Re: [gmx-users] nrexcl=3: ambiguous?

[Mark Abraham]

Hi,

Typically 1-4 interactions are regarded as bonded interactions implementing
a non-bonded functional form. So a request to exclude non-bonded
interactions between atoms connected by adjacent bonds does not apply. The
requirement for particular kinds of 1-4 interactions are imposed by
construction of the force field.

Mark

On Mon, Feb 19, 2018 at 6:34 AM Saumyak Mukherjee <
mukherjee.saumya...@gmail.com> wrote:

> Dear Users,
>
> As mentioned in the manual, *nrexcl = 3* means "*excluding non-bonded
> interactions between atoms that are no further than 3 bonds away*". This
> means, as I understand, 1-4 interactions are also excluded.
>
> However, after simulation when "gmx energy" is used, it gives output for
> 1-4 interactions. How is this possible?
>
> Any help/suggestion is appreciated.
>
> Thanks & regards,
>
> *Saumyak Mukherjee*
>
> Senior Research Fellow,
> Prof. Biman Bagchi's Lab,
> Solid State and Structural Chemistry Unit,
> Indian Institute of Science,
> Bangalore - 560012,
> Karnataka, India.
> --
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Re: [gmx-users] Regarding No more replaceable solvent!

[Dilip H N]

I have a system of 1aminoacid+511 water molecules (total is 512
molecules).and the box length is 2.52nm.

So, even if i replace by 45 Na+ and 45 Cl- ions (total is 90 ions) and
still i have 511-90 = 421 water molecules. and i think this is well within
the solubility...

How many water molecules are being removed for each ion..?? (when i
replaced 10Na+ and 10Cl- ions ie., 511-20=491 water molecules were there
and this system was being well, but now with 45 ions each, i am getting the
error...)

Then how do i solve this issue..??

Any suggestions.

Thank you.




‌
 Sent with Mailtrack


On Mon, Feb 19, 2018 at 11:49 AM, Alex  wrote:

> How about you actually open your 'glywi.gro' prior to adding more ions and
> count the number of water molecules, and then compare it with the number of
> ions you want to add? With concentration known and the knowledge of your
> box volume, this comparison shouldn't be a problem.
>
> Alex
>
>
> On 2/18/2018 11:14 PM, Dilip H N wrote:
>
>> Hello,
>> I added 10 Na+ and Cl- ions to the aminoacid-water system containing 512
>> molecules through the command
>> gmx genion -s em.tpr -o abc.gro -p topol.top -pname NA -nname CL -np 10
>> -nn
>> 10
>>
>> but now, i want to increase the concentration, so i want to add 45 Na+ and
>> Cl- ions (from calculation, the concentration for 45 ions is 5M...), but
>> when i give the commands:
>> gmx genion -s em.tpr -o glywi.gro -p topol.top -pname NA -nname CL -np 45
>> -nn 45
>>   (or)
>> gmx genion -s em.tpr -o glywi.gro -p topol.top -pname NA -nname CL -conc 5
>>
>> I am getting the error as:
>>
>> No more replaceable solvent!
>>
>> So, Is there any limit here..?? The maximum concentration that i can get
>> is
>> 2M (through -conc 2 command), and after that, if i change from -conc2 to
>> -conc3 etc., i am getting the same error as "No more replaceable
>> solvent!".
>>
>> Any suggestions are appreciated...
>>
>> Thank you
>>
>>
>>
> --
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With Best Regards,

DILIP.H.N
Ph.D Student
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Re: [gmx-users] Regarding No more replaceable solvent!

[Dilip H N]

Thank you sir...
Yes, I will post it in the group...




