[gmx-users] NPT not working
hanin_omar85 at yahoo.com
Wed Nov 14 12:07:42 CET 2018
Thank you Justin for your answer, i went back to my system and did all sort of tests, and the system works fine without the RDC restraint. Since the RDC values where used to generate the original pdb file of the protein i think the strongest option would be to say that i have an issue with the implementation of RDC constraints, so ill post how i implemented them and see if anyone cane pinpoint my mistakes:1) in the toplogy file:
; Include orientation restraint file
2) the RDC-restraint.itp had lines like these for 4 types of rdc (n-h , c-n, calpha-halpha, h-c):
[ orientation_restraints ]
; ai aj type exp. label alpha const. obs. weight
; Hz nm^3 Hz Hz^-2
; residue 1
5 6 1 1 1 3 -15.098 -15.0821 1
5 6 1 2 2 3 -15.098 10.8391 1
; residue 2
18 20 1 1 3 3 1.53 -1.145444 1
18 20 1 2 4 3 1.53 -1.128506 1
20 21 1 1 5 3 6.083 7.72483 1
20 21 1 2 6 3 6.083 7.27571 1
18 21 1 1 7 3 -15.098 0.187741325 1
18 21 1 2 8 3 -15.098 3.13646 1
22 23 1 1 9 3 -15.098 -12.31345 1
22 23 1 2 10 3 -15.098 15.355 1
3) in the mdp file for the simulation:
define = -DPOSRES ;use orientation restraint;Options for orientation restraint
orire = yes
orire-fc = 1 ; Orientation restraints force constant
orire-tau = 0 ; Turn off time averaging
orire-fitgrp = backbone
is the problem with my implementation that they are using the rdc restraints for the water as well as the protein, and if so how can i specify that they should be fitted to just the protein?THank you for the answerHain
On Thursday, November 1, 2018, 4:11:10 PM EDT, Justin Lemkul <jalemkul at vt.edu> wrote:
On 11/1/18 7:33 AM, Hanin Omar wrote:
> Dear all gromacs user;
> I am new to gromacs, and i desperatly need help. I want to use gromacs to calculate the internal dynamics trajectory within a protein.
> For my simulation i followed this protocol:
> 1)Use pdb2gmx to generate the gro file and topology ( i chose amber99SB and TIP3P water modrel)
> 2)Energy minimization in vacuum
> 3) set perodic boundery coditions
> 4)solvate the system
> 5) ADD ions to neutralize the system
> 6)Energy minimization of the solvated system
> 7) Position restrainted MD
> 8)Unrestraind MD ( NVT equiliberation)
> 9)Unrestraind MD ( NPT equiliberation)
> 10)Run MD simulation with the addition of RDC restraint in the topology like this
> ; Include Position restraint file
> #ifdef POSRES
> #include "RDC-restraint.itp"
> The problem is i always get the following eroor when i run the last step
> (Fatal error:
> Error: Too many iterations in routine JACOBI)
> I researched the error and some suggested that the system wasnt equiliberated enough, after checking it seems that the NPT part doesn't converge, i tried extending the time but that didnt solve it, i tired doing it in two steps: 1st NPT with thermostat = v - rescale and barostat = Berendsen for say 6.5 ps and then run 2ND NPT with thermostat = Nose-Hooover and barostat = Parinello -Rahman for 6.5 ps.But that also didnt help. can someone explain why is this happening( and if it has to do with the RDC constraints)? and how can i solve it?
If the introduction of RDC restraints causes a failure, then either (1)
the implementation of the restraints is incorrect or (2) your structure
is incompatible with those restraints, leading to the buildup of forces
and a crash.
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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