[gmx-users] NPT equilibration in KALP15-DPPC

[Shima Arasteh]

OK, but what about the index file after removing water molecules, updating .gro and .top file? Should it be generated again?




Sincerely,
Shima


________________________________
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: Monday, August 27, 2012 7:07 PM
Subject: Re: [gmx-users] NPT equilibration in KALP15-DPPC



On 8/27/12 10:27 AM, Shima Arasteh wrote:
> 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,
> Running:
> 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?
>

No.  There are three potential ways to fix this problem (all basically the 
same), depending on when the water molecules entered the bilayer.

1. If water molecules are in the bilayer after system construction, remove them 
even before running EM, modifying the topology and whatever coordinate file you 
have for your non-minimized structure.

2. If the water molecules leak in during NVT, modify nvt.gro and the topology 
and proceed to NPT.

3. Likewise, if water entered during NPT, modify npt.gro and the topology, and 
proceed with more NPT equilibration.

Any modification to the coordinate file requires that the number of atoms in the 
file be updated on the second line.  Thus if you delete two water molecules, the 
number should be accordingly decreased by 6.

-Justin

>
>
>
> Sincerely,
> Shima
>
>
> ----- Original Message -----
> From: Justin Lemkul <jalemkul at vt.edu>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc:
> 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:
>>
>>
>>     Hi,
>>
>> 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.
>
> -Justin
>
>> Thanks in advance.
>>
>> Sincerely,
>> Shima
>>
>>
>> ----- 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>
>> Cc:
>> 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:
>>>
>>>
>>> Hi,
>>>
>>> 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.
>>
>> -Justin
>>
>>>
>>> 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
>>> Reaction-Field-zero
>>>
>>> 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.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================