 Sent with Mailtrack


On Mon, Feb 19, 2018 at 12:17 PM, Alex  wrote:

> Please be kind to respond to the list and not to my email. I believe that
> 3-4 water molecules get removed per ion, depending on the insertion cutoff,
> so with 90 x 4, you're left in a situation where there's pretty much no
> water left. Gromacs is actually doing you a huge favor with this error,
> because it could manage to insert all the ions and you would end up
> simulating something nonsensical.
>
> Increase your box size appropriately.
>
> Alex
>
>
> On 2/18/2018 11:30 PM, Dilip H N wrote:
>
>> Sir,
>> In connection with the above-mentioned title...
>>
>> I have a system of 1glycine+511 water molecules (total is 512
>> molecules).and the box length is 2.51nm.
>>
>> So, even if i replace by 45 Na+ and 45 Cl- ions (total is 90 ions) and
>> still i have 511-90 = 421 water molecules. and i think this is well within
>> the solubility...
>>
>> Then how do i solve this issue..??
>>
>> Any suggestions sir.
>>
>> Thank you.
>>
>>
>>
>>
>>
>> --
>> With Best Regards,
>>
>> DILIP.H.N
>> Ph.D. Student
>>
>>
>>
>>  Sent with Mailtrack <
>> https://chrome.google.com/webstore/detail/mailtrack-for-gma
>> il-inbox/ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail&
>> utm_medium=signature_campaign=signaturevirality>
>>
>
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Ph.D Student
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Re: [gmx-users] Regarding No more replaceable solvent!

[Alex]

Please be kind to respond to the list and not to my email. I believe 
that 3-4 water molecules get removed per ion, depending on the insertion 
cutoff, so with 90 x 4, you're left in a situation where there's pretty 
much no water left. Gromacs is actually doing you a huge favor with this 
error, because it could manage to insert all the ions and you would end 
up simulating something nonsensical.


Increase your box size appropriately.

Alex


On 2/18/2018 11:30 PM, Dilip H N wrote:

Sir,
In connection with the above-mentioned title...

I have a system of 1glycine+511 water molecules (total is 512 
molecules).and the box length is 2.51nm.


So, even if i replace by 45 Na+ and 45 Cl- ions (total is 90 ions) and 
still i have 511-90 = 421 water molecules. and i think this is well 
within the solubility...


Then how do i solve this issue..??

Any suggestions sir.

Thank you.





--
With Best Regards,

DILIP.H.N
Ph.D. Student



 Sent with Mailtrack 
 



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Re: [gmx-users] Regarding No more replaceable solvent!

[Alex]

How about you actually open your 'glywi.gro' prior to adding more ions 
and count the number of water molecules, and then compare it with the 
number of ions you want to add? With concentration known and the 
knowledge of your box volume, this comparison shouldn't be a problem.


Alex


On 2/18/2018 11:14 PM, Dilip H N wrote:

Hello,
I added 10 Na+ and Cl- ions to the aminoacid-water system containing 512
molecules through the command
gmx genion -s em.tpr -o abc.gro -p topol.top -pname NA -nname CL -np 10 -nn
10

but now, i want to increase the concentration, so i want to add 45 Na+ and
Cl- ions (from calculation, the concentration for 45 ions is 5M...), but
when i give the commands:
gmx genion -s em.tpr -o glywi.gro -p topol.top -pname NA -nname CL -np 45
-nn 45
  (or)
gmx genion -s em.tpr -o glywi.gro -p topol.top -pname NA -nname CL -conc 5

I am getting the error as:

No more replaceable solvent!

So, Is there any limit here..?? The maximum concentration that i can get is
2M (through -conc 2 command), and after that, if i change from -conc2 to
-conc3 etc., i am getting the same error as "No more replaceable solvent!".

Any suggestions are appreciated...

Thank you




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[gmx-users] Regarding No more replaceable solvent!

[Dilip H N]

Hello,
I added 10 Na+ and Cl- ions to the aminoacid-water system containing 512
molecules through the command
gmx genion -s em.tpr -o abc.gro -p topol.top -pname NA -nname CL -np 10 -nn
10

but now, i want to increase the concentration, so i want to add 45 Na+ and
Cl- ions (from calculation, the concentration for 45 ions is 5M...), but
when i give the commands:
gmx genion -s em.tpr -o glywi.gro -p topol.top -pname NA -nname CL -np 45
-nn 45
 (or)
gmx genion -s em.tpr -o glywi.gro -p topol.top -pname NA -nname CL -conc 5

I am getting the error as:

No more replaceable solvent!

So, Is there any limit here..?? The maximum concentration that i can get is
2M (through -conc 2 command), and after that, if i change from -conc2 to
-conc3 etc., i am getting the same error as "No more replaceable solvent!".

