[gmx-users] Re: amber force field in Gromacs
Alan
alanwilter at gmail.com
Thu Dec 3 12:23:14 CET 2009
Dear Servaas,
Tested again in 'vacuum' and I saw no problems. Here goes what I did:
#----------------------------------
cat << EOF >| leap.in
verbosity 1
source leaprc.ff99SB
ad = sequence { DA5 DA DA3 }
saveamberparm ad da_amber.top da_amber.crd
savepdb ad DA.pdb
quit
EOF
tleap -f leap.in >| leap.out
acpypi -x da_amber.crd -p da_amber.top -d # acpypi generates em.mdp and
md.mdp
cat << EOF >| md.mdp
cpp = /usr/bin/cpp
define = ;-DFLEXIBLE
integrator = md
nsteps = 250000
constraints = none
emtol = 1000.0
emstep = 0.01
comm_mode = angular
ns_type = simple
nstlist = 0
rlist = 0
rcoulomb = 0
rvdw = 0
Tcoupl = no
Pcoupl = no
gen_vel = no
nstxout = 100
pbc = no
EOF
editconf -bt cubic -d 1.0 -f da_amber_GMX.gro -o da_amber_GMX.gro
#Single precision
grompp -f em.mdp -c da_amber_GMX.gro -p da_amber_GMX.top -o em.tpr
mdrun -v -deffnm em
grompp -f md.mdp -c em.gro -p da_amber_GMX.top -o md.tpr
mdrun -v -deffnm md
vmd md.gro md.trr
#----------------------------------
As you may suspect from the beginning it may be something in your mdp file.
Case the example above works, I would suggest you to try the mdp for solvent
box I sent before in a long simulation.
Good luck.
Regards,
Alan
On Wed, Dec 2, 2009 at 11:10, Alan <alanwilter at gmail.com> wrote:
> Dear Servaas,
>
> In tleap did you really did:
>
> TLEAP
> tleap -f leaprc.ff99SB
> ad = sequence { DA5 DA DA3 }
> saveamberparm da da_amber.top da_amber.crd
>
>
> If so, it's wrong, it should be:
>
> saveamberparm ad da_amber.top da_amber.crd
> ^^^
> and not 'da'
>
> Besides, I tried to reproduce what you did using what I think would be
> fine and... everything went fine! Energies after minimisation in
> single and double were almost identical and trajectories diverted
> normally.
>
> Please check what I did.
>
> # begin commands
>
> cat << EOF >| em.mdp
> define = -DFLEXIBLE
> integrator = cg ; steep
> nsteps = 200
> constraints = none
> emtol = 1000.0
> nstcgsteep = 10 ; do a steep every 10 steps of cg
> emstep = 0.01 ; used with steep
> nstcomm = 1
> coulombtype = PME
> ns_type = grid
> rlist = 1.0
> rcoulomb = 1.0
> rvdw = 1.4
> Tcoupl = no
> Pcoupl = no
> gen_vel = no
> nstxout = 0 ; write coords every # step
> optimize_fft = yes
> EOF
>
>
> cat << EOF >| md.mdp
> integrator = md
> nsteps = 1000
> dt = 0.002
> constraints = all-bonds
> nstcomm = 1
> ns_type = grid
> rlist = 1.2
> rcoulomb = 1.1
> rvdw = 1.0
> vdwtype = shift
> rvdw-switch = 0.9
> coulombtype = PME-Switch
> Tcoupl = v-rescale
> tau_t = 0.1 0.1
> tc-grps = protein non-protein
> ref_t = 300 300
> Pcoupl = parrinello-rahman
> Pcoupltype = isotropic
> tau_p = 0.5
> compressibility = 4.5e-5
> ref_p = 1.0
> gen_vel = yes
> nstxout = 2 ; write coords every # step
> lincs-iter = 2
> DispCorr = EnerPres
> optimize_fft = yes
> EOF
>
>
> cat << EOF >| leap.in
> verbosity 1
> source leaprc.ff99SB
> ad = sequence { DA5 DA DA3 }
> solvatebox ad TIP3PBOX 10.0
> addions ad Na+ 5
> addions ad Cl- 3
> saveamberparm ad da_amber.top da_amber.crd
> savepdb ad DA.pdb
> quit
> EOF
> tleap -f leap.in >| leap.out
>
> acpypi -x da_amber.crd -p da_amber.top -d
>
> #Single precision
> grompp -f em.mdp -c da_amber_GMX.gro -p da_amber_GMX.top -o em.tpr
> mdrun -v -deffnm em
>
> #Polak-Ribiere Conjugate Gradients converged to Fmax < 1000 in 22 steps
> #Potential Energy = -6.2280516e+04
> #Maximum force = 7.5868494e+02 on atom 98
> #Norm of force = 1.0447179e+02
>
