Re: [PyMOL] Pymol cavity detection error?

[Tsjerk Wassenaar]

Hi Kanika,

Try

set two_sided_lighting

Cheers,

Tsjerk

On Jun 28, 2017 17:14, "kanika sharma"  wrote:

> Dear PyMolers
>
> I want to see the cavities in my protein using the following steps:
>
> Setting → Surface → Cavities & Pockets Only.
> Show surface
> Cavity Detection Radius 5A
>
> But I see the surface as a black blob, if I colour it (say white), the
> external still remains black.
>
> Anyone has some suggestions why this happens?
>
> I attached a picture of what it looks like.
>
> --
> *Best,*
>
> *Kanika *
>
>
>
> 
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Re: [PyMOL] Problem with 'byring' selection

[Tsjerk Wassenaar]

Hi Vijay,

It is logic. 'byring elem N' selects all nitrogens and then expands the
selection to include the rings in which these participate. 'elem N and
byring elem N' does the same, but then intersects (and) to extract only
nitrogens. But that is the same as 'elem N'. If you want to have the
nitrogens from rings, you can do 'elem N and byring not elem N'. That
selects the non-nitrogen atoms and expands the selection over rings. So
only nitrogens in rings can be added to teh selection. Then intersecting to
get only nitrogens will yield only those that are members of rings.

Hope it helps,

Tsjerk

On Jun 3, 2017 5:45 AM, "Vijay Masand"  wrote:

> Dear PyMOL Users,
> I am using PyMOL 1.8.6 on Windows 10 (64 bit) with Python 2.7.12. I
> was working with small molecule
> (ClC1[OH+]C(Cl)=CN=C1C(=O)N([NH+]1CCC(SC1)F)CCN).
> When I tried to select all Nitrogen atoms which are exclusively in the
> ring only, I tried following command:
> abc=cmd.select('byring elem N')
> But, this selected not only Nitrogen atoms in the ring but Carbon
> atoms of the ring also.
> But, following command worked perfectly:
> abc=cmd.select('elem N & byring elem N')
> Is it a bug or something else?
> Cheers
> Vijay
>
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Re: [PyMOL] Is it possible in Pymol to determine Individual Bond, Dissociation Energy for any Bond in organic molecules?

[Tsjerk Wassenaar]

Dear Rajib,

Pymol reads atom labels and positions from a coordinate file. It then
determines which atoms are bonded based on distance criteria. That is used
to draw the molecule.
Pymol also has an internal library of molecules and fragments, with atoms
and bonds, which can be used to build bigger molecules.

QM methods are required to determine an optimal molecular geometry. But
that's not something Pymol does. Just read in coordinates and draw those.

Hope it helps,

Tsjerk

On Jun 1, 2017 21:27, "Susmita/Rajib"  wrote:

> No, Dr. Wassenaar, Sir! People have confused me. After two years, I am
> told that:
> [Quote]PyMol does not use QM methods. It also does not "determine the
> structures of molecules" [/Quote]
> I need my illustrious peers to clarify me regarding all my queries in
> all my posts in the present thread.
>
> 
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Re: [PyMOL] Is it possible in Pymol to determine Individual Bond, Dissociation Energy for any Bond in organic molecules?

[Tsjerk Wassenaar]

Hi Rajib,

The bonds are determined based on a distance cutoff.

Hope it helps,

Tsjerk


On Jun 1, 2017 21:15, "Susmita/Rajib"  wrote:

How come we see structures of molecules in PyMol?
https://en.wikipedia.org/wiki/PyMOL


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Re: [PyMOL] Pymol fab ss = 4 introduces bends in the structure

[Tsjerk Wassenaar]

Hi Ahmad,

Because the chain contains prolines. These typically cause kinks in a chain.

Cheers,

Tsjerk

On Fri, Apr 7, 2017 at 2:26 PM, Ahmad Abdelzaher 
wrote:

> Hello,
>
> I used cmd.fab('sequence', ss=4) to create 1baz_linear_protein.pdb,
> where sequence is the sequence extracted from 1baz.pdb.
>
> My question is, why does Pymol introduce the bends that you can see in
> 1baz_linear_protein.pdb attached below?
>
> Regards.
>
> 
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Re: [PyMOL] Calculating center of mass for the entire protein

[Tsjerk Wassenaar]

Hi Ahmad,

The center of mass of an atom is its position. A function like
cmd.centerofmass in the context of pymol only makes sense with a selection.
E.g.:

x,y,z = cmd.centerofmass('byres n. ca')
print "COM of protein:", x, y, z

Hope it helps,

Tsjerk

On Thu, Apr 6, 2017 at 6:30 AM, Ahmad Abdelzaher 
wrote:

> Well I'm assuming the selection goes in the argument of cmd.centerofmass(),
> however, does it have to be an atom? How should I calculate the center of
> mass for an entire protein?
>
> On Thu, Apr 6, 2017 at 4:48 AM, David Hall  wrote:
>
>> It returns the x, y, and z coordinates of the center of mass as a list of
>> 3 floats, presumably in that order?
>>
>> Is there another question? The page describes the arguments and their
>> defaults so I am unsure what is lacking.
>>
>> -David
>>
>> On Apr 5, 2017, at 10:29 PM, Ahmad Abdelzaher 
>> wrote:
>>
>> I find the documentation about the python api here to be a bit lacking.
>>
>> https://pymolwiki.org/index.php/Centerofmass
>>
>> I would appreciate more info on how to use this: cmd.centerofmass()
>> returns a list of 3 floats.
>>
>> 
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>
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Re: [PyMOL] Scripting coloring method via own calculations

[Tsjerk Wassenaar]

Hey :)

Just as sidenote, the spectrum command takes arbitrary color schemes. Just
combine colors separated by underscores. Also fun in combination with
set_color :)

Cheers,

Tsjerk

On Feb 14, 2017 5:46 PM, "Robert Campbell" 
wrote:

Hello Peleg,

I think there are other possibilities, but my data2bfactor.py script will
do that for you.  You create a file with whitespace-separated columns
(spaces and/or tabs) in which each line contains:

chain resi resn name data

(i.e. chain, residue number, residue name, atom name and value to be
applied to the B-factor column).

The number can also be applied to the occupancy column instead if you want
to keep the B-factor intact.

Then you can use the spectrum command or my color_b.py script to colour
each atom according to the data value.  My color_b.py script has a few more
options than the spectrum command, including the ability to define a custom
colour gradient scheme.

You can find my scripts here:

http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

Cheers,
Rob

On Tue, 2017-02-14 17:12  +0100,  Peleg Bar-Sapir  wrote:

> Hello,
>
> I wish to write a script that will take the molecule loaded in PyMol,
> and color the molecule according to values I will calculate using the
> molecules' parameters (in the end there will be one floating number
> per atom). Then, I would like to display that using surface mode.
>
> Could anyone direct me to a way of doing that? I saw scripts coloring
> by atom type, but I'm not sure how to apply it for a molecule already
> loaded in PyMol.
>
> Best,
>
> Peleg




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Re: [PyMOL] Pseudoatom for a cavity

[Tsjerk Wassenaar]

Hi Kanika,

That's been quite a while! Nice to see you again and to see you're still
your determined self, still a bit impatient, reposting a message within a
day :)

The issue with the second question is not about center_of_mass, but about
center_of_no_mass, which is a bit harder (and I don't think there's an
import for that). You can have a look at hollow.sourceforge.net or so. If
they're channels, connected to the surface of the protein, you can also
have a look at the Mole plugin on the Pymol wiki. Alternatively, I have
some bits of code that could be forged together to get something similar
and which would allow for getting a center_of_no_mass, but I probably won't
be able to do the forging before next week.