Any suggestions are appreciated...

Thank you


-- 
With Best Regards,

DILIP.H.N
Ph.D. Student



‌
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[gmx-users] nrexcl=3: ambiguous?

[Saumyak Mukherjee]

Dear Users,

As mentioned in the manual, *nrexcl = 3* means "*excluding non-bonded
interactions between atoms that are no further than 3 bonds away*". This
means, as I understand, 1-4 interactions are also excluded.

However, after simulation when "gmx energy" is used, it gives output for
1-4 interactions. How is this possible?

Any help/suggestion is appreciated.

Thanks & regards,

*Saumyak Mukherjee*

Senior Research Fellow,
Prof. Biman Bagchi's Lab,
Solid State and Structural Chemistry Unit,
Indian Institute of Science,
Bangalore - 560012,
Karnataka, India.
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Re: [gmx-users] Fwd: ion channel in lipid bilayer

[Kroon, P.C.]

Hi Alex,

Try either insane.py, or charmm-gui. I can't provide links, since I'm on my
phone.

You may need to generate the topology (itp) of the protein, which you can
do with calling pdb2gmx on just the protein. You should have a topology
(itp) of your favourite lipid.

Peter

On 18 Feb 2018 13:54, "alex rayevsky"  wrote:

> I'm sorry for repeat, but nobody answered the question and I decided to
> duplicate the request. Maybe it is a problem with a form of question or its
> content, please, point me the mistake.
>
> Hi all!
>
> I have a question concerning immersion of the ion channel (four subunits
> with extracellular domains and a bundles of helixes)  into the lipid
> bilayer. 6 years ago I used some tutorial or mailing lists, which described
> the way from KALP15 tutor. With CCR5 model there were no problems at all.
> Now I have a not 'cylindric'  protein with a complex shape and overhanging
> domains.
> the forcefield is CHARMM36, lipid type - POPG.
>
> I tried Membrane builder, but couldn't orient the plane of the membrane by
> changing XYZ principles many times in different combinations.. Thus I used
> a slightly modified KALP15 method (other .itps, lipids and water
> molecules).  First of all after pdb2gmx for protein a series of topologies
> were generated with identifiers in the name, as it was assigned in each
> chain. However editconf produced a new pdb from the outpu gro without any
> ID or terminators for the chains, in Pymol it is represented with a
> tetramer entirely highlithing if a single chain is selected (maybe it is a
> reason of faults at later stages).
>
> Well, it works fine until the perl script execution. Beside some problems
> with the output (system_inflated.gro was corrupted, but I repaired it with
> simple python scripting and got a pretty protein in the center of rare
> molecules, which looks reliable enough) I started to compact the bilayer to
> rich the lipid area of ~53A^2. I finished it on the 13 stage of perl
> execution - the distance between nearest lipids was about 16A, however, the
> layer was really holey. At the same time the protein was not surrounded
> from all sides. But if I try to put lipids closely one to other, they are
> simultaneously penetrate the protein body.
>
> Is it the correct method for such kind of simmulations? Could I increase
> the number of POPG molecules after getting inflated.gro file with scaled up
> bilayer (the initial step for tightning) before scaling iterations? I can
> do it manually by copy of the layer (all lipid coordinates) and its
> rotation around Y axis in any soft to enlarge the number of molecules in
> the cell (even 200 mols is more than 128). Of course I will make changes in
> a topology file. It seems, that I will obtain a fully wrapped protein
> without anxiety about clashes or presure in cavities...
>
> What do You think? Thank You in advance!
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[gmx-users] Fwd: ion channel in lipid bilayer

[alex rayevsky]

I'm sorry for repeat, but nobody answered the question and I decided to
duplicate the request. Maybe it is a problem with a form of question or its
content, please, point me the mistake.

Hi all!

I have a question concerning immersion of the ion channel (four subunits
with extracellular domains and a bundles of helixes)  into the lipid
bilayer. 6 years ago I used some tutorial or mailing lists, which described
the way from KALP15 tutor. With CCR5 model there were no problems at all.
Now I have a not 'cylindric'  protein with a complex shape and overhanging
domains.
the forcefield is CHARMM36, lipid type - POPG.

