date:20180118




On 1/18/18 7:02 AM, za...@tezu.ernet.in wrote:

Send gromacs.org_gmx-users mailing list submissions to
gromacs.org_gmx-users@maillist.sys.kth.se

To subscribe or unsubscribe via the World Wide Web, visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
or, via email, send a message with subject or body 'help' to
gromacs.org_gmx-users-requ...@maillist.sys.kth.se

You can reach the person managing the list at
gromacs.org_gmx-users-ow...@maillist.sys.kth.se

When replying, please edit your Subject line so it is more specific
than "Re: Contents of gromacs.org_gmx-users digest..."


Today's Topics:

1. Re: -inter command (Jo?o Henriques)
2. Rupture force definition (Rakesh Mishra)
3. Re: Can I get the fraction of solvent accessible surface area
   using "gmx sasa"? (=?ISO-8859-1?B?WkhBTkcgQ2hlbmc=?=)


--

Message: 1
Date: Tue, 16 Jan 2018 08:30:10 +0100
From: Jo?o Henriques 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] -inter command
Message-ID:

Re: [gmx-users] six member ring won't stay flat




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 always an in vacuo geometry optimization (QM vs. MM comparison) to
make sure the topology is sensible. If that doesn't check out, there are
problems that can be easily spotted before subjecting the new residue to
any other complicating factors like water and other parts of the protein.

-Justin


Thank you Justin. What would you look at to make a judgement to see if
the topology is sensible after the vacuo geometry optimization? Or as long
as there were no errors or bad notes along the run it should be good?


You look at the structure to see if it is sensible (and here, sensible 
is defined as properly reproducing QM-optimized geometries and/or known 
high-resolution experimental geometries - start with QM and compare 
against empirical evidence later).


The absence of errors or notes when executing grompp tells you precisely 
nothing about the integrity of the physical model; it only tells you if 
you've forgotten to do something. I can populate every parameter field 
with absolute garbage and grompp will happily carry on preparing my 
doomed simulation :)


-Justin

--
==

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

==

--
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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] six member ring won't stay flat

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
 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 and stream file contains an
>>> ASCII
>>> drawing and full name of every species in the residue entries.
>>>
>>>
>>> -Justin
>>>
>>> Justin, the CHARMM forcefield I downloaded has a folder of files
>> including
>> merged.rtp, ffbonded.itp... but I didn't see any rtf file or any file that
>> has ASCII drawings. I am sure I am missing something obvious here. Do you
>> mind giving me a quick link/example please?
>>
>
> You need to be looking at the CHARMM files, not GROMACS files.
>
> http://mackerell.umaryland.edu/charmm_ff.shtml#charmm
>
> -Justin
>
>
> --
> ==
>
> 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
>
> ==
>
> --
> 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
>
> * For (un)subscribe requests visit
> 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

* 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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] six member ring won't stay flat

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 geometry optimization (QM vs. MM comparison) to
> make sure the topology is sensible. If that doesn't check out, there are
> problems that can be easily spotted before subjecting the new residue to
> any other complicating factors like water and other parts of the protein.
>
> -Justin
>

Thank you Justin. What would you look at to make a judgement to see if
the topology is sensible after the vacuo geometry optimization? Or as long
as there were no errors or bad notes along the run it should be good?
Thank you,
Ming

>
> --
> ==
>
> 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
>
> ==
>
> --
> 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
>
> * For (un)subscribe requests visit
> 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

* 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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] SDS initial setup




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 side of the box.

I have used the following command to insert the sds molecules:

gmx insert-molecules -f prot.gro -ci sds.pdb -nmol 200 -o comp.gro

Will it be appropriate to run simulation with this initial setup? Or do I
need to make sure that entire sds molecules are inside the box.


There is no such thing as "outside" a periodic box.

-Justin

--
==

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

==

--
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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] regarding pbc issue

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 criterion and clue to say that:"that's enough, you shouldn't pull it
MORE?"