Hope it helps,

Tsjerk

On Thu, Jan 26, 2017 at 10:14 PM, Hitesh Patel 
wrote:

> Hi,
>
> For your 2nd question:
> You can make pseudoatom at Center of mass or center of geometry (for an
> object or probably selection too) using the following script:
> https://pymolwiki.org/index.php/Center_of_mass
>
> In your case you mat try:
>
> import center_of_mass
>
> com SelectionObjectName, state=1#Create a pseudoatom representing the Object 
> COG and store it as "SelectionObjectName_COM"
>
>
>
> On Thu, Jan 26, 2017 at 4:52 AM kanika sharma 
> wrote:
>
>> Dear PyMol Users,
>>
>> I am struggling here two things.
>> 1). I want to place a pseudoatom in the charge centre of a non aromatic
>> residue, like arginine.
>> 2). Is it possible to place another pseudoatom in the centre of a cavity
>> in the protein? I am thinking how can I define the co ordinates of the
>> position where I wan t to place the pseudoatom?
>>
>> ​Thanks ​
>>
>> --
>> *Best,*
>>
>> *Kanika*
>>
>>
>> 
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>
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Re: [PyMOL] making a plane

[Tsjerk Wassenaar]

Hi Vitaly,

You have several options, but if the loops are nicely bent, the best is
probably doing PCA on the coordinate sets of the loops and calculate the
angle between the smallest eigenvectors.

Is that enough information? Do you insist on drawing the planes?

Cheers,

Tsjerk

On Jan 17, 2017 15:11, "chemocev marker"  wrote:

> Hi
> I am analyzing the dynamics of the loop and interested to define the loop
> as plane. Is there is a way in the pymol, if I can define the loop as plane
> and can measure the angle between these plane in different model??
>
> Best
> J. Vitali
>
> 
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Re: [PyMOL] default water bond lengths in PyMOL

[Tsjerk Wassenaar]

Hi Tom,

Do consider that

1. the PDB format only allows four digits for residue numbers, such that
water molecules must get the same number of there are more than  of
them.

2. periodic boundary conditions may cause water molecules to be split,
making water molecules seem to miss an atom or hydrogen atoms appear alone.

3. The residue number is read from the PDB file as is, and if a hydrogen
atom gets a different number than the other two atoms from the same water
molecule, either the program used to generate the PDB file is at fault or
the file format is somehow broken.

Hope it helps,

Tsjerk

On Tue, Jan 3, 2017 at 2:35 PM, Thomas Holder  wrote:

> Hi Tom,
>
> There is the "connect_cutoff" setting, see
> https://pymolwiki.org/index.php/connect_cutoff
>
> The bonds do not affect residue numbers in PyMOL, those should be
> unchanged and identical to your original input file.
>
> Cheers,
>   Thomas
>
> On 03 Jan 2017, at 07:07, Thomas Charles Pochapsky 
> wrote:
>
> > Hi, I exported a PDB file from PyMOL that includes explicit water from a
> > dynamics track.  However, many of the solvent molecules are either
> > doubled (same residue number for two different waters) or truncated
> > (missing a hydrogen, or a hydrogen given a separate residue number).   I
> > am assuming that PyMOL assigns bonds based on distance between atoms, is
> > there a way to minimize this?  The RCSB doesn't like my current PDB file!
> >
> > Thanks, Tom Pochapsky
>
> --
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> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
> 
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Re: [PyMOL] how to show PBC box?

[Tsjerk Wassenaar]

Hi Albert,

You can do:

show cell

Cheers,

Tsjerk

On Dec 7, 2016 8:44 PM, "Albert"  wrote:

> Hello:
>
> I am visualizing a MD simulation system in PyMOL. It contains the PBC
> information. I am just wondering how can we show the PBC box in PyMOL?
> As far as I know the PBC box can be shown in VMD using the following
> command line:
>
>  >pbc box
>
> Is there any similar command line in PyMOL?
>
> Thank you very much.
>
> Albert
>
>
> 
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Re: [PyMOL] Starting PyMol in interactive IPython Session

[Tsjerk Wassenaar]

Hi Leonhard,

I would guess it's the formatting setting of numpy in IPython. You can see
what one float really is:

print(cmd.get_coords("1xyz")[0,0])

Cheers,

Tsjerk

On Thu, Dec 1, 2016 at 1:40 PM, Leonhard Heizinger  wrote:

> I guess formatting didn't work out as i expected. So once again and
> hopefully formatted:
>
>
> Hi!
>
> I stumbled upon some odd behavior when starting PyMol in an interactive
> IPython Session.
>
> PyMol can be launched from interactive IPython like this:
>
> In [1]: import pymol
> In [2]: from pymol import cmd
> In [3]: pymol.finish_launching()
> In [4]: cmd.fetch("1xyz")
>
> So far, everything is normal.
> However, when I want to get the coordinates of the structure the following
> happens:
>
> In [5]: cmd.get_coords("1xyz")
> Out[5]:
> array([[ 41., 25., 36.],
> [ 40., 25., 35.],
> [ 39., 24., 35.], ...,
> [ 11., 26., 67.],
> [ 4., 32., 95.],
> [ 22., 45., 49.]], dtype=float32)
>
> Even though the datatype is float32 apparently the decimals got lost
> somehow.
> The coordinates of the first atom should be: 41.511  25.152  36.876
>
> Repeating the above in a normal interactive Python Session everything
> works just fine:
>
> >>> import pymol
> >>> from pymol import cmd
> >>> pymol.finish_launching()
> >>> cmd.fetch("1xyz")
> >>> cmd.get_coords("1xyz")
> array([[ 41.51100159, 25.15200043, 36.87599945],
> [ 40.9070015 , 25.55500031, 35.56299973],
> [ 39.68399811, 24.70700073, 35.10599899], ...,
> [ 11.8878, 26.97699928, 67.03900146],
> [ 4.45699978, 32.77299881, 95.16600037],
> [ 22.64100075, 45.7840004 , 49.03900146]], dtype=float32)
>
> As I use IPython only for debugging of PyMol scripts/plugins this is not a
> very big problem.
> Still I'm interested in what causes this strange behavior. Is it a
> problem/bug in IPython or in PyMol?
> Maybe someone has more insights here and can give clarity!
>
> Using Python 2.7.12, IPython 5.1.0 and PyMol 1.8.4.0
>
> Thanks!
>
> regards
> Leonhard
>
> 
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Re: [PyMOL] Scripts don't work any longer after upgrade to v1.8.4

[Tsjerk Wassenaar]

Hi Thomas,

Yeah, this one catches me off-guard now and again. Chain labels were made
case-sensitive, as assemblies sometimes become so large that more than 26
labels are required. So, you'll probably need to specify 'chain A' in stead
of 'chain a'.

Hope it helps,

Tsjerk

On Mon, Nov 28, 2016 at 3:13 PM, <reubold.tho...@mh-hannover.de> wrote:

> Dear Tsjerk,
>
> thank you for your reply.
>
>
>
> The very simple script
>
>
>
> bg_color white
>
> load 2j6o-coot-0.pdb
>
>
>
> works fine as the pdb-file is loaded and displayed as line model (as it
> should) with v.1.8.40.
>
>
>
> Adding the line
>
>
>
> select SH3, resi 2-58 and chain a
>
>
>
> yields  a selection called SH3 (as expected) but this does not contain any
> atoms. As I already wrote, the same script (plus lots of additional lines)
> works flawlessly using v1.8.07.
>
>
>
> I will be happy about any possibly helpful suggestion.
>
>
>
> Best
>
> Thomas
>
>
>
>
>
>
>
> *Von:* Tsjerk Wassenaar [mailto:tsje...@gmail.com]
> *Gesendet:* Donnerstag, 24. November 2016 15:36
> *An:* Reubold, Thomas Dr.
> *Cc:* pymol-users
> *Betreff:* Re: [PyMOL] Scripts don't work any longer after upgrade to
> v1.8.4
>
>
>
> Hi Thomas,
>
>
>
> Can you give more information? What is in the script? Is something written
> in the terminal?
>
> FWIW, I have not encountered problems, and certainly not with selections.
> My guess is that the script breaks before getting to the selection.
>
>
>
> Cheers,
>
>
>
> Tsjerk
>
>
>
> On Thu, Nov 24, 2016 at 2:13 PM, <reubold.tho...@mh-hannover.de> wrote:
>
> Hello all,
>
>
>
> after installation of Pymol v.1.8.4 on our Linux system, scripts that used
> to work fine with v.1.8.0.7 do not work anymore. Even a simple selection
> does not work.
>
> Is this a known problem? If so, is there a way to fix it?
>
> Any help is greatly appreciated.
>
>
>
> Best,
>
> Thomas
>
>
> 
> --
>
> ___
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
>
>
>
>
> --
>
> Tsjerk A. Wassenaar, Ph.D.
>



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Re: [PyMOL] Scripts don't work any longer after upgrade to v1.8.4

[Tsjerk Wassenaar]

Hi Thomas,

Can you give more information? What is in the script? Is something written
in the terminal?
FWIW, I have not encountered problems, and certainly not with selections.
My guess is that the script breaks before getting to the selection.

