estions. Do
you mean that the steep integrator is not good to do energy minimization
for this type of simulation?
Would you please help me to fix these problems?
Regards,
Mahsa
On Sat, Feb 24, 2018 at 8:54 AM, Mark Abraham
wrote:
> Hi,
>
> Even if there are minima on the surface that have negati
ions,
should I use pbc or not and which of the mdp files in my first post is
correct?
Regards,
Mahsa
On Sun, Feb 25, 2018 at 3:39 PM, Justin Lemkul wrote:
>
>
> On 2/25/18 9:26 AM, Mahsa wrote:
>
>> Dear Mark,
>>
>> Thank you for your reply. However, this is not cl
Hi,
Thanks for your help, Justin!
Regards,
Mahsa
On Sun, Feb 25, 2018 at 5:53 PM, Justin Lemkul wrote:
>
>
> On 2/25/18 10:15 AM, Mahsa wrote:
>
>> Dear Justin,
>>
>> Thank you for your reply!
>>
>> In general, is it a good approach to first use ste
specify
the O of the side chain in the index file to tell it apart from the other O
atoms?
Besides there are around 500 of this atom in the system so changing
something manually is not a good option either.
Best regards,
Mahsa
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with this approach I get both O types
in a group while I should have them separately. Could you help me with this
problem? I don't know how to specify this one for the RDF calculations.
Best regards,
Mahsa
On Sat, Aug 11, 2018 at 12:22 PM, Mark Abraham
wrote:
> Hi,
>
> Making a
Dear Mark,
Could you please comment on my previous question? I would really appreciate
it.
Best regards,
Mahsa
On Sat, Aug 11, 2018 at 12:52 PM, Mahsa wrote:
> Hi Mark,
>
> Thank you for your reply!
>
> I tried gmx make_ndx -f topol.tpr -o index.ndx before and then selected
Thank you for your reply!
Best regards,
Mahsa
On Mon, Aug 13, 2018 at 2:47 PM, Mark Abraham
wrote:
> Hi,
>
> You need a composite selection, eg of an atomtype and residue type or
> molecule type. Make a selection of the atomtype and another of whatever
> seems suitable, a
and then the polymer group.
The generated file numcont.xvg which is more related to what I am looking
for, gives number of contacts vs time. How can I get the information which
I look for from this analysis?
Best regards,
Mahsa
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the same approach to get the distribution of
coordination number for the first coordination shell of ions and special
atoms of the polymers?
Best regards,
Mahsa
On Sun, Feb 17, 2019 at 1:39 PM Justin Lemkul wrote:
>
>
> On 2/17/19 7:21 AM, Mahsa wrote:
> > Dear Gromacs users,
&g
Hi Justin,
Could you please comment on my questions in the previous post?
Best regards,
Mahsa
-- Forwarded message -
From: Mahsa
Date: Sun, Feb 17, 2019 at 2:36 PM
Subject: Re: [gmx-users] Probability of number of atomic contacts
To:
Thank you very much, Justin!
I tried
Thank you very much for your comments!
How would it be possible to get probability vs. number of contacts or
probability vs coordination number averaged across the simulations? Can it
be done directly with Gromacs tools or I need some scripts for that?
Best regards,
Mahsa
On Thu, Feb 28, 2019
of particles within a distance
r.
Best regards,
Mahsa
On Fri, Mar 1, 2019 at 5:04 AM Mark Abraham
wrote:
> Hi,
>
> Which GROMACS tools documentation did you check to see whether it can be
> done already? :-) I don't know the answer, but that's where to start!
>
> Ma
shell coordination number for specific groups during the simulation time.
Is this correct? because the coordination number from gmx rdf gives the
average number of particles within a distance r.
Best regards,
Mahsa
On Fri, Mar 1, 2019 at 12:11 PM Mahsa wrote:
> Hi Mark,
>
> Thank you
lar question:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2011-June/062181.html
Does this means that I should consider the second column of y values in the
contac_ac.xvg file instead of the first one?
Best regards,
Mahsa
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the reported sigma value in the output of
dsp.xvg should be multiplied by 10^-12 manually.
It took sometime for me to understand what is going on in the output :-)
Please correct me if I'm wrong or missed something in these comments.
Best regards,
Mahsa
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Gromacs Users mailing list
* P
Hi again,
Something went wrong with the equations which I tried to show.
