Dear Gromacs users,
I was trying to extract electrostatics and van der Waals interactions for
specific lipid molecules in the system I simulated. I assume you can get
the coulomb and LJ values from energy. But why is there more than one
options to select for both Coulomb and LJ from the list.?
Dear all,
I would like to calculate surface tension/pressure of my monolayer
simulation. I have two monolayers of lipid each side of a water box. So
four interfaces; vaccum/lipid, lipid/water, water/lipid and lipid/vaccum. I
used NVT simulation. Is there a way to calculate surface
rmation as reference).
>
> Hope this helps.
>
> Regards,
>
> On 15 March 2017 at 21:28, Merril Mathew <mmath...@mail.bbk.ac.uk> wrote:
>
> > Dear all,
> >
> > I want to calculate how much my lipid heads emerse into water in a
> > monolayer afte
Dear all,
I want to calculate how much my lipid heads emerse into water in a
monolayer after simulation. I want to compare the movement of the lipids
from the intial conformation to the final conformation. Is there a way to
calculate such movement using GROMACS?
Merril.
--
Gromacs Users mailing
Is the modified parameter file for POPG from your work available online?
Merril.
On 10 Mar 2017 7:05 a.m., "Merril Mathew" <mmath...@mail.bbk.ac.uk> wrote:
> many thanks Tom.
>
> On 10 Mar 2017 1:35 a.m., "Thomas Piggot" <t.pig...@soton.ac.uk> wrote:
&g
suppl/10.1021/jp207013v) but I cannot remember
> off the top of my head the impact they made.
>
> Up to you to decide with the density calculation.
>
> Cheers
>
> Tom
>
> On 10/03/17 00:45, Merril Mathew wrote:
>
>> The POPG .itp and .pdb files were obtained from,
>&g
thanks Justin.
On 8 Mar 2017 13:09, "Justin Lemkul" <jalem...@vt.edu> wrote:
>
>
> On 3/8/17 8:06 AM, Merril Mathew wrote:
>
>> I dont know what I am doing wrong. There is no Box-X or Box-Y when
>
I also used the same POPG .itp and .pdb files to edit and create an
oxidised version of the molecule with aldehyde group replacing the double
bond. Is there a problem associated with parameters from A Kukol for POPG?
On 10 Mar 2017 00:45, "Merril Mathew" <mmath...@mail.bbk
gmx traj). For the thickness, you can probably use gmx density to
> create a density profile of your monolayer and work out a thickness from
> that.
>
> Tom
>
> On 10/03/17 00:24, Merril Mathew wrote:
>
>> I am using Berger lipid from Dr.Tielemens website and modified the
pid force field per say but there are PG
> compatible lipids (Kukol, different Berger variants, GROMOS-CKP). Which
> lipid parameters are you using? Lots of them don't work well at all.
>
> Cheers
>
> Tom
>
> On 10/03/17 00:10, Merril Mathew wrote:
>
>> Hi,
>>
>&g
orrectly (even when using the -unsat option).
>
> Out of interest, is this a united-atom or all-atom force field you are
> using?
>
> Cheers
>
> Tom
>
> On 09/03/17 23:51, Merril Mathew wrote:
>
>> Hi,
>>
>> I followed turorials found on Bevanlab by Justin.
Hi,
I followed turorials found on Bevanlab by Justin. I successfully calculated
order parameter for DPPC molecules in my system following the tutorial. My
question is whether the same calculation can be applied for a POPG molecule
with a double bond in the acyl chain.? can I group all the carbon
are the coupling groups I used.
Merril.
On 8 March 2017 at 12:56, Justin Lemkul <jalem...@vt.edu> wrote:
>
>
> On 3/8/17 7:52 AM, Merril Mathew wrote:
>
>> I am not sure what command to use to extract the X and Y box vector. is it
>> gmx energy -f md.edr -o .xvg?
&g
I am not sure what command to use to extract the X and Y box vector. is it
gmx energy -f md.edr -o .xvg?
and which option should I choose from the list?
On 8 Mar 2017 12:44 p.m., "Justin Lemkul" <jalem...@vt.edu> wrote:
>
>
> On 3/8/17 7:28 AM, Merril Mathew wrote:
&g
I have a system that I simulated using GROMACS v5.0.4. The system is two
monolayers of lipid on each side of a box of water. I would like to know if
there is a way to calculate area per lipid and monolayer thickness. I read
that one can use gmx energy to find box size in X and Y and you divide the
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