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Dear Gromacs Users
I am trying to simulate a protein with 200 SDS molecules.
After inserting 200 molecules inside the box with the protein at the
center (size of the cubic box is 324 nm3), few of the SDS molecules are
outside the box from each side of the box.
I have used the following command t
On 1/18/18 7:02 AM, za...@tezu.ernet.in wrote:
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On 1/18/18 7:28 AM, za...@tezu.ernet.in wrote:
Dear Gromacs Users
I am trying to simulate a protein with 200 SDS molecules.
After inserting 200 molecules inside the box with the protein at the
center (size of the cubic box is 324 nm3), few of the SDS molecules are
outside the box from each si
On 1/18/18 12:38 AM, kordza...@aut.ac.ir wrote:
Hi all
when we use "gmx energy" what is the difference between LJ-(SR),
LJ-14, Coulomb-14, Coulomb(SR)?
those mentioned energies, give us energy interaction of total system. right?
Not necessarily, because there may be long-range terms from P
On 1/18/18 12:37 AM, Moradzadeh, Alireza wrote:
Hi!
I am trying to do umbrella sampling between two 2D-sheets. I did it according
bevan lab tutorial the problem I encounter is that after pulling steps. I
perform umbrella sampling with rate of 0.0 however, two sheets get back
together and i
On 1/18/18 12:24 AM, Mohsen Ramezanpour wrote:
Dear Gromacs users,
I am interested in calculation of tilt angle for the POPC headgroup (angle
distribution between the P-N vector and Z axis).
I am not sure if my approach is correct as my angle distribution does not
seem reasonable.
Given a bil
On 1/17/18 6:11 PM, Mark Abraham wrote:
Hi,
If you poke your finger into something, it isn't going to stay flat. :-)
And to add on to this, in the CHARMM parametrization protocol, the first
step is always an in vacuo geometry optimization (QM vs. MM comparison)
to make sure the topology is
On 1/17/18 12:06 PM, Rose wrote:
Thank you so much,I've got it now.
we know that for example 2 molecule can not stick to each other they just close
enough till repulse each other.
Now, imagine pulling, if I can not see "really broken" structures in classicalMD , so
what would be my criterio
I know what you mean, but I didn't see any other molecules getting too
close to the ring :)
On Wed, Jan 17, 2018 at 6:11 PM, Mark Abraham
wrote:
> Hi,
>
> If you poke your finger into something, it isn't going to stay flat. :-)
>
> Mark
>
> On Wed, Jan 17, 2018 at 9:44 PM MD wrote:
>
> > Hi Mar
On Thu, Jan 18, 2018 at 7:43 AM, Justin Lemkul wrote:
>
>
> On 1/17/18 6:11 PM, Mark Abraham wrote:
>
>> Hi,
>>
>> If you poke your finger into something, it isn't going to stay flat. :-)
>>
>
> And to add on to this, in the CHARMM parametrization protocol, the first
> step is always an in vacuo
On 1/18/18 7:51 AM, MD wrote:
On Thu, Jan 18, 2018 at 7:43 AM, Justin Lemkul wrote:
On 1/17/18 6:11 PM, Mark Abraham wrote:
Hi,
If you poke your finger into something, it isn't going to stay flat. :-)
And to add on to this, in the CHARMM parametrization protocol, the first
step is alwa
Dear GROMACS community,
evaluating the diffusivity of as single dodecyl sulfate (DS) anion, I
use a small trajectory chunk "md_1.trr" 5 ps (500 frames) long for
testing purposes. The .trr has been stripped of any atoms except the 42
ones forming the DS chain (12H25SO4). What is more, I pre
Coolbeans! Thank you Justin :)
Ming
On Jan 18, 2018 7:54 AM, "Justin Lemkul" wrote:
>
>
> On 1/18/18 7:51 AM, MD wrote:
>
>> On Thu, Jan 18, 2018 at 7:43 AM, Justin Lemkul wrote:
>>
>>
>>> On 1/17/18 6:11 PM, Mark Abraham wrote:
>>>
>>> Hi,
If you poke your finger into something, it i
I have a question related to charmm. Does charmm have a name/structure
chart for all the parametrized molecules? I want to borrow some parameters
info from those molecules but often I can't quickly figure out what they
are.