So for the first equation please see eq. 9 in this paper:
https://aip.scitation.org/doi/10.1063/1.2868752
and the second missing formula is:
1 / 6*V*K_B*T = 7.20677e-12
Best regards,
Mahsa
On Wed, Jun 12, 2019 at 3:12
Hi Mark,
Thank you for your reply!
I opened a new issue with this information in the link you mentioned.
Best regards,
Mahsa
On Wed, Jun 12, 2019 at 10:26 PM Mark Abraham
wrote:
> Hi Mahsa,
>
> Thanks very much for your feedback. Those look like useful changes to the
> code. Ca
Hi,
I think the selection keywords in the manual are helpful:
http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html#selection-examples
/Mahsa
On Tue, Feb 20, 2018 at 5:53 PM, Dilip H N
wrote:
> Hello,
> How to get RDF within a certain distance..??
>
> Say for
y wrong in the simulation which I'm not aware of?
Regards,
Mahsa
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conformation with different angles and dihedrals than in the monomer.
In general, how can I use the topology file of a monomer for the longer
chain of a polymer ?
Could you please advise me?
Best regards,
Mahsa
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conformation with different angles and dihedrals than in the monomer.
In general, how can I use the topology file of a monomer for the longer
chain of a polymer?
Could you please advise me?
Best regards,
Mahsa
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generate the .itp file
for a longer chain of polymer (like 25 units)?
Your kind help on this is very much appreciated.
Best regards,
Mahsa
On Sun, Aug 6, 2017 at 2:34 AM, Justin Lemkul wrote:
>
>
> On 8/5/17 8:12 AM, Mahsa E wrote:
>
>> Dear gmx-users,
>>
>> I am tryi
Thank you for your help!
Best regards,
Mahsa
On Mon, Aug 7, 2017 at 4:35 PM, Justin Lemkul wrote:
>
>
> On 8/6/17 8:35 PM, Mahsa E wrote:
>
>> Hello Justin,
>>
>> Thank you so much for your reply!
>>
>> I followed what you suggested. Please correct me
gthening
lincs_warnangle = 30; [degrees] maximum angle that a
bond can rotate before LINCS will complain
Best regards,
Mahsa
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* Can'
another
polymer, I didn't see this difference in the systems after the production
run, so I'm wondering if this is related to the stability of the system?
Best regards,
Mahsa
On Mon, Sep 18, 2017 at 12:10 AM, Dallas Warren
wrote:
> Because that is how the system changed within t
Thank you for you quick reply, Justin and Dallas! Very good point!
Best regards,
Mahsa
On Mon, Sep 18, 2017 at 1:00 AM, Justin Lemkul wrote:
>
>
> On 9/17/17 6:57 PM, Mahsa E wrote:
>
>> Could you please see the link below for the input and output simulation
&
Thank you very much for the links!
Best regards,
Mahsa
On Mon, Sep 18, 2017 at 1:30 AM, Dallas Warren
wrote:
> These two images will help you see what is going on:
>
> https://twitter.com/dr_dbw/status/909559339366572032 - shows a
> molecule that appears to be outside the bo
Dear gromacs users,
I am using following pull code in md simulation
for pulling a ligand across the plasma membrane model.
Ligand passes through the membrane,but along simulation,
the size of axis z increases.
My size box is 8.52807 8.52807 14.0.
And the pull distance is less than one-half
.
Regards
Mahsa.
Does it do that without using the pull code, i.e. just performing NPT
simulation? What is physically happening? Sounds like the bilayer is
unstable. What forcefield is this?
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences
the membrane .
Thank you .
Regards
Mahsa
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Dear gromacs users,
Sorry for repeating my question.
I didn't receive any email so I couldn't reply and I missed
them.
I am using following pull code in md simulation
for pulling a ligand across the plasma membrane model.
Ligand passes through the membrane,but along simulation,
the size of axi
Dear gromacs users,
Sorry for repeating my question.
I didn't receive any email so I couldn't reply and I missed
them.
I am using following pull code in md simulation
for pulling a ligand across the plasma membrane model.
Ligand passes through the membrane,but along simulation,
the size of axis
Dear gromacs users,
I am using following pull code in md simulation
for pulling a ligand across the plasma membrane model.
My size box is 8.52807 8.52807 14.0.
And the pull distance is less than one-half the length of the box vector
along.pull distance is 6 nm.
when I execute this command,
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