Cheers,

Tsjerk

On Thu, Nov 24, 2016 at 2:13 PM,  wrote:

> Hello all,
>
>
>
> after installation of Pymol v.1.8.4 on our Linux system, scripts that used
> to work fine with v.1.8.0.7 do not work anymore. Even a simple selection
> does not work.
>
> Is this a known problem? If so, is there a way to fix it?
>
> Any help is greatly appreciated.
>
>
>
> Best,
>
> Thomas
>
> 
> --
>
> ___
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>



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Re: [gmx-users] D-amino acids' force fields

[Tsjerk Wassenaar]

Hi Mijidorj,

You can see that the modified improper uses the C atom from the previous
residue (-C) in stead of the one of the own residue (C). Whether these
parameters are reliable, I can't tell.

Cheers,

Tsjerk

On Mon, Oct 24, 2016 at 10:04 AM, Mijiddorj Batsaikhan <
b.mijidd...@gmail.com> wrote:

> Hi Tsjerk,
>
> Thank you for your reply. How can I invert the improper dihedral at the CA?
> I found the D_aminoacids parameters of gromacs which supported by
> SwissParam. I compaired
>
> *ILE’s improper  of Charmm22.ff *
>
>
>
> [ impropers ]
>
> N C CA HN
>
>   C CA  +N O
>
> [ cmap ]
>
> -CN CA  C +N
>
>
>
> *DIL’s improper  of SwissParam modified Charmm22.ff *
>
> [ impropers ]
>
> N -CCA  HN
>
> C CA  +N  O
>
>  [ cmap ]
>
> -CN CA  C +N
>
>
>
> How are the swissparam parameters reliable?
>
>
> Best regards,
>
>
> Mijiddorj
>
> --
>
> Message: 5
> Date: Sat, 22 Oct 2016 10:11:50 +0200
> From: Tsjerk Wassenaar <tsje...@gmail.com>
> To: Discussion list for GROMACS users <gmx-us...@gromacs.org>
> Subject: Re: [gmx-users] D-amino acids' force fields
> Message-ID:
> <CABzE1Sh3MgjP8puni4mF9sk720JjaAyxaZZGg0W55vHiDaS4sA@mail.
> gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Mijidorj,
>
> These amino acids are chemically and topologically equivalent to their L
> counterparts. For united atom force fields you only need to invert the
> improper dihedral at the C-alpha. For atomistic force fields you don't need
> to change anything, except the CMAP stuff in Charmm for the backbone
> dihedral, and you need to reset the hydrogen position if you used pdb2gmx
> for building the topology and the hydrogens.
>
> Cheers,
>
> Tsjerk
>
> On Oct 22, 2016 8:03 AM, "Mijiddorj Batsaikhan" <b.mijidd...@gmail.com>
> wrote:
>
> > Dear users,
> >
> > Hello, Is there any force field that contains parameters of D-amino
> acids?
> > In my case I need to D-ILE and D-Phe amino acids simulation. Please,
> advice
> > me.
> >
> > Best regards,
> >
> > Mijiddorj
> > --
> > 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
>
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>
> End of gromacs.org_gmx-users Digest, Vol 150, Issue 98
> **
> --
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>
> * 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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Re: [gmx-users] D-amino acids' force fields

[Tsjerk Wassenaar]

Hi Mijidorj,

These amino acids are chemically and topologically equivalent to their L
counterparts. For united atom force fields you only need to invert the
improper dihedral at the C-alpha. For atomistic force fields you don't need
to change anything, except the CMAP stuff in Charmm for the backbone
dihedral, and you need to reset the hydrogen position if you used pdb2gmx
for building the topology and the hydrogens.

Cheers,

Tsjerk

On Oct 22, 2016 8:03 AM, "Mijiddorj Batsaikhan" 
wrote:

> Dear users,
>
> Hello, Is there any force field that contains parameters of D-amino acids?
> In my case I need to D-ILE and D-Phe amino acids simulation. Please, advice
> me.
>
> Best regards,
>
> Mijiddorj
> --
> 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.
>
-- 
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Re: [gmx-users] g_membed failure

[Tsjerk Wassenaar]

Hi Sophia,

I can't help out with mdrun -membed, but I did write a tool (insane) to
avoid just the hassle you seem to face. It builds a coarse grained system,
but that can be converted to atomistic. Depending on what exactly you need
to do, it may be trivial or less so. In either case, if you care, you can
contact me offline and we can see whether this could be a useful route for
you.

Best,

Tsjerk


On Mon, Oct 17, 2016 at 1:56 PM, Sophia Kuriakidi 
wrote:

