Re: [gmx-users] Normal-mode analysis in Gromacs

[Kevin C Chan]

Thank you David for your reply. In fact, I have already been using the
double precision version of Gromacs.

I will greatly appreciate it if other questions could also be covered.

Thanks,
Kevin


Den 2018-03-08 kl. 00:53, skrev Kevin C Chan:
> >* Dear Users, *> >* I have encountered several questions when I try to
> perform NMA on a protein *>* structure from an equilibrated MD
> simulation. I were basically referred to *>* the gromacs manual ( *>*
> http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis
> ) and
> some *>* threads in the mailing list. *> >* First, Gromacs (and in some
> literature) suggest to have L-BFGS energy *>* minimization (sometimes
> after steep and cg calculations) of the structure *>* before NMA and
> L-BFGS generally requires shifted/switched interactions. *>* However, for
> vdW the option should have been changed by introducing the *>*
> vdw-modifier and l-bfgs seems to still recognize it as cutoff. *> >*
> Second, for electrostatics, the option has been improved by *>*
> Reaction-field-zero but is it still suitable for NMA calculation? *> >*
> Third, I have achieved a maximum force of 9.78750e-01 using cg and still *
> >* got the warning: "The force is probably not small enough to ensure
> that you *>* are at a minimum." Usually how stable do we have to achieve
> in order to *>* avoid the warning? *> >* Thanks in advance for any
> experience shared. *You need to compile gromacs in double precision to
> get to low forces. > >* Kevin *>* OSU Pharmacy *> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
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Re: [gmx-users] Normal-mode analysis in Gromacs

[David van der Spoel]

Den 2018-03-08 kl. 00:53, skrev Kevin C Chan:

Dear Users,

I have encountered several questions when I try to perform NMA on a protein
structure from an equilibrated MD simulation. I were basically referred to
the gromacs manual (
http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis) and some
threads in the mailing list.

First, Gromacs (and in some literature) suggest to have L-BFGS energy
minimization (sometimes after steep and cg calculations) of the structure
before NMA and L-BFGS generally requires shifted/switched interactions.
However, for vdW the option should have been changed by introducing the
vdw-modifier and l-bfgs seems to still recognize it as cutoff.

Second, for electrostatics, the option has been improved by
Reaction-field-zero but is it still suitable for NMA calculation?

Third, I have achieved a maximum force of 9.78750e-01 using cg and still
got the warning: "The force is probably not small enough to ensure that you
are at a minimum." Usually how stable do we have to achieve in order to
avoid the warning?

Thanks in advance for any experience shared.

You need to compile gromacs in double precision to get to low forces.



Kevin
OSU Pharmacy




--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
--
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Re: [gmx-users] Normal Mode Analysis with Gromacs 4.6

[Mark Abraham]

Why are you using PME-switch? Without explicitly choosing a switch?

Mark


On Thu, Dec 12, 2013 at 6:45 PM, mcfc1301 mcfc1...@gmail.com wrote:

 Hello Everyone，

 I'm confused about Normal Mode Analysis of Gromacs. I have googled a lot
 but
 find little useful.
 My Gromacs was installed in a Linux cluster.

 Follows is my steps to do normal mode analysis:

 • pdb2gmx -ignh -ff  forcefield  -f protein.pdb -o mut.gro -p topol.top
 • editconf -f mut.gro -o box.gro -d 1.5
 • grompp -f em.mdp -c box.gro -p topol.top -o em.tpr
 • mdrun -s em.tpr -deffnm em -c em.g96 -v
 • grompp -f nm.mdp -c em.g96 -o nm.tpr
   ---WARNING 1 [file nm.mdp]:
 The switching range for PME-Switch should be 5% or
 less, energy
 conservation will be good anyhow, since ewald_rtol
 =
 1e-05

 I have taken advises from the forum that I should not genbox and should use
 cg instead steep for em in order to do Normal Mode Analysis, but now I am
 facing problem of PME-Switch.

 Does anyone have any experience on this?

 Thanks in advance.

 Kevin


 ==Attached is em.mdp and nm.mdp=
 em.mdp

 define  =  -DFLEXIBLE
 constraints =  none
 integrator  =  cg
 dt  =  0.002; ps !
 nsteps  =  400
 nstlist =  10
 ns_type =  grid
 rlist   =  1.0
 coulombtype =  PME
 rcoulomb=  1.0
 vdwtype =  cut-off
 rvdw=  1.4
 optimize_fft=  yes
 emtol   =  1000
 emstep  =  0.01

 ---
 nm.mdp
 constraints =  none
 integrator  =  nm
 dt  =  0.002; ps !
 nsteps  =  400
 nstlist =  10
 ns_type =  grid
 rlist   =  1.2
 coulombtype =  PME-Switch
 rcoulomb=  1.0
 vdwtype =  Cut-off
 rvdw=  1.4

 --
 View this message in context:
 http://gromacs.5086.x6.nabble.com/Normal-Mode-Analysis-with-Gromacs-4-6-tp5013240p5013276.html
 Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Re: [gmx-users] Normal Mode Analysis with Gromacs 4.6

[mcfc1301]

Hello Everyone， 

I'm confused about Normal Mode Analysis of Gromacs. I have googled a lot but
find little useful. 
My Gromacs was installed in a Linux cluster. 

Follows is my steps to do normal mode analysis: 

• pdb2gmx -ignh -ff  forcefield  -f protein.pdb -o mut.gro -p topol.top 
• editconf -f mut.gro -o box.gro -d 1.5 
• grompp -f em.mdp -c box.gro -p topol.top -o em.tpr 
• mdrun -s em.tpr -deffnm em -c em.g96 -v 
• grompp -f nm.mdp -c em.g96 -o nm.tpr 
  ---WARNING 1 [file nm.mdp]: 
The switching range for PME-Switch should be 5% or
less, energy 
conservation will be good anyhow, since ewald_rtol =
1e-05

I have taken advises from the forum that I should not genbox and should use
cg instead steep for em in order to do Normal Mode Analysis, but now I am
facing problem of PME-Switch. 

Does anyone have any experience on this? 
  
Thanks in advance. 

Kevin 


==Attached is em.mdp and nm.mdp= 
em.mdp 

define  =  -DFLEXIBLE 
constraints =  none 
integrator  =  cg 
dt  =  0.002; ps ! 
nsteps  =  400 
nstlist =  10 
ns_type =  grid 
rlist   =  1.0 
coulombtype =  PME 
rcoulomb=  1.0 
vdwtype =  cut-off 
rvdw=  1.4 
optimize_fft=  yes 
emtol   =  1000 
emstep  =  0.01 

--- 
nm.mdp
constraints =  none 
integrator  =  nm 
dt  =  0.002; ps ! 
nsteps  =  400 
nstlist =  10 
ns_type =  grid 
rlist   =  1.2 
coulombtype =  PME-Switch 
rcoulomb=  1.0 
vdwtype =  Cut-off 
rvdw=  1.4

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http://gromacs.5086.x6.nabble.com/Normal-Mode-Analysis-with-Gromacs-4-6-tp5013240p5013276.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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