Totally, how can i know the Max pulling ?

I have PMF schemes which show repulsion( after interaction distance the
potential get less minus and tend to get more positive but they just stop in
0kJ and not any positive potential. It happened for every AA which i pull it
through sheet, so i doubt to my results.

A PMF of zero means the biased groups are (effectively) no longer
interacting. You should expect this.

This thread is well off topic of the original post; if you have further
questions, start a new thread to avoid hijacking this one and
complicating the archive further.

-Justin

Sorry for poor english

With regards
Sent from my iPhone

On Jan 17, 2018, at 19:57, Justin Lemkul wrote:

On 1/17/18 11:23 AM, Rose wrote:
I mean, sometimes structures may really break or collapse, in these situations
trjconv won't show these broken structures whole yes?
just will show them broken (as they really are) yes?

In the context of the question I was answering, "broken" means that it appears bonds have broken
and molecules appear at either side of a periodic boundary. That instance is always fixed by proper use of
trjconv. Bonds can't break or form during classical MD, so if trjconv leaves "broken" molecules
behind, then you've got a topology issue. But I'd wager that about 99.999% of the cases that involve
"broken" molecules are normal PBC issues and nothing more.

But, to answer your question, no, trjconv won't fix a situation in which the
user has supplied an incorrect topology.

-Justin

Sent from my iPhone

On Jan 17, 2018, at 18:15, Justin Lemkul wrote:

On 1/17/18 9:40 AM, Rose wrote:
You mean if -pbc could make molecule whole,everything is ok, but if not it
means the molecule was broken from first, yes?

mdrun writes "broken" coordinates because the physics does not depend on our
visualization convenience. Most programs account for PBC. Some don't. It is generally a
safe practice to just make molecules whole as your first step in trjconv and avoid any
ambiguity.

-Justin

Sent from my iPhone

On Jan 17, 2018, at 16:19, Justin Lemkul wrote:

On 1/17/18 5:51 AM, Vidya R wrote:
Hi Justin,

I got the same result as you said.

What confused me was, when I viewed movie.pdb file generated by the
following command,

gmx trjconv -pbc nojump -s PRD-SMP3.gro -f PRD-SMP3.xtc -e 1.0 -n
index.ndx -o movie.pdb

two hydrogen molecules of my organic compound, were unbonded to my molecule
(which is not supposed to be). They are far away from molecules (their
bonds were broken)

Is it a pbc problem?

Because, when I used

gmx trjconv -pbc whole -s PRD.tpr -f PRD.xtc -o trajwhole.xtc
gmx trjconv -pbc nojump -s PRD.tpr -f trajwhole.xtc -o trajcluster.xtc
gmx trjconv -pbc mol -center -s PRD.tpr -f trajcluster.xtc -o newtraj.xtc

and created a .pdb file with newtraj.xtc, the whole molecule was intact.

Making molecules whole should always be the first step. If you try to remove jumps with
"broken" molecules, what you visualize will be garbage. A separate issue is
with respect to the analysis programs - many are PBC-aware and can handle the original
trajectory without manipulation.

-Justin

--
==

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

--
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

* For (un)subscribe requests visit
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

--
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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] six member ring won't stay flat




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 sensible. If that doesn't check out, there 
are problems that can be easily spotted before subjecting the new 
residue to any other complicating factors like water and other parts of 
the protein.


-Justin

--
==

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

==

--
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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] tilt angle for POPC




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 bilayer with 200 lipids (100 lipids in each leaflet with
resides 1-100 and 101-200 for upper and lower leaflets, respectively)
simulated for 200 ns:

gmx make_ndx -f SYSTEM.gro  -o index.ndx
keep 0
r 1-100
name 1 upperleaflet
1 & a P
1 & a N
2 | 3
name 4 vector
q

Next, I use:
gmx gangle  -f  md.xtc  -s  md.tpr  -n  index.ndx  -g1  vector  -g2  z   -b
  10   -group1  -oh histogram.xvg   -binw  0.01

and choose index group 4 and then Ctrl+D.