> Hi again! Anyone with any suggestions? I am totally stuck with this...
>
> 2016-10-03 12:15 GMT+03:00 Sophia Kuriakidi :
>
> > Hi Mark,
> >
> > Yes I started with the tutorial you mentioned. From which I understood I
> > need some kind of embed.dat file and that my .mdp file has to have this
> > part:
> > integrator = md
> > energygrps = Protein_Lig (since I have a ligand and I have grouped it
> > with the protein using an index file)
> > freezegrps = Protein_Lig
> > freezedim  = Y Y Y
> > energygrp_excl = Protein_Lig Protein_Lig
> >
> > I copied this to the embed file:
> > xyinit (0.5) Resize factor for the protein in the xy dimension before
> > starting embedding.
> > -
> >
> > xyend 1.0
> > zinit 1.0
> > -
> >
> > zend 1.0
> > -
> >
> > nxy 1000
> > -
> >
> > nz 0
> > -
> >
> > rad 0.22
> > -
> >
> > pieces 1
> > -
> >
> > asymmetry no
> > -
> >
> > ndiff 0
> > -
> >
> > maxwarn 0
> > -
> > - Is that correct? And what is the appropriate command in order to
> > actually run the simulation?
> > - I am sorry if I am asking something obvious, I am completely new to
> > gromacs! Thanks!
> >
> > 2016-10-02 19:28 GMT+03:00 Mark Abraham :
> >
> >> Hi,
> >>
> >> Did you start with
> >> http://manual.gromacs.org/documentation/5.1/user-guide/mdrun
> >> -features.html#running-a-membrane-protein-embedding-simulation?
> >>
> >>
> >> Mark
> >>
> >> On Sun, 2 Oct 2016 17:13 Sophia Kuriakidi  wrote:
> >>
> >> > Hi again to all of you!
> >> > I am trying to run at last this membrane simulation. I am trying to
> use
> >> the
> >> > -membed option but I can't figure out how to. Can anyone provide me
> >> with an
> >> > example input line? e.g. gmx mdrun -membed -input file -n index.ndx -p
> >> > topol.top -o output file etc ? And also, can anyone provide with an
> >> example
> >> > embed.dat? Thanks a lot in advance!
> >> >
> >> > 2016-09-22 10:38 GMT+03:00 Sophia Kuriakidi :
> >> >
> >> > > Thank you so much Tom, I will try that!
> >> > >
> >> > > 2016-09-21 21:11 GMT+03:00 Thomas Piggot :
> >> > >
> >> > >> g_membed is now part of mdrun, so you would need to use mdrun with
> >> the
> >> > >> -membed option. From mdrun -h:
> >> > >>
> >> > >> /"The option -membed does what used to be g_membed, i.e. embed a
> >> protein
> >> > >> into a//
> >> > >> //membrane. This module requires a number of settings that are
> >> provided
> >> > >> in a//
> >> > >> //data file that is the argument of this option. For more details
> in
> >> > >> membrane//
> >> > >> //embedding, see the documentation in the user guide. The options
> -mn
> >> > and
> >> > >> -mp//
> >> > >> //are used to provide the index and topology files used for the
> >> > >> embedding."/
> >> > >>
> >> > >> Cheers
> >> > >>
> >> > >> Tom
> >> > >>
> >> > >>
> >> > >> On 21/09/16 18:36, Sophia Kuriakidi wrote:
> >> > >>
> >> > >>> Thank you for your responses!
> >> > >>>
> >> > >>> Sotirios:"Also the way this worked for me was to use an index
> file.
> >> I
> >> > >>> made
> >> > >>> an index of the prot + lig + crystallographic waters and I used it
> >> in
> >> > >>> both
> >> > >>> grompp and g_membed. In the latter I just used the group and then
> >> > >>> selected
> >> > >>> the POPC. You must also include the group's name in the mdp in
> order
> >> > for
> >> > >>> it
> >> > >>> to work."
> >> > >>> I also have grouped the ligand with the protein (but not any
> waters)
> >> > and
> >> > >>> I
> >> > >>> included the index in the mdp file.
> >> > >>>
> >> > >>> Thomas:"My guess is that you probably also have an older version
> of
> >> the
> >> > >>> g_membed program installed on your system and as you are trying to
> >> use
> >> > a
> >> > >>> more recent tpr (from version 5.1.2), this might be what is
> causing
> >> the
> >> > >>> segmentation fault. That said, if I try a tpr from GROMACS 5.0.6
> >> with
> >> > >>> g_membed 4.5.7 it does give me a warning about a mismatch of
> >> versions
> >> > so
> >> > >>> I
> >> > >>> could be wrong (but what you say you are doing shouldn't be
> >> possible)."
> >> > >>>
> >> > >>> It seems that this is the case because I am using 5.1.2. How
> could I
> >> > >>> resolve this problem? How coould I use g_membed in 5.1.2? Or how I
> >> > could
> >> > >>> alternatively insert my protein into a membrane bilayer?
> >> > >>>
> >> > >>> Thanks again!
> >> > >>>
> >> > >>>
> >> > >>>
> >> > >>> 2016-09-14 13:47 GMT+03:00 Thomas 

Re: [PyMOL] External file for writing with multiple data

[Tsjerk Wassenaar]

Hi Daniel,

Use \t in stead of \n to separate the numbers from one measurement with
tabs, in stead of newlines. Do write one newline before the new series:
f.write('\n')

However, you might want to be a bit smarter in writing code. So you're
trying to get one angle for all states?:

f = open('NE_S_C.txt','w')
angles = [ cmd.get_angle('39/NE2', '144/SG', '221/C', state) for state in
range(1,cmd.count_states()+1) ]
f.write("\t".join(["%.3f"%angle for angle in angles]))
f.write('\n')
...
f.close()

Hope it helps,

Tsjerk


On Thu, Oct 13, 2016 at 8:31 PM, Daniel Munoz Escudero 
wrote:

> Hello!
>
> I'm trying to get multiple measures of angles and distances between some
> residues for 232 states of the same molecule in PyMOL . I'm using this
> command for that:
>
> f=open('NE_S_C.txt','w')
> var1=cmd.get_angle('39/NE2', '144/SG', '221/C', 1)
> f.write("%8.3f\n"%var1)
> var2=cmd.get_angle('39/NE2', '144/SG', '221/C', 2)
> f.write("%8.3f\n"%var2)
> ...
> f.close()
>
> That creates a file called NE_S_C.txt with all my angles in one column.
> This means that in order to get the another measures, I repeat the process
> over again changing the angle command by the atoms I want. I'd like to do
> the another measures in the same script but I don't know how to print them
> in the same file separated by columns. I imagine it has something to do
> with the "f.write" part, but I just can't figure it out yet.
>
> I'd be glad if anyone could give me a help.
>
> Thank you.
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
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Re: [PyMOL] Placing pseudo atom on COM and saving it as pdb

[Tsjerk Wassenaar]

Hi Subha,

Sorry, my bad. It should've been object='pseudo' and not name='pseudo'.
Should've tested it first.

Cheers,

Tsjerk

On Wed, Oct 12, 2016 at 9:56 PM, Subha K <subhal...@gmail.com> wrote:

> Thanks David and Tsjerk for the kind reply and suggestion.
>
> I Figured a solution by combining both of your suggestions
>
> def center(selection, com=True):
>
> model = cmd.get_model(selection)
>
> xyz = np.array(model.get_coord_list())
>
> mass = [i.get_mass() for i in model.atom]
>
> xyz_m = xyz * np.array([mass]).T
>
> if com:
>
> return tuple(np.sum(xyz_m, 0)/model.get_mass())
>
> else:
>
> return tuple(np.average(xyz, 0))
>
>
> with open("./out") as f:
>
> for line in f:
>
> in_pdb_file = line.strip()
>
> print in_pdb_file
>
> cmd.load(in_pdb_file, 'tmp')
>
> COM = center('resn UNK')
>
> cmd.pseudoatom('ligCOM', pos=COM)
>
> cmd.save(in_pdb_file[:-4] + "_dummy.pdb", "all")
>
> cmd.delete('ligCOM')
>
> cmd.delete('tmp')
>
>
> @Tsjerk: Don't know why I got an error: Selector-Error: Invalid selection
> name "pseudo".
> pseudo<--
>
> Thanks again for the support.
>
> Best Regards,
> Subha
>
>
>
>
>
> On Wed, Oct 12, 2016 at 12:53 PM, Tsjerk Wassenaar <tsje...@gmail.com>
> wrote:
>
>>
>> Hi Subha,
>>
>> Probably this will get close:
>>
>> for pdb in open('./out').readlines():
>> pdb = pdb.strip()
>> cmd.load(pdb,'tmp')
>> cmd.pseudoatom('tmp',name='pseudo')
>> cmd.save(pdb[:-4]+'-pseudo.pdb','pseudo')
>> cmd.delete('tmp')
>> cmd.delete('pseudo')
>>
>> ... Just a bit too much for a oneliner ;)
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>>
>> On Wed, Oct 12, 2016 at 8:16 PM, Subha K <subhal...@gmail.com> wrote:
>>
>>> Hi There,
>>>
>>> I am looking to automate the calculation of centre of mass and placing a
>>> pseudo atom on the COM and save it as a pdb file . Going through the forum [
>>> https://sourceforge.net/p/pymol/mailman/message/34458943/] , I found
>>> some useful scripts for this, but, I am having trouble getting it done for
>>> all files in a directory. My script does what I need for the first file
>>> alone. Some looping or other is not correct. Or there could be an easy and
>>> better way to do it. I couldn't figure that out.  So, could some one please
>>> help me solve this?
>>>
>>> I have 100 files F01, F02, F100 ... in the directory dockout. I would
>>> like to calculate the COM and place a pseudo atom on the COM and save it as
>>> a pdb for all the 100 files.
>>> 'out' in the script corresponds to the list of all the 100 files.
>>>
>>> import pymol
>>>
>>> from pymol import cmd
>>>
>>> pymol.finish_launching()
>>>
>>> import numpy as np
>>>
>>> import glob
>>>
>>> import fileinput
>>>
>>> def center(selection, com=True):
>>>
>>> model = cmd.get_model(selection)
>>>
>>> xyz = np.array(model.get_coord_list())
>>>
>>> mass = [i.get_mass() for i in model.atom]
>>>
>>> xyz_m = xyz * np.array([mass]).T
>>>
>>> if com:
>>>
>>> return tuple(np.sum(xyz_m, 0)/model.get_mass())
>>>
>>> else:
>>>
>>> return tuple(np.average(xyz, 0))
>>>
>>>
>>> def GetListOfFiles (filename):
>>>
>>> l = []
>>>
>>> for line in fileinput.input( filename ):
>>>
>>> tokens = line.split( )
>>>
>>> l.append(tokens)
>>>
>>> return l
>>>
>>>
>>> def Calculate_COM (list):
>>>
>>> for i in range (len(list)):
>>>
>>> print list[i][0]
>>>
>>> X=1
>>>
>>> if (X<101):
>>>
>>> os.system("cp ./dockout/F"+ str(X).zfill(2)+ " ./lig.pdb")
>>>
>>> for pdb in glob.glob("lig.pdb"):
>>>
>>> cmd.load(pdb)
>>>
>>> COM = center('resn UNK')
>>>
>>> cmd.pseudoatom('ligCOM', pos=COM)
>>>
>>> cmd.save("complex_dummy.pdb&q

