Yuri Garmay wrote:
Hi, all!
I am trying to simulate a system of peptide, water, NaCl and DMSO.
I used pdb2gmx to generate .top file for DMSO and then created this .itp:
(initial DMSO structure had been minimized before it was used for box
generation)
[ moleculetype ]
; Name nrexcl
DMSO 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
; residue 1 DMSO rtp DMSO q 0.0
1 SDmso 1 DMSO SDmso 1 0.12753 32.06 ;
qtot 0.1275
2 ODmso 1 DMSO ODmso 1 -0.44753 15.9994 ;
qtot -0.32
3 CDmso 1 DMSO CDms1 1 0.16 15.035 ;
qtot -0.16
4 CDmso 1 DMSO CDms2 1 0.16 15.035 ;
qtot 0
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 2 gb_41
1 3 2 gb_42
1 4 2 gb_42
2 3 2 gb_49
2 4 2 gb_49
3 4 2 gb_50
Corresponding record
in /usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp is:
[ DMSO ]
[ atoms ]
SDmso SDmso 0.12753 0
ODmso ODmso -0.44753 0
CDms1 CDmso 0.16000 0
CDms2 CDmso 0.16000 0
[ bonds ]
SDmso ODmso gb_41
SDmso CDms1 gb_42
SDmso CDms2 gb_42
ODmso CDms1 gb_49
ODmso CDms2 gb_49
CDms1 CDms2 gb_50
[ angles ]
; ai aj ak gromos type
[ impropers ]
; ai aj ak al gromos type
[ dihedrals ]
; ai aj ak al gromos type
Then I created box with genbox using -ci and -cs options. I did add
following strings in system .top file:
before [ system ]
; Include DMSO topology
#include "dmso.itp"
after [ molecules ]
DMSO 69
Parameters what I used for energy minimization was:
; Parameters describing how to find the neighbors of each atom and how
to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range forces
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.0 ; Cut-off for making neighbor list (short range forces)
coulombtype = PME ; Treatment of long range electrostatic interactions
pme_order = 4 ; cubic interpolation
fourierspacing = 0.12 ; grid spacing for FFT
rcoulomb = 1.0 ; Short-range electrostatic cut-off
rvdw = 1.0 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
Then I get minimization crushed after such warnings:
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.646692, max 1.998582 (between atoms 237 and 236)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
223 222 148.1 0.1535 0.0548 0.1530
When I set constraints = h-bonds minimization was successful.
It seems LINCS algorithm has limitations on the molecule topology. I
didn't know details of this method and need help.
LINCS is actually quite stable, but will crash if the system is not ;)
What should I do for simulation works? Is there need to change DMSO
topology or maybe it is better to use constraints = h-bonds option?
Try minimizing again now with all bonds constrained using the output of the EM
that ran. Generally, if EM crashes, your system contains some unresolvable
clash or inappropriate geometry. Perhaps you have now relaxed the bad
interactions sufficiently to proceed.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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