Please let me know your opinion. I think I am doing something wrong,
especially with the construction of P-N vector.


What results do you get from this approach?

What happens if you try to analyze only a single lipid?

-Justin

--
==

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

==

--
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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] six member ring won't stay flat




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 and stream file contains an 
ASCII drawing and full name of every species in the residue entries.


-Justin

--
==

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

==

--
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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] gmx enenrgy




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 PME or 
dispersion correction.



if I want to determine interaction enenrgy for example, LJ, between two special 
species, not in total system, what should I do?


Define energygrps in the .mdp file and re-evaluate the energies of the 
trajectory with mdrun -rerun. Note that for most force fields, this 
value has no physical significance.


-Justin

--
==

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

==

--
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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] six member ring won't stay flat

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 :)
> 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 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 sensible. If that doesn't check out, there are
 problems that can be easily spotted before subjecting the new residue to
 any other complicating factors like water and other parts of the
 protein.

 -Justin

 Thank you Justin. What would you look at to make a judgement to see if
>>> the topology is sensible after the vacuo geometry optimization? Or as
>>> long
>>> as there were no errors or bad notes along the run it should be good?
>>>
>>
>> You look at the structure to see if it is sensible (and here, sensible is
>> defined as properly reproducing QM-optimized geometries and/or known
>> high-resolution experimental geometries - start with QM and compare against
>> empirical evidence later).
>>
>> The absence of errors or notes when executing grompp tells you precisely
>> nothing about the integrity of the physical model; it only tells you if
>> you've forgotten to do something. I can populate every parameter field with
>> absolute garbage and grompp will happily carry on preparing my doomed
>> simulation :)
>>
>> -Justin
>>
>> --
>> ==
>>
>> 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
>>
>> ==
>>
>> --
>> 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
>>
>> * For (un)subscribe requests visit
>> 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

* 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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] six member ring won't stay flat




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 often I can't quickly figure out what they
are.


Not in one places, but every CHARMM RTF and stream file contains an ASCII
drawing and full name of every species in the residue entries.


-Justin


Justin, the CHARMM forcefield I downloaded has a folder of files including
merged.rtp, ffbonded.itp... but I didn't see any rtf file or any file that
has ASCII drawings. I am sure I am missing something obvious here. Do you
mind giving me a quick link/example please?


You need to be looking at the CHARMM files, not GROMACS files.

http://mackerell.umaryland.edu/charmm_ff.shtml#charmm

-Justin

--
==

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

==

--
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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] gmx enenrgy

2018-01-18 Thread kordzadeh

Hello Dr.Lemkul

Thank you very much for your answer 

I try to do it.

Regards

Azadeh

-- 
This email was Anti Virus checked by  Security Gateway.
-- 
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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Recentering a protein

2018-01-18 Thread Ahmed Mashaly

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 Na+ to NA and WAT to SOL 
and H and O of water to HW1 HW2 and OW04. Doing a CG minimization again with 
gromacs.05. Doing a NPT with gromacs06. Running MD simulation with gromacs.
Is this procedure correct or do I need any modification?
In Amber we used to run MD for 5 ns, then recenter then relaunch from the last 
rst file. The same case will be with gromacs.Is there a script I can find to 
recenter and relunch the process automatically?

Another thing after doing the minimization, I cannot recenter the protein by 
trjconv command gmx trjconv -f em.gro -s em.tpr -o em_1.gro -center -pbc mol 
-ur compact>> selecting 1 to center protein>> selecting 0 to get the whole 
system output
https://drive.google.com/open?id=13lGcj52NpteRPTBHFJOKlXZ9dUliezqd
In this link you have The acp.gro and acp.top file produced from Acpype with 
modifications to Na and watermdp files for Min, NPT, MD, please check themAnd 
the em.gro the file produced after minimization which cannot be centered
Many thanks
Kind Regards,Ahmed 

-- 
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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] tilt angle for POPC

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.ndx
keep 0
r 1-100
name 1 upperleaflet
1 & a N P
name 2 vector
q

The index file (i.e. the order and numbers in the index file) for group 2
is exactly the same, i.e. will give the N->P vector, not P->N.
So, I think this is why there was a shift to more than 90 degrees.
doing (180-alpha) gave the P->N angle distribution.

