[gmx-users] Error with CHARMM36 force field
laurenmr at bii.a-star.edu.sg
Tue Mar 13 10:25:17 CET 2018
Thanks for the reply.
I use GROMACS-5.1.4 and I just use standard Linux editors. Please find
my mdp file attached.
When I check in the file "old_c36_cmap.itp" I do find very long lines (>
4095 characters). Could this mean that this force field file is not
compatible with this version of GROMACS?
On 13/03/2018 17:07, Mark Abraham wrote:
> What version of GROMACS is this? Did you edit your file using an unsuitable
> editor, such as anything on Windows?
> On Tue, Mar 13, 2018 at 9:20 AM laurenmr <laurenmr at bii.a-star.edu.sg> wrote:
>> Hi Gromacs Users,
>> I have downloaded the latest version of the CHARMM36M force field. My
>> aim is to compare a simulation using CHARMM36M and CHARMM36. In the
>> forcefield.itp there is an 'if' statement allowing the user to switch to
>> the old CHARMM36 force field by directing to the old cmap itp:
>> ; Allow the user to specify CHARMM36 parameters, instead
>> ; Default behavior is to use CHARMM36m
>> #ifdef USE_OLD_C36
>> #include "old_c36_cmap.itp"
>> #include "cmap.itp"
>> However, when I include "define = -DUSE_OLD_C36" in my .mdp file I
>> receive this error at the grompp command:
>> Fatal error:
>> An input file contains a line longer than 4095 characters, while the
>> buffer passed to fgets2 has size 4095. The line starts with: 'C NH1 CT1
>> C NH1 1 24'
>> Could anyone suggest a way around this or should I download an older
>> version of CHARMM36 (before CHARMM36M)?
>> Thanks in advance for the help!
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; ions.mdp - used as input into grompp to generate ions.tpr
; Parameters describing what to do, when to stop and what to save
define = -DUSE_OLD_C36 ; Don't use cmap corrections
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep = 0.01 ; Energy step size
nsteps = 50000 ; Maximum number of (minimization) steps to perform
; 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
cutoff-scheme = Verlet
ns_type = grid ; Method to determine neighbor list (simple, grid)
coulombtype = PME ; Treatment of long range electrostatic interactions
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)
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