Re: [PyMOL] Placing pseudo atom on COM and saving it as pdb

[Tsjerk Wassenaar]

Hi Subha,

Probably this will get close:

for pdb in open('./out').readlines():
pdb = pdb.strip()
cmd.load(pdb,'tmp')
cmd.pseudoatom('tmp',name='pseudo')
cmd.save(pdb[:-4]+'-pseudo.pdb','pseudo')
cmd.delete('tmp')
cmd.delete('pseudo')

... Just a bit too much for a oneliner ;)

Hope it helps,

Tsjerk


On Wed, Oct 12, 2016 at 8:16 PM, Subha K  wrote:

> Hi There,
>
> I am looking to automate the calculation of centre of mass and placing a
> pseudo atom on the COM and save it as a pdb file . Going through the forum [
> https://sourceforge.net/p/pymol/mailman/message/34458943/] , I found some
> useful scripts for this, but, I am having trouble getting it done for all
> files in a directory. My script does what I need for the first file alone.
> Some looping or other is not correct. Or there could be an easy and better
> way to do it. I couldn't figure that out.  So, could some one please help
> me solve this?
>
> I have 100 files F01, F02, F100 ... in the directory dockout. I would like
> to calculate the COM and place a pseudo atom on the COM and save it as a
> pdb for all the 100 files.
> 'out' in the script corresponds to the list of all the 100 files.
>
> import pymol
>
> from pymol import cmd
>
> pymol.finish_launching()
>
> import numpy as np
>
> import glob
>
> import fileinput
>
> def center(selection, com=True):
>
> model = cmd.get_model(selection)
>
> xyz = np.array(model.get_coord_list())
>
> mass = [i.get_mass() for i in model.atom]
>
> xyz_m = xyz * np.array([mass]).T
>
> if com:
>
> return tuple(np.sum(xyz_m, 0)/model.get_mass())
>
> else:
>
> return tuple(np.average(xyz, 0))
>
>
> def GetListOfFiles (filename):
>
> l = []
>
> for line in fileinput.input( filename ):
>
> tokens = line.split( )
>
> l.append(tokens)
>
> return l
>
>
> def Calculate_COM (list):
>
> for i in range (len(list)):
>
> print list[i][0]
>
> X=1
>
> if (X<101):
>
> os.system("cp ./dockout/F"+ str(X).zfill(2)+ " ./lig.pdb")
>
> for pdb in glob.glob("lig.pdb"):
>
> cmd.load(pdb)
>
> COM = center('resn UNK')
>
> cmd.pseudoatom('ligCOM', pos=COM)
>
> cmd.save("complex_dummy.pdb", "all")
>
> os.system("mv complex_dummy.pdb complex_" + str(X).zfill(2)
> + "_dummy.pdb")
>
> os.system("rm lig.pdb")
>
> X=X+1
>
> else:
>
> break
>
> listofFiles = GetListOfFiles ("./out")
>
> print listofFiles
>
> Calculate_COM(listofFiles)
>
>
>
> Thanks,
> Subha
>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> ___
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>



-- 
Tsjerk A. Wassenaar, Ph.D.
--
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Re: [gmx-users] principal component analysis chain break (Tsjerk Wassenaar)

[Tsjerk Wassenaar]

Hi Jie,

Knowing a few words is not yet knowing the language :)
It's a bit odd that the extreme projections, or any projection for that
matter, has breaks where the original has bonds. Projecting on any subset
of principal components is a reduction of dimensionality and distances
between particles can thus only become smaller. Have you visually checked
the trajectory? What's the difference between md_backbone.xtc and
md1_backbone.xtc?

Cheers,

Tsjerk



On Sat, Oct 8, 2016 at 3:33 PM, 胡杰 <huji...@mails.ucas.ac.cn> wrote:

> Hi Tsjerk,
> Thanks for your reply. It's amazing you know my language!
> I'm sure PBC is processed, and the input trajectory is whole. But, chain
> do break in extreme projection.
> By the way could you please give me some suggestions about meaningful PCA
> output.
> Sincerely yours
> Jie
>
>
> > -原始邮件-
> > 发件人: gromacs.org_gmx-users-requ...@maillist.sys.kth.se
> > 发送时间: 2016年10月7日 星期五
> > 收件人: gromacs.org_gmx-users@maillist.sys.kth.se
> > 抄送:
> > 主题: gromacs.org_gmx-users Digest, Vol 150, Issue 35
> >
> > 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. Umbrella sampling tutorial (gozde ergin)
> >2. principal  component analysis chain break (??)
> >3. Re: principal component analysis chain break (Tsjerk Wassenaar)
> >
> >
> > --
> >
> > Message: 1
> > Date: Fri, 7 Oct 2016 10:41:36 +0200
> > From: gozde ergin <gozdeeer...@gmail.com>
> > To: gromacs.org_gmx-users@maillist.sys.kth.se
> > Subject: [gmx-users] Umbrella sampling tutorial
> > Message-ID: <db4c74ad-bc61-436b-877e-5d940f83f...@gmail.com>
> > Content-Type: text/plain; charset=utf-8
> >
> > Dear all,
> >
> > I would like to ask a question about Justin?s tutorial.
> > By using the POSRES_B, a restraint is applied on chain B in order to
> immobile it. Is the effect of this restraint removed during the WHAM?
> >
> > I want to do a similar thing by applying restraint force on the organic
> molecule on the bulk water in order to inhibit their movement inside the
> bulk. Should I consider the removing of the restraint in PMF?
> >
> > Thanks in advance.
> >
> > --
> >
> > Message: 2
> > Date: Fri, 7 Oct 2016 17:20:53 +0800 (GMT+08:00)
> > From: ?? <huji...@mails.ucas.ac.cn>
> > To: gmx-us...@gromacs.org
> > Subject: [gmx-users] principal  component analysis chain break
> > Message-ID:
> >  <612918.790a.1579e71fe59.coremail.huji...@mails.ucas.ac.cn>
> > Content-Type: text/plain; charset=GBK
> >
> > Dear Gromacs community,
> >
> > It's a question about principal  component analysis(PCA).
> > Starting with a tRNA trajectory xtc file and a reference pdb file I use
> the following command, :
> > 1. g_covar -s ref_backbone.pdb -f md_backbone.xtc
> > 2. g_anaeig -s ref_backbone.pdb -f md1_backbone.xtc -extr extreme1.pdb
> -first 1 -last 1 -nframes 30
> >
> > extreme1.pdb is what I want, but the chain of the structure break at
> some place showing from PLMOL or VMD. What's the matter. Could you please
> tell me how to get the compelet structure of extreme1.pdb.
> >
> > best regards
> > Jie
> >
> >
> >
> >
> >
> >
> >
> > --
> >
> > Message: 3
> > Date: Fri, 7 Oct 2016 11:34:46 +0200
> > From: Tsjerk Wassenaar <tsje...@gmail.com>
> > To: Discussion list for GROMACS users <gmx-us...@gromacs.org>
> > Subject: Re: [gmx-users] principal component analysis chain break
> > Message-ID:
> >  

Re: [gmx-users] principal component analysis chain break

[Tsjerk Wassenaar]

Ni hao Jie,

The extreme projections are typically pretty meaningless. But if you want
them or the more meaningful PCA output, do make sure you remove jumps over
PBC from your input trajectory and have the molecules whole/clustered.