I tried Membrane builder, but couldn't orient the plane of the membrane by
changing XYZ principles many times in different combinations.. Thus I used
a slightly modified KALP15 method (other .itps, lipids and water
molecules).  First of all after pdb2gmx for protein a series of topologies
were generated with identifiers in the name, as it was assigned in each
chain. However editconf produced a new pdb from the outpu gro without any
ID or terminators for the chains, in Pymol it is represented with a
tetramer entirely highlithing if a single chain is selected (maybe it is a
reason of faults at later stages).

Well, it works fine until the perl script execution. Beside some problems
with the output (system_inflated.gro was corrupted, but I repaired it with
simple python scripting and got a pretty protein in the center of rare
molecules, which looks reliable enough) I started to compact the bilayer to
rich the lipid area of ~53A^2. I finished it on the 13 stage of perl
execution - the distance between nearest lipids was about 16A, however, the
layer was really holey. At the same time the protein was not surrounded
from all sides. But if I try to put lipids closely one to other, they are
simultaneously penetrate the protein body.

Is it the correct method for such kind of simmulations? Could I increase
the number of POPG molecules after getting inflated.gro file with scaled up
bilayer (the initial step for tightning) before scaling iterations? I can
do it manually by copy of the layer (all lipid coordinates) and its
rotation around Y axis in any soft to enlarge the number of molecules in
the cell (even 200 mols is more than 128). Of course I will make changes in
a topology file. It seems, that I will obtain a fully wrapped protein
without anxiety about clashes or presure in cavities...

What do You think? Thank You in advance!
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Re: [gmx-users] Electric Field

[Mark Abraham]

Hi,

Suggestion, get the git version of gromacs and use

 git grep -i -G"electric field"

src/gromacs/applied-forces

Mark

On Sun, Feb 18, 2018 at 7:36 PM Ali Ahmed  wrote:

> Dear Mark,
> I could not find the electric field calculation code. In 2016 version, the
> code was in mdlib/sim_util.cpp but in 2018 version I could not find it.
> Is it elsewhere? can you tell me, please?
> Thanks
>
> On Fri, Jan 19, 2018 at 12:25 PM, Ali Ahmed  wrote:
>
> > Dear Mark,
> > Thank you. this is good I will study it.
> >
> >
> > On Fri, Jan 19, 2018 at 10:21 AM, Mark Abraham  >
> > wrote:
> >
> >> Hi,
> >>
> >> See section 6.7 of the 2018 reference manual for what is supported.
> >>
> >> MArk
> >>
> >> On Fri, Jan 19, 2018 at 3:17 PM Ali Ahmed  wrote:
> >>
> >> > Hello GROMACS users
> >> > I have looked through GROMACS user manual to understand the theory
> >> behind
> >> > applying external electric field but I did not find any description.
> >> Also,
> >> > I looked at the source code in  sim_util.cpp file but found only the
> >> > time-dependent electric field.
> >> > My question does GROMACS consider Lorentz force for applying external
> >> > electric field or using another theory?
> >> > Thanks
> >> > Ali
> >> > --
> >> > Gromacs Users mailing list
> >> >
> >> > * Please search the archive at
> >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> > posting!
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> >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> > send a mail to gmx-users-requ...@gromacs.org.
> >> >
> >> --
> >> Gromacs Users mailing list
> >>
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> >>
> >
> >
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Re: [gmx-users] PROBLEM IN COORDINATES

[Alex]

Hi,

The error is informative. Check the number of entries in the gro file 
and compare it with the [ atoms ] section in your topology, together 
with anything that's added under [ system ]. The total numbers need to 
match.


Alex


On 2/18/2018 11:34 AM, neelam wafa wrote:

Dear gmx users,

I am doing the tutorial of protein ligand simmulation given at
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/com.
when I give following command, I get an error.

gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr

the error says the number of coordinates in the sol.gro file and
topol.top file does not match. How to fix it.

Help me out please.

Thanks in advance.