Ming
On Jan 18, 2018 8:18 AM, "MD" wrote:
> Coolbeans! Thank you Justin
On 1/18/18 8:46 AM, MD wrote:
I have a question related to charmm. Does charmm have a name/structure
chart for all the parametrized molecules? I want to borrow some parameters
info from those molecules but often I can't quickly figure out what they
are.
Not in one places, but every CHARMM RTF
Besides the fact that there cannot be molecules outside a periodic box, are
you sure that you want such a high SDS concentration? You are nearly 15
times over the cmc, in the real world you would most likely end up with a
hydrated SDS crystals (Mol. Cryst. Liq. Cryst., Vol. 549:pp. 160–165, 2011)
On Thu, Jan 18, 2018 at 8:48 AM, Justin Lemkul wrote:
>
>
> On 1/18/18 8:46 AM, MD wrote:
>
>> I have a question related to charmm. Does charmm have a name/structure
>> chart for all the parametrized molecules? I want to borrow some parameters
>> info from those molecules but often I can't quickl
On 1/18/18 9:04 AM, MD wrote:
On Thu, Jan 18, 2018 at 8:48 AM, Justin Lemkul wrote:
On 1/18/18 8:46 AM, MD wrote:
I have a question related to charmm. Does charmm have a name/structure
chart for all the parametrized molecules? I want to borrow some parameters
info from those molecules but
whoops, Thank you :))
On Thu, Jan 18, 2018 at 9:05 AM, Justin Lemkul wrote:
>
>
> On 1/18/18 9:04 AM, MD wrote:
>
>> On Thu, Jan 18, 2018 at 8:48 AM, Justin Lemkul wrote:
>>
>>
>>> On 1/18/18 8:46 AM, MD wrote:
>>>
>>> I have a question related to charmm. Does charmm have a name/structure
Hello Dr.Lemkul
Thank you very much for your answer
I try to do it.
Regards
Azadeh
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Hi
I am new to gromacs (using v. 2016.4) and need to check the following steps for
my system.
01. I have prepared the system with Amber 14, minimized, heated to 300K,
equilibrated 02. Then I used Acpype to convert the amber top and equilibrated
rst file to gromacs .top and .gro files03. Changing
Hi Justin,
On Thu, Jan 18, 2018 at 5:42 AM, Justin Lemkul wrote:
>
>
> On 1/18/18 12:24 AM, Mohsen Ramezanpour wrote:
>
>> Dear Gromacs users,
>>
>> I am interested in calculation of tilt angle for the POPC headgroup (angle
>> distribution between the P-N vector and Z axis).
>> I am not sure if
And, I used Charmm36 FF for simulations in Gromacs v. 2016.3
Cheers,
Mohsen
On Thu, Jan 18, 2018 at 11:28 AM, Mohsen Ramezanpour <
ramezanpour.moh...@gmail.com> wrote:
> Hi Justin,
>
> On Thu, Jan 18, 2018 at 5:42 AM, Justin Lemkul wrote:
>
>>
>>
>> On 1/18/18 12:24 AM, Mohsen Ramezanpour wrote
Looking at index file made in the above mentioned way, as way as the
following way:
gmx make_ndx -f SYSTEM.gro -o index.ndx
keep 0
r 1-100
name 1 upperleaflet
1 & a P N
name 2 vector
q
gave the same results.
Interestingly, even if I make the index file like:
gmx make_ndx -f SYSTEM.gro -o index.
I did more tests and here are the conclusions for the pick mentioned
earlier.
The pick appears when the -binw gets smaller and smaller.
For the default value of gangle (which is 1), one cannot detect such a pick
and you will get a normal distribution.
Even for a -binw of 0.1 everything looks fine.
Hi gromacs users:
I just wrote this to share that I write a conda package let you to install
gromacs 4.5.5 on 64-bit linux system:
https://anaconda.org/hsiaoyi0504/gromacs
The objective of this package is to let people build applications based on
gromacs more easier, such as prediction system bas
Why 4.5.5?
On Thu, Jan 18, 2018 at 11:26 PM, 蕭毅 wrote:
> Hi gromacs users:
>
> I just wrote this to share that I write a conda package let you to install
> gromacs 4.5.5 on 64-bit linux system:
> https://anaconda.org/hsiaoyi0504/gromacs
>
> The objective of this package is to let people build ap
Dear Justin
Thanks for your explanation . Yes I am agree that it will depend on the k
value and path direction.
Let suppose we map the experimental spring constant and rate then it will
be some how relevant for my study.
My another query is the same from umbrella sampling of puling code.
If I res
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