Cheers,

Tsjerk

On Oct 7, 2016 11:21 AM, "胡杰"  wrote:

> Dear Gromacs community,
>
> It's a question about principal  component analysis(PCA).
> Starting with a tRNA trajectory xtc file and a reference pdb file I use
> the following command, :
> 1. g_covar -s ref_backbone.pdb -f md_backbone.xtc
> 2. g_anaeig -s ref_backbone.pdb -f md1_backbone.xtc -extr extreme1.pdb
> -first 1 -last 1 -nframes 30
>
> extreme1.pdb is what I want, but the chain of the structure break at some
> place showing from PLMOL or VMD. What's the matter. Could you please tell
> me how to get the compelet structure of extreme1.pdb.
>
> best regards
> Jie
>
>
>
>
>
> --
> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/
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[PyMOL] Leap Motion

[Tsjerk Wassenaar]

Hey :)

We've been playing recently with a Leap Motion controller for PyMol and are
now wondering how we would emulate a mouse click event, based on the screen
coordinates. Does anyone know?

Thanks in advance,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.
--
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Re: [gmx-users] RMSD of energy minimized structure

[Tsjerk Wassenaar]

Hi Surya,

The first part ss a warning, not an error. It also says (implicitly) that
if the molecules are not broken across PBC then there's nothing to worry
about whatsoever. So just assert that your molecules are not split over
PBC. Have a look at the trajectory. If there are frames with one part of
the structure on one side of the box and another on the other side, then
run gmx trjconv -pbc mol on the trajectory, using a .tpr file as reference
structure.

Why it doesn't give any output is impossible to say without getting more
information. Please paste the command line and the output from the terminal
in a mail and send that to us, so we can see what happened.

Cheers,

Tsjerk

On Fri, Sep 30, 2016 at 7:33 AM, Seera Suryanarayana 
wrote:

> Dear gromacs users,
>
> I have done energy minimization of clustered PDBs. When I try to
> calculate the RMSD between the minimized clustered PDB and the
> starting structure of MD simulations I got the following warning.
>
> If there are molecules in the input tarjectory file that are broken
> across periodic boundaries, they cannot be made whole (or treadted as
> whole) without you providing a run input file.
>
> I did not get what does it mean. I have not get any output for RMSD.
> Where I did wrong? Kindly tell me.
>
> Thanks in advance
> Surya
> Graduate student
> India.
> --
> 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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>



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Re: [gmx-users] question

[Tsjerk Wassenaar]

Hi Alvaro,

gmx genconf

Hope it helps,

Tsjerk

On Sep 29, 2016 4:59 PM, "ÁLVARO RODRIGO RUIZ FERNÁNDEZ" <
arr...@ug.uchile.cl> wrote:

> Dear gromacs users:
>
> How I can multiply a box full of molecules from 1x1 to 2x2 ?, I know  I can
> use Avogadro but in this case it does not work, I think for the
> periodic boundary
> conditions. Thank you very much
>
> --
>
>
>
>
>
> *Álvaro Rodrigo Ruiz Fernández Laboratorio Fisicoquimica
> MolecularDepartamento de QuímicaFacultad de CienciasUniversidad de
> Chile*Mobile:
> +56-9-75643659
> Office: +56-2-9787443
> arr...@ug.uchile.cl
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>
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Re: [gmx-users] Cluster Analysis

[Tsjerk Wassenaar]

Hi Sanket,

gmx trjconv allows writing frames based on a frame index file or using a
xvg file and threshold. Check the help of trjconv on it.

Hope it helps,

Tsjerk

On Thu, Sep 29, 2016 at 9:05 AM, Sanket Ghawali 
wrote:

> Dear, gmx-users,
>
> I performed a cluster analysis using gmx cluster. I found a total of 178
> clusters with the highest cluster having 63 members. I wish to save these
> members to a .trr or .pdb file in order to perform analysis on all these
> members as a whole and not on the representative structure which is
> generated using the -cl option.
>
> Any suggestions on how to go about doing this?
>
>
> Thanks,
>
> Sanket
> --
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>
> * Please search the archive at http://www.gromacs.org/
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>
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>



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Re: [gmx-users] Problem in PCA of protein ligand system

[Tsjerk Wassenaar]

Hi Ashutosh,

If you want to look at specific motions, like a dihedral, then just look at
that (gmx angle).

Cheers,

Tsjerk

On Mon, Sep 26, 2016 at 11:10 AM, ashutosh srivastava <ashu4...@gmail.com>
wrote:

> Dear Tsjerk
>
> Thank you so much for the detailed explanation.
> So is there a way to extract motions of only ligand, along a particular
> direction (say rotation along a dihedral in ligand) from this trajectory?
>
> Best Regards
> Ashutosh
>
> On Mon, Sep 26, 2016 at 3:52 PM, Tsjerk Wassenaar <tsje...@gmail.com>
> wrote:
>
> > Hi Ashutosh,
> >
> > To simplify this, let's do PCA of two balls on opposite ends of a stick
> I'm
> > rotating. The mean position of both ends is right at the center of
> > rotation, and the relative positions I can describe with X and Y
> > coordinates only. Now, the essence of PCA is the question 'which single
> > direction can I find that explains most of the spread of my points?'.
> Since
> > this is pure rotation, any direction is as good as any other, so I just
> > pick the horizontal line through the center. I then project my trajectory
> > onto this axis. Surprise: I find that the principal component describes
> > lengthening and contraction of my stick along the horizontal direction.
> > What? Let's check the other component, orthogonal to the first. That too
> > describes lengthening and contraction, but anticorrelated with the
> > projection onto the first. The thing is, I can't ever describe a
> > ((semi-)rigid) rotation with a single component. The projection needs to
> go
> > through the center and come out the other end, looking like a contraction
> > and expansion. Likewise, the mean structure is halfway, so it's the most
> > distorted configuration along the axis.
> >
> > I hope this clarifies your observations.
> >
> > Cheers,
> >
> > Tsjerk
> >
> > On Mon, Sep 26, 2016 at 4:32 AM, ashutosh srivastava <ashu4...@gmail.com
> >
> > wrote:
> >
> > > Dear all
> > >
> > > I have performed a 200 ns simulation on a protein ligand  (MOL) system
> in
> > > gromacs 5.1.2. Is it possible to get low frequency motions of only the
> > > ligand?
> > > When I am looking at the filtered trajectory (along PC1) after
> performing
> > > PCA on the protein+MOL the small molecule looks distorted. There is an
> > > aromatic ring in the molecule that collapses and expands during the
> > course
> > > of trajectory and the methyl groups are all collapsed throughout the
> > > trajectory.
> > > Following is the command that I am using
> > >
> > > covar -f "$TRAJ" -s "$TPR" -o
> > > ck2_go289_eigval_${first_frame}_${interval}.xvg -v
> > > ck2_go289_eigvec_${first_frame}_${interval}.trr -av
> > > ck2_go289_eigavg_${first_frame}_${interval}.pdb -l
> > > ck2_go289_eiglog_${first_frame}_${interval}.log -ascii
> > > ck2_go289_eigcovar_${first_frame}_${interval}.dat -xpm
> > > ck2_go289_eigcovar_${first_frame}_${interval}.xpm -xpma
> > > ck2_go289_eigcovara_${first_frame}_${interval}.xpm -b $first_frame -e
> > > $interval
> > >
> > > anaeig -v ck2_go289_eigvec_${first_frame}_${interval}.trr -f "$TRAJ"
> -s
> > > "$TPR" -eig ck2_go289_eigval_${first_frame}_${interval}.xvg -comp
> > > ck2_go289_eigcomp1_${first_frame}_${interval}.xvg -rmsf
> > > ck2_go289_eigrmsf1_${first_frame}_${interval}.xvg -proj
> > > ck2_go289_eigproj1_${first_frame}_${interval}.xvg -filt
> > > ck2_go289_eigfilt1_${first_frame}_${interval}.xtc -first 1 -last 1 -b
> > > $first_frame -e $interval
> > >
> > > I have also tried giving -extr option and the extracting 2000 frames
> > along
> > > the PC1, the molecule looks distorted even in this.
> > >
> > > I have tried following
> > > 1) Fitting CA and MOL and covariance analysis on CA and MOL
> > > 2) Fittting CA only and covariance on MOL only
> > > 3) Fitting MOL only and covariance on MOL only
> > > 4) Isolating the MOL trajectory separately and then performing PCA on
> > this
> > > trajectory.
> > > 5) Fitting all atoms and covariance analysis on all atoms
> (protein+MOL).
> > >
> > > Before all this I performed following PBC corrections on the
> trajectory.
> > >
> > > trjconv -s prod_0-10.tpr -f prod_0-100.xtc -o whole_100ns.xtc -pbc
> whole
> > >
> > > trjconv -s prod_0-10.tpr -f whole_100ns.xtc -o nojump_100ns.xtc -pbc
> > nojump
> > >
&g