STILL, I do not know why there is a pick standing out around 90 degrees. It
is very sharp narrow pick.
Other tilt angle distributions I have seem do not show such a pick.

Thanks in advance for your comments and help

On Thu, Jan 18, 2018 at 11:29 AM, Mohsen Ramezanpour <
ramezanpour.moh...@gmail.com> wrote:

> 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:
>>>
 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 bilayer with 200 lipids (100 lipids in each leaflet with
 resides 1-100 and 101-200 for upper and lower leaflets, respectively)
 simulated for 200 ns:

 gmx make_ndx -f SYSTEM.gro  -o index.ndx
 keep 0
 r 1-100
 name 1 upperleaflet
 1 & a P
 1 & a N
 2 | 3
 name 4 vector
 q

 Next, I use:
 gmx gangle  -f  md.xtc  -s  md.tpr  -n  index.ndx  -g1  vector  -g2  z
  -b
   10   -group1  -oh histogram.xvg   -binw  0.01

 and choose index group 4 and then Ctrl+D.

 Please let me know your opinion. I think I am doing something wrong,
 especially with the construction of P-N vector.

>>>
>>> What results do you get from this approach?
>>>
>> A normal distribution centered around 105 with a high pick standing out
>> around 90.
>> I expected it to be around ~73-77
>>
>>
>>>
>>> What happens if you try to analyze only a single lipid?
>>>
>> I get an approximate normal distribution centered around 100 degrees.
>>
>>
>> I have two systems, one is salt free and the other one has 0.15 M NaCL
>> salt.
>> The shape of histograms is the same.
>>
>> I had to separate the leaflets, right?
>> So, any idea why this is happening?
>>
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> 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
>>>
>>> ==
>>>
>>> --
>>> 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
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>
>>
>>
>> --
>> *Rewards work better than punishment ...*
>>
>
>
>
> --
> *Rewards work better than punishment ...*
>

-- 
*Rewards work better than punishment ...*
-- 
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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] tilt angle for POPC

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:
>>
>>> 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 bilayer with 200 lipids (100 lipids in each leaflet with
>>> resides 1-100 and 101-200 for upper and lower leaflets, respectively)
>>> simulated for 200 ns:
>>>
>>> gmx make_ndx -f SYSTEM.gro  -o index.ndx
>>> keep 0
>>> r 1-100
>>> name 1 upperleaflet
>>> 1 & a P
>>> 1 & a N
>>> 2 | 3
>>> name 4 vector
>>> q
>>>
>>> Next, I use:
>>> gmx gangle  -f  md.xtc  -s  md.tpr  -n  index.ndx  -g1  vector  -g2  z
>>>  -b
>>>   10   -group1  -oh histogram.xvg   -binw  0.01
>>>
>>> and choose index group 4 and then Ctrl+D.
>>>
>>> Please let me know your opinion. I think I am doing something wrong,
>>> especially with the construction of P-N vector.
>>>
>>
>> What results do you get from this approach?
>>
> A normal distribution centered around 105 with a high pick standing out
> around 90.
> I expected it to be around ~73-77
>
>
>>
>> What happens if you try to analyze only a single lipid?
>>
> I get an approximate normal distribution centered around 100 degrees.
>
>
> I have two systems, one is salt free and the other one has 0.15 M NaCL
> salt.
> The shape of histograms is the same.
>
> I had to separate the leaflets, right?
> So, any idea why this is happening?
>
>>
>> -Justin
>>
>> --
>> ==
>>
>> 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
>>
>> ==
>>
>> --
>> 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
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
>
> --
> *Rewards work better than punishment ...*
>