Regards


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Re: [gmx-users] PROBLEM IN COORDINATES

[Ali Ahmed]

check your sol.gro if you have molecules more or less than given in your
topology
Best

On Sun, Feb 18, 2018 at 12:34 PM, neelam wafa  wrote:

> Dear gmx users,
>
> I am doing the tutorial of protein ligand simmulation given at
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/com
> .
> when I give following command, I get an error.
>
> gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr
>
> the error says the number of coordinates in the sol.gro file and
> topol.top file does not match. How to fix it.
>
> Help me out please.
>
> Thanks in advance.
>
> Regards
> --
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Re: [gmx-users] Electric Field

[Ali Ahmed]

Dear Mark,
I could not find the electric field calculation code. In 2016 version, the
code was in mdlib/sim_util.cpp but in 2018 version I could not find it.
Is it elsewhere? can you tell me, please?
Thanks

On Fri, Jan 19, 2018 at 12:25 PM, Ali Ahmed  wrote:

> Dear Mark,
> Thank you. this is good I will study it.
>
>
> On Fri, Jan 19, 2018 at 10:21 AM, Mark Abraham 
> wrote:
>
>> Hi,
>>
>> See section 6.7 of the 2018 reference manual for what is supported.
>>
>> MArk
>>
>> On Fri, Jan 19, 2018 at 3:17 PM Ali Ahmed  wrote:
>>
>> > Hello GROMACS users
>> > I have looked through GROMACS user manual to understand the theory
>> behind
>> > applying external electric field but I did not find any description.
>> Also,
>> > I looked at the source code in  sim_util.cpp file but found only the
>> > time-dependent electric field.
>> > My question does GROMACS consider Lorentz force for applying external
>> > electric field or using another theory?
>> > Thanks
>> > Ali
>> > --
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[gmx-users] PROBLEM IN COORDINATES

[neelam wafa]

Dear gmx users,

I am doing the tutorial of protein ligand simmulation given at
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/com.
when I give following command, I get an error.

gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr

the error says the number of coordinates in the sol.gro file and
topol.top file does not match. How to fix it.

Help me out please.

Thanks in advance.

Regards
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[gmx-users] do the results seem logical for intreaction zno nanoparticle and human serum album in gromacs?

[Marziyeh hassanian96]

Hi,I am studying the toxicity effect of ZnO nanoparticle (with a partial 
charges of +1.026 and -1.026 for Zinc and Oxygen atoms, respectively) on the 
Albumin structure by Gromacs. For MD simulation the nanoparticle was placed at 
a distance of 1nm of protein, after running pdb2gmx, the simulation box was 
solvated by TIP3P waters. The net charge of protein in physiological condition 
is -14 that was neutralized by adding sodium and chloride ions to box. Then, 
energy minimization, NVT and NPT were done. From the beginning of md 
simulation, the protein structure began to be unfolded slowly before binding 
nanoparticle to it and after binding, the protein structure changed 
dramatically. I cannot consider the charge of ZnO as zero like silver or gold 
nanoparticles. So, I am confused that whether the study method is correct or 
wrong for this interaction? Do the results seem logical?
Thanks

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Re: [gmx-users] Secondary structure propensity.

[Justin Lemkul]

On 2/18/18 6:05 AM, Sundari wrote:

Thank You :)

I have a little doubt now. If I want total percentage of all 8 secondary
structures separately i.e SS (%) than I can get this by simply averaging
the propensities of ss ?



No, that will give you a constant number. All residues have to be in one 
type of secondary structure (including coil) and they can only 
interconvert between them. If you do any sort of averaging over the 8 
types, you get a constant. The calculation I gave before will do what 
you want.


-Justin




On Fri, Feb 16, 2018 at 6:21 PM, Justin Lemkul  wrote:



On 2/16/18 3:40 AM, Subhomoi Borkotoky wrote:


Hello,

I believe *do_dssp* will do the trick. Generate the *.xpm* matrix file ,
it
contains the required information.


Only indirectly, but scount.xvg has all that is needed, the number of
residues in a given secondary structure as a function of time. From that,
percentage over time is a trivial scripting task, [(# in SS) / (# of
residues)]*100.

-Justin

Regards,

S. Borkotoky

On Fri, Feb 16, 2018 at 1:30 PM, Sundari  wrote:

Dear gromacs users,

can any one please tell me that how we get the secondary structure
propensity or secondary structure content(%) as a function of simulation
time.

