[gmx-users] NPT equilibration in KALP15-DPPC
shima_arasteh2001 at yahoo.com
Mon Aug 27 16:27:18 CEST 2012
I removed the water molecules located between carbon chains of lipids. Then updated the top file. Should the atom numbers of "nvt.gro" be changed? This is not clear for me.
I updated the nvt.gro,
grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -n index.ndx -o npt.tpr
but it gives me an error about one of the atoms in index file!
Or I am supposed to run mdrun without a new grompp?
----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Monday, August 27, 2012 2:33 PM
Subject: Re: [gmx-users] NPT equilibration in KALP15-DPPC
On 8/27/12 2:30 AM, Shima Arasteh wrote:
> After the NPT mdrun, I visulized the npt.gro.
> I need to know if this npt.gro is the final result of equilibration?
From mdrun -h:
"The structure file (-c) contains the coordinates and velocities of the last step."
> I see 2,3 water molecules between the lipid chains. Should I remove them? Can I remove them? Or it's not the step that I can make such a decision?
You can remove them. Update the topology and the number of atoms at the top of
the .gro file, then re-equilibrate.
> Thanks in advance.
> ----- Original Message -----
> From: Justin Lemkul <jalemkul at vt.edu>
> To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Sunday, August 26, 2012 5:29 PM
> Subject: Re: [gmx-users] NPT equilibration in KALP15-DPPC
> On 8/26/12 8:54 AM, Shima Arasteh wrote:
>> For NPT equilibration of KALP15 in DPPC following the Justin's tutorial, when
>> I run the grompp command, I get 4 notes. Is it necessary to pay attention to
>> the notes ? Are they notable?
> Notes are generally notable, yes ;) Never ignore anything grompp tells you,
> that's my rule of thumb. Some messages are less critical than others. The ones
> shown here are quite important.
> These warnings cannot possibly be produced by the .mdp file in the tutorial, and
> they suggest that you are not doing NPT under any sort of stable conditions.
> You're using plain cutoffs, no constraints, and attempting to produce NVE, which
> will surely fail.
>> NOTE 1 [file npt.mdp]: You are using a cut-off for VdW interactions with NVE,
>> for good energy conservation use vdwtype = Shift (possibly with DispCorr)
>> NOTE 2 [file npt.mdp]: You are using a cut-off for electrostatics with NVE,
>> for good energy conservation use coulombtype = PME-Switch or
>> Generated 837 of the 2346 non-bonded parameter combinations Excluding 3
>> bonded neighbours molecule type 'Protein' Excluding 3 bonded neighbours
>> molecule type 'DPPC' Excluding 2 bonded neighbours molecule type 'SOL'
>> Excluding 1 bonded neighbours molecule type 'CL'
>> NOTE 3 [file topol.top, line 929]: The bond in molecule-type Protein between
>> atoms 4 N and 5 H has an estimated oscillational period of 1.0e-02 ps, which
>> is less than 10 times the time step of 1.0e-03 ps. Maybe you forgot to change
>> the constraints mdp option.
>> Number of degrees of freedom in T-Coupling group rest is 33897.00
>> NOTE 4 [file npt.mdp]: You are using a plain Coulomb cut-off, which might
>> produce artifacts. You might want to consider using PME electrostatics.
>> Reading Coordinates, Velocities and Box size from old trajectory Will read
>> whole trajectory Last frame -1 time 100.000 Using frame at t = 100
>> ps Starting time for run is 0 ps Largest charge group radii for Van der
>> Waals: 0.239, 0.234 nm Largest charge group radii for Coulomb: 0.239,
>> 0.234 nm This run will generate roughly 1 Mb of data
>> There were 4 notes
>> Thanks for your suggestions in advance.
>> Sincerely, Shima
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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