < 10<br>
<br>
Double precision normally gives you higher accuracy.<br>
<br>
writing lowest energy coordinates.<br>
<br>
Back Off! I just backed up em.gro to ./#em.gro.1#<br>
<br>
Steepest Descents converged to machine precision in 15 steps,<br>
but did not reach the requested Fmax < 10.<br>
Potential Energy = 9.0435262e+19<br>
Maximum force = inf on atom 2781<br>
Norm of force = inf<br>
<br>
<br>
The reason behind this was that DHB molecules were on top of each other, highly dense system ( viewed in VMD)<br>
So, to reduce the density of DHB molecules, I tried using-vdwd option of genbox (changed from default value of 0.105 to 0.5)<br>
But, I got almost same number of DHB molecules using genbox.<br>
<br>
</blockquote>
<br></div>
The -vdwd option has no effect unless you're using atom names that are not found in vdwradii.dat (see the genbox help description). Your DHB molecule should be unaffected by the use of -vdwd.<div><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
What is the best solution to this problem as I understand, reducing the density of DHB molecules around the protein as a solvent or there is some other problem?<br>
<br>
</blockquote>
<br></div>
You need to generate a configuration in which molecules aren't overlapping. There are several ways to accomplish this. You can manually place molecules within a box at a desired location with editconf -center, otherwise genbox -ci -nmol. If the locations of the molecules are not what you desire with genbox, change the value of -seed and try again.<br>
<br>
-Justin<br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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