-- 
*Rewards work better than punishment ...*
-- 
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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] tilt angle for POPC

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 my approach is correct as my angle distribution does not
>> seem reasonable.
>>
>> Given a bilayer with 200 lipids (100 lipids in each leaflet with
>> resides 1-100 and 101-200 for upper and lower leaflets, respectively)
>> simulated for 200 ns:
>>
>> gmx make_ndx -f SYSTEM.gro  -o index.ndx
>> keep 0
>> r 1-100
>> name 1 upperleaflet
>> 1 & a P
>> 1 & a N
>> 2 | 3
>> name 4 vector
>> q
>>
>> Next, I use:
>> gmx gangle  -f  md.xtc  -s  md.tpr  -n  index.ndx  -g1  vector  -g2  z
>>  -b
>>   10   -group1  -oh histogram.xvg   -binw  0.01
>>
>> and choose index group 4 and then Ctrl+D.
>>
>> Please let me know your opinion. I think I am doing something wrong,
>> especially with the construction of P-N vector.
>>
>
> What results do you get from this approach?
>
A normal distribution centered around 105 with a high pick standing out
around 90.
I expected it to be around ~73-77


>
> What happens if you try to analyze only a single lipid?
>
I get an approximate normal distribution centered around 100 degrees.


I have two systems, one is salt free and the other one has 0.15 M NaCL salt.
The shape of histograms is the same.

I had to separate the leaflets, right?
So, any idea why this is happening?

>
> -Justin
>
> --
> ==
>
> 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
>
> ==
>
> --
> 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
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
*Rewards work better than punishment ...*
-- 
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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] tilt angle for POPC

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.
However, for -binw of lower than 0.1, e.g. 0.5 or so, the picks appear.

Well, is this a problem with POPC simulation, POPC topology, POPC
parameters, the algorithm behind gangle, or it is what is really happening
and we do not detect it due to the NOT enough Small value of -binw in the
histogram?
I vote for the last option.

Cheers,



On Thu, Jan 18, 2018 at 12:07 PM, Mohsen Ramezanpour <
ramezanpour.moh...@gmail.com> 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.ndx
> keep 0
> r 1-100
> name 1 upperleaflet
> 1 & a N P
> name 2 vector
> q
>
>
> The index file (i.e. the order and numbers in the index file) for group 2
> is exactly the same, i.e. will give the N->P vector, not P->N.
> So, I think this is why there was a shift to more than 90 degrees.
> doing (180-alpha) gave the P->N angle distribution.
>
> STILL, I do not know why there is a pick standing out around 90 degrees.
> It is very sharp narrow pick.
> Other tilt angle distributions I have seem do not show such a pick.
>
> Thanks in advance for your comments and help
>
>
> On Thu, Jan 18, 2018 at 11:29 AM, Mohsen Ramezanpour <
> ramezanpour.moh...@gmail.com> wrote:
>
>> 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:

> 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 bilayer with 200 lipids (100 lipids in each leaflet with
> resides 1-100 and 101-200 for upper and lower leaflets, respectively)
> simulated for 200 ns:
>
> gmx make_ndx -f SYSTEM.gro  -o index.ndx
> keep 0
> r 1-100
> name 1 upperleaflet
> 1 & a P
> 1 & a N
> 2 | 3
> name 4 vector
> q
>
> Next, I use:
> gmx gangle  -f  md.xtc  -s  md.tpr  -n  index.ndx  -g1  vector  -g2
> z   -b
>   10   -group1  -oh histogram.xvg   -binw  0.01
>
> and choose index group 4 and then Ctrl+D.
>
> Please let me know your opinion. I think I am doing something wrong,
> especially with the construction of P-N vector.
>

 What results do you get from this approach?

>>> A normal distribution centered around 105 with a high pick standing out
>>> around 90.
>>> I expected it to be around ~73-77
>>>
>>>

 What happens if you try to analyze only a single lipid?