> grompp -f md.mdp -c em.gro -p da_amber_GMX.top -o md.tpr
> mdrun -v -deffnm md
>
> #Double precision
> grompp_d -f em.mdp -c da_amber_GMX.gro -p da_amber_GMX.top -o em.tpr
> mdrun_d -v -deffnm em
>
> #Polak-Ribiere Conjugate Gradients converged to Fmax < 1000 in 22 steps
> #Potential Energy = -6.22813514022256e+04
> #Maximum force = 7.58238100790309e+02 on atom 98
> #Norm of force = 1.04358667410458e+02
>
> grompp_d -f md.mdp -c em.gro -p da_amber_GMX.top -o md.tpr
> mdrun_d -v -deffnm md
>
> # end commands
>
> Regards,
>
> Alan
>
> On Tue, Dec 1, 2009 at 13:56, Alan <alanwilter at gmail.com> wrote:
> > Dear Servaas,
> >
> > I've been following your thread. I am the developer of acpypi and
> > thanks for giving a try.
> >
> > So, as you may already know, you are trying acpypi as amb2gmx.pl so
> > far, but you also seemed to have read acpypi wikis and realise that
> > acpypi can help you to generate the whole topology for a ligand.
> >
> > However, AFAIU you have only regular NA and not modified ones neither
> > ligands, right? But then why are you using RED?
> >
> > I understand your approach about using tleap to create your whole
> > system and then convert it to GMX. It should work at first but it is
> > clearly not as you reported.
> >
> > So, here goes some of my recommendations:
> >
> > 1) GMX is vacuum is unrealistic and prone for errors. There's no GB
> > implementation as far as I know.
> >
> > 2) Have you try to use pdb2gmx to generate your files from your pdb
> > directly to GMX?
> >
> > 3) When you say that gmx double precision works, is your system in
> > vacuum or with solvent?
> >
> > 4) if using tleap, create your system with solvent and ions and then
> > use acpypi to convert to gmx.
> >
> > The use of amb2gmx or acpypi is to give you a system to be run
> > immediately in gromacs doing just a grompp and mdrun. Using editconf
> > will change the parameters of your box and it may have serious
> > implications besides that in amber we don't have dodecahedron, so if
> > doing what you're doing then you're not replicating the conditions you
> > have in amber with those in gmx (although it puzzles me that gmx
> > double works, with the commands you gave in gmx?).
> >
> > I would ask you to give more details and even a detailed step by step
> > of commands of what you're doing including tleap.
> >
> > Regards,
> > Alan
> >
> >
> >
> > On Tue, Dec 1, 2009 at 11:00, <gmx-users-request at gromacs.org> wrote:
> >>
> >> Thanks for your suggestion, I tried without success and I also tried
> >> shake. But this is also rather fighting the symptoms than the cause...
> >> And amber simulations in vacuum do work fine... My personal guess was
> >> that another parameter in my mdp file was not compatible with the amber
> >> force field, but I could not figure out which one. I also tried
> >> different settings, e.g. the one I found on the acpypi wiki.
> >>
> >
> > --
> > Alan Wilter Sousa da Silva, D.Sc.
> > PDBe group, PiMS project http://www.pims-lims.org/
> > EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
> > +44 (0)1223 492 583 (office)
> >
>
>
>
> --
> Alan Wilter Sousa da Silva, D.Sc.
> PDBe group, PiMS project http://www.pims-lims.org/
> EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
> +44 (0)1223 492 583 (office)
>
--
Alan Wilter Sousa da Silva, D.Sc.
PDBe group, PiMS project http://www.pims-lims.org/
EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
+44 (0)1223 492 583 (office)
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