Hello Justin and everybody,<br><br>I created a system of charged polyhistdine, counter anions and just 1 DHB molecule is a box without making any change in the vdwradii.dat file. <br>This system does not energy minimize, it stops with the same message:<br>
<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>What can be done to fix this problem?<br><br><br>The part of DHB itp file is:<br>[ moleculetype ]<br>; Name nrexcl<br>DHB 3<br><br>[ atoms ]<br>; nr type resnr resid atom cgnr charge mass<br>
1 OM 1 DHB OAA 1 -0.567 15.9994<br> 2 C 1 DHB CAH 1 1.135 12.0110<br> 3 OM 1 DHB OAD 1 -0.568 15.9994<br> 4 C 1 DHB CAK 2 -0.004 12.0110<br>
5 CR1 1 DHB CAG 2 0.004 12.0110<br> 6 HC 1 DHB HAG 2 0.033 1.0080<br> 7 C 1 DHB CAI 2 0.141 12.0110<br> 8 OA 1 DHB OAB 2 -0.179 15.9994<br>
9 H 1 DHB HAB 2 0.005 1.0080<br> 10 CR1 1 DHB CAE 3 0.000 12.0110<br> 11 HC 1 DHB HAE 3 0.000 1.0080<br> 12 CR1 1 DHB CAF 3 0.000 12.0110<br>
13 HC 1 DHB HAF 3 0.000 1.0080<br> 14 C 1 DHB CAJ 4 0.082 12.0110<br> 15 OA 1 DHB OAC 4 -0.113 15.9994<br> 16 H 1 DHB HAC 4 0.031 1.0080<br>
<br><br><br><br><br>If I have the water/methanol or water:methanol in the system as the solvent, the system runs fine.<br><br>Please help.<br><br>Thanks,<br>SN<br><br><br><br><br><br><br><div class="gmail_quote">On Tue, Jun 14, 2011 at 3:13 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">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;"><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;"><div><div></div><div class="h5">
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>
*DHB C 0.5<br>
DHB H 0.5<br>
DHB O 0.5*<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></div></div>
/var/spool/pbs/mom_priv/jobs/<a href="http://1869547.lionxj.rcc.psu.edu.SC" target="_blank">1869547.lionxj.rcc.psu.edu.SC</a> <<a href="http://1869547.lionxj.rcc.psu.edu.SC" target="_blank">http://1869547.lionxj.rcc.psu.edu.SC</a>>: line 14: 2359 Segmentation fault mdrun -deffnm npt<div class="im">
<br>
<br>
<br>
<br>
<br>
So, I have three questions:<br>
<br>
1. Is the starting structure bad?<br>
</div></blockquote>
<br>
Probably.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
2. Did I change the vdwd radii by a lot (0.105 to 0.5)<br>
</blockquote>
<br></div>
Yes. And you shouldn't use those artificial values for anything else. Remove them after you've inserted the DHB into your system. This is, of course, no guarantee that the system is stable, either.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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>
</blockquote>
<br></div>
Do not adjust the table extension. If the system is blowing up, there's no reason to troubleshoot the constraints; they're not your problem.<div><div></div><div class="h5"><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>
========================================<br>
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