>>> I get an approximate normal distribution centered around 100 degrees.
>>>
>>>
>>> I have two systems, one is salt free and the other one has 0.15 M NaCL
>>> salt.
>>> The shape of histograms is the same.
>>>
>>> I had to separate the leaflets, right?
>>> So, any idea why this is happening?
>>>

 -Justin

 --
 ==

 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

 ==

 --
 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

 * For (un)subscribe requests visit
 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
 send a mail to gmx-users-requ...@gromacs.org.

>>>
>>>
>>>
>>> --
>>> *Rewards work better than punishment ...*
>>>
>>
>>
>>
>> --
>> *Rewards work better than punishment ...*
>>
>
>
>
> --
> *Rewards work better than punishment ...*
>



-- 
*Rewards work better than punishment ...*
-- 
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

* For (un)subscribe requests visit

[gmx-users] SDS initial setup

2018-01-18 Thread zaved

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 to insert the sds molecules:

gmx insert-molecules -f prot.gro -ci sds.pdb -nmol 200 -o comp.gro

Will it be appropriate to run simulation with this initial setup? Or do I
need to make sure that entire sds molecules are inside the box.

Kindly guide me.

Thank You

Regards
Zaved H.


* * * D I S C L A I M E R * * *
This e-mail may contain privileged information and is intended solely for the 
individual named. If you are not the named addressee you should not 
disseminate, distribute or copy this e-mail. Please notify the sender 
immediately by e-mail if you have received this e-mail in error and destroy it 
from your system. Though considerable effort has been made to deliver error 
free e-mail messages but it can not be guaranteed to be secure or error-free as 
information could be intercepted, corrupted, lost, destroyed, delayed, or may 
contain viruses. The recipient must verify the integrity of this e-mail message.
-- 
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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Umbrella Sampling




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 initial configuration and final configuration are totally 
different. Z_start = 0.91 nm and Z_Final = 0.51 nm. Any possible solution?


Use a stronger force constant.

-Justin

--
==

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

==

--
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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] six member ring won't stay flat

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 Mark,
> > Can you tell me more details about the ring's atoms interacting with an
> > environment? What interactions did you mean?
> > Thanks,
> > Ming
> >
> > On Tue, Jan 16, 2018 at 6:43 AM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > You still have many sources of problems (e.g. the warnings you
> > suppressed,
> > > the fact that your ring's atoms interact with an environment). What
> > happens
> > > when you minimize a capped peptide in vacuo?
> > >
> > > Mark
> > >
> > > On Tue, Jan 16, 2018 at 12:39 PM MD  wrote:
> > >
> > > > Hi Justin,
> > > >
> > > > I got the itp and parameters of my side chain modified amino acid
> from
> > > > CHARMM-GUI and incorporated it into my protein structure, labeled
> with
> > > > HETATM. I made the atom types names consistent with charmm forcefield
> > > which
> > > > I used with gromacs and made sure overall the parameters look decent
> > for
> > > > now. After some fixing the grompp would run with no warnings, and I
> > did a
> > > > quick energy minimization, but ended up with a distorted six member
> > > ring. I
> > > > have the picture and my parameters attached. Your time is appreciated
> > :)
> > > >
> > > >
> > > > https://docs.google.com/document/d/1bjSq55HDLRsSVGqm5i0MRwI-
> > > rgIesxy0QdIHm7tqTug/edit?usp=sharing
> > > >
> > > > Ming
> > > >
> > > > On Mon, Jan 15, 2018 at 7:53 PM, Justin Lemkul 
> > wrote:
> > > >
> > > > >
> > > > >
> > > > > On 1/15/18 7:45 PM, MD wrote:
> > > > >
> > > > >> Hi Gromacs,
> > > > >>
> > > > >> I have a modified side chain amino acid and it has a six member
> ring
> > > > >> attached to it. Regarding this ring I had dihedral angles taken
> care
> > > > with
> > > > >> some 0s and some 180s. However, after minimization my structure
> > looks
> > > > very
> > > > >> strange, the ring is not flat and the dihedral angles in my
> settings
> > > > >> didn't
> > > > >> seem to apply to the minimized structure at all. Any thoughts?
> > > > >>
> > > > >
> > > > > You're going to have to provide a lot more detail. You're
> > parametrizing
> > > > > something nonstandard, so there are plenty of places to make
> > mistakes.
> > > > > Without knowing your structure, the actual parameters and how
> derived
> > > and
> > > > > validated them, there's nothing to do but guess.
> > > > >
> > > > > Keep in mind that rings are not necessarily perfectly planar, and
> the
> > > > > values set for dihedral phase offsets do not strictly mean the
> values
> > > > that
> > > > > the dihedrals must adopt.
> > > > >
> > > > > -Justin
> > > > >
> > > > > --
> > > > > ==
> > > > >
> > > > > 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
> > > > >
> > > > > ==
> > > > >
> > > > > --
> > > > > 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
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > 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
> > > >
> > > > * 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
> > > >
> > > > * For (un)subscribe requests visit
> > > > 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
> > >
> > > * 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
> > >
> > > * For (un)subscribe requests visit
> > > 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
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post?