I used "gmx do_dssp" but it gives me number of residues forming the
secondary structure vs simulation time. is it same thing or something
different?

Thank you in advance..
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--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==


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==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] Secondary structure propensity.

[Subhomoi Borkotoky]

Thanks for the addition.

On 16 Feb 2018 6:22 pm, "Justin Lemkul"  wrote:

>
>
> On 2/16/18 3:40 AM, Subhomoi Borkotoky wrote:
>
>> Hello,
>>
>> I believe *do_dssp* will do the trick. Generate the *.xpm* matrix file ,
>> it
>> contains the required information.
>>
>
> Only indirectly, but scount.xvg has all that is needed, the number of
> residues in a given secondary structure as a function of time. From that,
> percentage over time is a trivial scripting task, [(# in SS) / (# of
> residues)]*100.
>
> -Justin
>
> Regards,
>>
>> S. Borkotoky
>>
>> On Fri, Feb 16, 2018 at 1:30 PM, Sundari  wrote:
>>
>> Dear gromacs users,
>>>
>>> can any one please tell me that how we get the secondary structure
>>> propensity or secondary structure content(%) as a function of simulation
>>> time.
>>>
>>> I used "gmx do_dssp" but it gives me number of residues forming the
>>> secondary structure vs simulation time. is it same thing or something
>>> different?
>>>
>>> Thank you in advance..
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/
>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
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>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
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Re: [gmx-users] 2016H66 force field

[Patrick Fuchs]

Hi Anjana,
if you use the files from 2016H66 (see my previous message) and the 
statement #include "ffG2016h66.itp" in your top file, no need to change 
anything (provided you use a correct itp file for your molecule, e.g. 
the CiEj on my github website). All the parameters that were changed 
from 53A6 to 53A6_OXY are properly included in the 2016H66 files.

Best,

Patrick

Le 18/02/2018 à 04:55, Anjana Jayasinghe a écrit :

Dear All,
I would like to know that do we need to change bond lengths and bond angles 
such as gb_1, gb_18, ga_12 and ga_15 (according to OXY) for MD simulations of 
CiEj or PEO molecules when we use 2016H66 force field?
Thank you.


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Re: [gmx-users] Secondary structure propensity.

[Sundari]

Thank You :)

I have a little doubt now. If I want total percentage of all 8 secondary
structures separately i.e SS (%) than I can get this by simply averaging
the propensities of ss ?




On Fri, Feb 16, 2018 at 6:21 PM, Justin Lemkul  wrote:

>
>
> On 2/16/18 3:40 AM, Subhomoi Borkotoky wrote:
>
>> Hello,
>>
>> I believe *do_dssp* will do the trick. Generate the *.xpm* matrix file ,
>> it
>> contains the required information.
>>
>
> Only indirectly, but scount.xvg has all that is needed, the number of
> residues in a given secondary structure as a function of time. From that,
> percentage over time is a trivial scripting task, [(# in SS) / (# of
> residues)]*100.
>
> -Justin
>
> Regards,
>>
>> S. Borkotoky
>>
>> On Fri, Feb 16, 2018 at 1:30 PM, Sundari  wrote:
>>
>> Dear gromacs users,
>>>
>>> can any one please tell me that how we get the secondary structure
>>> propensity or secondary structure content(%) as a function of simulation
>>> time.
>>>
>>> I used "gmx do_dssp" but it gives me number of residues forming the
>>> secondary structure vs simulation time. is it same thing or something
>>> different?
>>>
>>> Thank you in advance..
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/
>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
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>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
>
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Re: [gmx-users] SS Content?

[Sundari]

my problem resolved :)

Thank you

On Sun, Feb 18, 2018 at 4:22 PM, Sundari  wrote:

> Dear gromacs users,
>
> can any one please tell me that how we get the secondary structure
> propensity or secondary structure content(%) as a function of simulation
> time.
>
> I used "gmx do_dssp" but it gives me number of residues forming the
> secondary structure vs simulation time. is it same thing or something
> different?
>
> Thank you in advance..
>
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