[gmx-users] Three different diffusivities by "gmx msd" /

2018-01-18 Thread Johannes Hörmann


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 prepared an index 
file DS_selection.ndx with the content


    [ Surfactant ]
       1    2    3    4    5    6    7    8    9   10   11   12 13   
14   15
      16   17   18   19   20   21   22   23   24   25   26   27 28   
29   30

      31   32   33   34   35   36   37   38   39   40   41   42

in order to select the molecule of interest explicitly. As far as I 
understand the GMX 2016.4 manual and help, the commad


    gmx msd -f md_1.trr -s md.tpr -o atom_wise_msd.xvg -n 
DS_selection.ndx


should yield the atom-wise evaluated MSD averaged over all 42 atoms for 
each timestep. "atom_wise_msd.xvg" contains the comment


    
    # MSD gathered over 4.99 ps with 1 restarts
    # Diffusion constants fitted from time 0.5 to 4.49 ps
    # D[Surfactant] = 1.8305 (+/- 1.3704) (1e-5 cm^2/s)
    

which I understand  as the atom-averaged diffusivity. On the other hand,

    gmx msd -f md_1.trr -s md.tpr -o mol_wise_msd.xvg -mol 
mol_wise_D.xvg -n DS_selection.ndx


should yield MSD (and diffusivity D) for the molecule's COM, and 
consequently a different value D


    
    # MSD gathered over 4.99 ps with 1 restarts
    # Diffusion constants fitted from time 0.5 to 4.49 ps
    # D[Surfactant] = 1.5575 (+/- 1.3521) (1e-5 cm^2/s)
    

is found within "mol_wise_msd.xvg". So far, so good, my understanding is 
correct up until here?


Now, looking at the latter command's stdout, I have

     = 1.1395 Std. Dev. = -nan Error = -nan
    Fitting from 0.5 to 4.49 ps

    D[Surfactant] 1.5575 (+/- 1.3521) 1e-5 cm^2/s

and in the file "mol_wise_D.xvg" of course just one entry for the single 
DS molecule


    
    @    title "Diffusion Coefficients / Molecule"
    @    xaxis  label "Molecule"
    @    yaxis  label "D"
    @TYPE xy
 0 1.13953

Here, I am confused. How does the third value for D arise? Naturally, I 
would have expected "mol_wise_D.xvg" to list the same value of D = 
1.5575 as found within the comment of "mol_wise_msd.xvg".


I am looking forward to a clarifying answer, as I could not find any 
notes on this discrepancy in the documentation. Is it maybe possible 
that the  = 1.1395 is evaluated over all 5ps, whereas D[Surfactant] = 
1.5575is fitted only on the 80% trajectory from 0.5 to 4.49 ps? If so, 
some clear hint towards this fact would be appreciated in the "gmx help 
msd" text.


A different topic: I could not find any option for "gmx msd" to evaluate 
a trajectory frame-wise without loading the whole file into memory. When 
applied onto a several GB .trr, even with relatively small "-trestart”， 
GMX would continuously eat up memory until the job would be canceled due 
to running out of the node's 128 GB RAM. Maybe any undocumented option 
hidden somewhere?


Here the output of "gmx --version"

    GROMACS:  gmx, version 2016.4
    Executable: 
/work/ws/nemo/fr_lp1029-IMTEK_SIMULATION-0/gromacs_2016.4_gnu/bin/gmx
    Data prefix: 
/work/ws/nemo/fr_lp1029-IMTEK_SIMULATION-0/gromacs_2016.4_gnu
    Working dir: 
/work/ws/nemo/fr_jh1130-201708-0/jobs/gmxlab/sds/201801/farafonov2017developing/1ds/rtp/GAFF-SPC

    Command line:
  gmx --version

    GROMACS version:    2016.4
    Precision:  single
    Memory model:   64 bit
    MPI library:    thread_mpi
    OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
    GPU support:    disabled
    SIMD instructions:  AVX2_256
    FFT library:    fftw-3.3.7-sse2-avx-avx2-avx2_128
    RDTSCP usage:   enabled
    TNG support:    enabled
    Hwloc support:  hwloc-1.11.0
    Tracing support:    disabled
    Built on:   Wed Dec 13 10:46:41 CET 2017
    Built by:   fr_jh1...@int02.nemo.privat [CMAKE]
    Build OS/arch:  Linux 3.10.0-693.5.2.el7.x86_64 x86_64
    Build CPU vendor:   Intel
    Build CPU brand:    Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz
    Build CPU family:   6   Model: 79   Stepping: 1
    Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma 
hle htt lahf mmx msr nonstop_tsc pcid    pclmuldq pdcm pdpe1gb popcnt 
pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic

    C compiler: /opt/bwhpc/common/compiler/gnu/5.2.0/bin/gcc GNU 5.2.0
    C compiler flags:    -march=core-avx2 -O3 -DNDEBUG 
-funroll-all-loops -fexcess-precision=fast

    C++ compiler: /opt/bwhpc/common/compiler/gnu/5.2.0/bin/g++ GNU 5.2.0
    C++ compiler flags:  -march=core-avx2    -std=c++0x   -O3 -DNDEBUG 
-funroll-all-loops -fexcess-precision=fast


Thanks for your help.

Best regards,

--
Johannes Hörmann

University of Freiburg
IMTEK - Department of Microsystems Engineering
Laboratory for Simulation
Georges-Köhler-Allee 103, Room 03 020
79110

Re: [gmx-users] six member ring won't stay flat

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 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 sensible. If that doesn't check out, there are
>>> problems that can be easily spotted before subjecting the new residue to
>>> any other complicating factors like water and other parts of the protein.
>>>
>>> -Justin
>>>
>>> Thank you Justin. What would you look at to make a judgement to see if
>> the topology is sensible after the vacuo geometry optimization? Or as long
>> as there were no errors or bad notes along the run it should be good?
>>
>
> You look at the structure to see if it is sensible (and here, sensible is
> defined as properly reproducing QM-optimized geometries and/or known
> high-resolution experimental geometries - start with QM and compare against
> empirical evidence later).
>
> The absence of errors or notes when executing grompp tells you precisely
> nothing about the integrity of the physical model; it only tells you if
> you've forgotten to do something. I can populate every parameter field with
> absolute garbage and grompp will happily carry on preparing my doomed
> simulation :)
>
> -Justin
>
> --
> ==
>
> 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
>
> ==
>
> --
> 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
>
> * For (un)subscribe requests visit
> 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

* 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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] six member ring won't stay flat