Re: [gmx-users] Problem in PCA of protein ligand system

[Tsjerk Wassenaar]

Hi Ashutosh,

To simplify this, let's do PCA of two balls on opposite ends of a stick I'm
rotating. The mean position of both ends is right at the center of
rotation, and the relative positions I can describe with X and Y
coordinates only. Now, the essence of PCA is the question 'which single
direction can I find that explains most of the spread of my points?'. Since
this is pure rotation, any direction is as good as any other, so I just
pick the horizontal line through the center. I then project my trajectory
onto this axis. Surprise: I find that the principal component describes
lengthening and contraction of my stick along the horizontal direction.
What? Let's check the other component, orthogonal to the first. That too
describes lengthening and contraction, but anticorrelated with the
projection onto the first. The thing is, I can't ever describe a
((semi-)rigid) rotation with a single component. The projection needs to go
through the center and come out the other end, looking like a contraction
and expansion. Likewise, the mean structure is halfway, so it's the most
distorted configuration along the axis.

I hope this clarifies your observations.

Cheers,

Tsjerk

On Mon, Sep 26, 2016 at 4:32 AM, ashutosh srivastava 
wrote:

> Dear all
>
> I have performed a 200 ns simulation on a protein ligand  (MOL) system in
> gromacs 5.1.2. Is it possible to get low frequency motions of only the
> ligand?
> When I am looking at the filtered trajectory (along PC1) after performing
> PCA on the protein+MOL the small molecule looks distorted. There is an
> aromatic ring in the molecule that collapses and expands during the course
> of trajectory and the methyl groups are all collapsed throughout the
> trajectory.
> Following is the command that I am using
>
> covar -f "$TRAJ" -s "$TPR" -o
> ck2_go289_eigval_${first_frame}_${interval}.xvg -v
> ck2_go289_eigvec_${first_frame}_${interval}.trr -av
> ck2_go289_eigavg_${first_frame}_${interval}.pdb -l
> ck2_go289_eiglog_${first_frame}_${interval}.log -ascii
> ck2_go289_eigcovar_${first_frame}_${interval}.dat -xpm
> ck2_go289_eigcovar_${first_frame}_${interval}.xpm -xpma
> ck2_go289_eigcovara_${first_frame}_${interval}.xpm -b $first_frame -e
> $interval
>
> anaeig -v ck2_go289_eigvec_${first_frame}_${interval}.trr -f "$TRAJ" -s
> "$TPR" -eig ck2_go289_eigval_${first_frame}_${interval}.xvg -comp
> ck2_go289_eigcomp1_${first_frame}_${interval}.xvg -rmsf
> ck2_go289_eigrmsf1_${first_frame}_${interval}.xvg -proj
> ck2_go289_eigproj1_${first_frame}_${interval}.xvg -filt
> ck2_go289_eigfilt1_${first_frame}_${interval}.xtc -first 1 -last 1 -b
> $first_frame -e $interval
>
> I have also tried giving -extr option and the extracting 2000 frames along
> the PC1, the molecule looks distorted even in this.
>
> I have tried following
> 1) Fitting CA and MOL and covariance analysis on CA and MOL
> 2) Fittting CA only and covariance on MOL only
> 3) Fitting MOL only and covariance on MOL only
> 4) Isolating the MOL trajectory separately and then performing PCA on this
> trajectory.
> 5) Fitting all atoms and covariance analysis on all atoms (protein+MOL).
>
> Before all this I performed following PBC corrections on the trajectory.
>
> trjconv -s prod_0-10.tpr -f prod_0-100.xtc -o whole_100ns.xtc -pbc whole
>
> trjconv -s prod_0-10.tpr -f whole_100ns.xtc -o nojump_100ns.xtc -pbc nojump
>
> trjconv -s prod_0-10.tpr -f nojump_100ns.xtc -o center_mol_ur_compact.xtc
> -pbc mol -center -ur compact -n index.ndx
>
> trjconv -s prod_0-10.tpr -f center_mol_ur_compact.xtc -o
> fit_center_mol_ur_compact.xtc -n index.ndx -fit rot+trans
>
> I have done mass weighted analysis and the result is the same.
> In all the cases the MOL becomes distorted in the filtered trajectory.
> In order to visualize the trajectory I am extracting the 0th frame of the
> trajectory (CA and MOL) from the actual trajectory and then loading
> filtered trajectory on top of that.
> I also tried extracting the 0th frame of filtered trajectory and then
> loading the trajectory on top of that.
> I have looked at the actual trajectory  and the small molecule as well as
> protein is fine in that with no weird motions.
>
> What am I doing wrong here?
>
> Kindly let me know if anymore details are required.
>
> Thank you
>
> Ashutosh.
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Re: [gmx-users] Large (600k particle) semi-isotropic lipid bilayer system transformed into vacuum-separated coordinates by grompp and mdrun

[Tsjerk Wassenaar]

Hi George,

Oh, quadrants over PBC, so it just completely ruptured. It means the area
per lipid is really off in your starting structure. Where did you get it
from?

Cheers,

Tsjerk

On Sep 8, 2016 3:54 PM, "George Pantelopulos" 
wrote:

> Dear Tsjerk and Erik,
>
> Thank you for the responses!
>
> The initial structure is a complete bilayer with no vacuum in a rectangular
> box.
>
> The quadrants are due to distribution over cores/nodes. You can try EM on a
> > single core for a few steps, but it seems that the system is too
> stretched
> > anyway, so I think that won't really solve your problem.
>
>
> I had thought this as well, at first, but even running on a single
> processor for one step produces this problem -- it is for this reason that
> I think it has something to do with how GROMACS is interpreting the system.
>
> Is this not just a visualisation issue because of periodic boundary
> > conditions? Are you sure that the vacuum was not present in the input
> > coordinate file?
>
>
> I am sure that there was no vacuum present in the input coordinate file. I
> had thought that it might be a bizarre visualization issue, but after a
> very rigorous minimization and annealing from 0K, the system not only
> remains split into quadrants, but the edges of each quadrant deform from
> squares into more smoothly curved shapes. If I look at the system in VMD
> with periodic images, it seems like the outer edges of all of the quadrants
> align perfectly to make one complete bilayer with the nighboring over the
> neighboring, but the vacuums are still there.
>
> On Thu, Sep 8, 2016 at 5:42 AM, Erik Marklund 
> wrote:
>
> > Dear George,
> >
> > Is this not just a visualisation issue because of periodic boundary
> > conditions? Are you sure that the vacuum was not present in the input
> > coordinate file?
> >
> > Kind regards,
> > Erik
> >
> > > On 7 Sep 2016, at 23:58, George Pantelopulos 
> > wrote:
> > >
> > > Dear all,
> > >
> > > I have been trying to equilibrate a very large lipid bilayer system for
> > the
> > > past few days, but I have not been able to move past a very curious
> error
> > > that happens when producing a tpr file and running miminization or MD.
> > >
> > > The system ends up being split in to 8 quadrants, leaving sizeable
> > vacuums
> > > between each quadrant, and the coordinates of the system are
> transposed.
> > > I've tried to resolve this via various combinations of minimization and
> > > equilibration schemes but have had no success. At this point, I think I
> > may
> > > only turn to the mailing list for advice.
> > >
> > > Does anyone have an idea of what might be going on and how I could
> > resolve
> > > this?
> > > Thank you for the help,
> > > George Pantelopulos
> > > --
> > > Gromacs Users mailing list
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Re: [gmx-users] Large (600k particle) semi-isotropic lipid bilayer system transformed into vacuum-separated coordinates by grompp and mdrun

[Tsjerk Wassenaar]

Hi George,

How did you build the starting structure?

The quadrants are due to distribution over cores/nodes. You can try EM on a
single core for a few steps, but it seems that the system is too stretched
anyway, so I think that won't really solve your problem.

Cheers,

Tsjerk

On Sep 7, 2016 11:58 PM, "George Pantelopulos" 
wrote:

Dear all,

I have been trying to equilibrate a very large lipid bilayer system for the
past few days, but I have not been able to move past a very curious error
that happens when producing a tpr file and running miminization or MD.

The system ends up being split in to 8 quadrants, leaving sizeable vacuums
between each quadrant, and the coordinates of the system are transposed.
I've tried to resolve this via various combinations of minimization and
equilibration schemes but have had no success. At this point, I think I may
only turn to the mailing list for advice.

Does anyone have an idea of what might be going on and how I could resolve
this?
Thank you for the help,
George Pantelopulos
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Re: [gmx-users] Odd behaviour of editconf or VMD?

[Tsjerk Wassenaar]

Hi Jernej,

This is simpler in two dimensions:
Consider a hexagonal unit cell.
Draw it, together with the surrounding copies (7 hexagons total).
Now connect the central hexagon with the right horizontal neighbor, and
with the 'northeast' neighbour.
Connect these two neighbors with their other common neighbor.
You drew a parallelogram.
Check that the contents of the parallelogram is the same as that of any
hexagon.
Now think of how it works with a rhombic dodecahedron and a parallelepiped.

Cheers,

Tsjerk


On Tue, Aug 30, 2016 at 10:17 AM, Jernej Zidar 
wrote:

> Hi,
>   I am trying to solvate a small DNA molecule. Since I don't want so
> simulate more waters than what is really neccessary, I decided to try the
> dodecahdron and octahedron unit cells.
>
>   After I added waters I went to examine the resulting structures in VMD
> only to find that the octahedron and dodecahedron cells are completely
> wrong. Instead of the familiar shape (roughly a cube with trimmed edges for
> dodeachedron), I am greeted with a parallelepiped-like shape.
>
>   I tried Gromacs 5.0.7, 5.1.3, 2016 but the results seem to be always the
> same. Is this an expected behaviour? How do I "reconstitute" the resulting
> structure?
>
> Thanks,
> Jernej
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Re: [gmx-users] X Amino Acids for Building CG Structure

[Tsjerk Wassenaar]

Hi Elka,

Methyl asparagine is not known by DSSP and is not availble in Martini.
You're probably best off replacing it by asparagine:

sed '/^ATOM/s/MEN/ASN/' 1HG0.pdb > out.pdb

Cheers,

Tsjerk

On Fri, Aug 26, 2016 at 11:26 AM, Elka Firmanda  wrote:

> Hi, I just got "X" amino acids on DSSP, what does it means ? when I use the
> DSSP file to build coarse grained structure with martini 2.2 force field, I
> lost some amino acids because of this "x" amino acids on DSSP. So, how to
> build CG structure if I have this "x" amino acids ? I want to build CG
> structure for phycocyanin (1GH0) chain A-F. The "x" amino acids refers to
> modified residues called "MEN", L-Peptide Linking. Thank you for your help.
>
>
> *Elka Firmanda*
> Graduate Student
> Biophysics Division,
> ​ ​
> Department of Physics
> Faculty of Mathematics and Natural Sciences
> Bogor Agricultural University, Indonesia 16680
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Re: [gmx-users] COM-COM distance: PBC problem

[Tsjerk Wassenaar]

Hi Arnost,

When you fit with rotation the coordinates and the box are not on par
anymore. Anything you do after that tries using PBC will fail. I guess that
Plumed is trying to use the box to get the COM-COM distance. The only
(practical) solution: don't fit.

Cheers,

Tsjerk

On Aug 17, 2016 00:24, "Arnost Mladek"  wrote:

> Dear Plumed users,
>
> I've encountered one problem I'm unable to resolve. I use combination of
> Gromacs 5.0.4 and Plumed 2.1.3 and what I want is to calculate restrained
> distance between two center of masses (COMs) corresponding to two chains
> within a dimeric protein. If I let Plumed to calculate COM-COM distances
> "on-the-fly" (ie. during the simulation), I get correct results, let say
> distances in the interval of (4,9 ; 5.3) with the average value of 5.1 nm
> corresponding to the minimum of the restraining potential.
>
> If I use Plumed as a stand-alone software and calculate the distances
> along the trajectory via "plumed driver --mf_xtc trajectory.xtc --plumed
> pl.dat", I get the same correct results. Up to this point, no problem.
>
> However if I fit (rot+trans) the trajectory frames to chain-A using
> GROMACS trjconv command (trjconv -f trajectory.xtc -s reference.tpr -o
> fitted_trajectory.xtc -fit rot+trans -center) and then run the plumed
> driver to calculate the distances from the fitted trajectory there are huge
> jumps of several nm. It is obvious that the problem is somehow associated
> with PBC and "WHOLEMOLECULES STRIDE=1 ENTITY0=protein" command within the
> plumed script is unable to resolve it. I've tried various trajectory
> transformations as suggested on GROMACS web page (http://www.gromacs.org/
> Documentation/Terminology/Periodic_Boundary_Conditions), like "-pbc mol
> -ur compact", "-pbc whole", "-pbc nojumps", etc. but nothing helped. As I
> am unable to get the COM-COM distances using GROMACS alone, I am not sure
> whether the problem relates to GROMACS or Plumed.
>
> Thank you so much for your help.
>
> AM
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Re: [gmx-users] Box dimensions variation

[Tsjerk Wassenaar]

Hi Yasser,

Probably you're using semi-isotropic pressure coupling, which you should
only do if you have a membrane like structure aligned with the XY plane (or
a somewhat stiffish wire like structure aligned along z).

Cheers,

Tsjerk

On Wed, Aug 10, 2016 at 3:52 PM, Yasser Almeida Hernández <
yasser.almeida.hernan...@chemie.uni-hamburg.de> wrote:

> Hi all,
> I have a coarse grained system (membrane protein/water/ions/polymer) in a
> 20 nm box, running during 2 us. During the run the box dimensions varies
> significantly, increasing in Z and decreasing in X and Y (identically) to
> almost the same XY dimensions of my protein.
>
> Any ideas?
>
> Thanks in advance
>
> --
> Yasser Almeida Hernández
> PhD student
> Institute of Biochemistry and Molecular Biology
> Department of Chemistry
> University of Hamburg
> Martin-Luther-King-Platz 6
> 20146 Hamburg
> Germany
> +49 40 42838 2845
> yasser.almeida.hernan...@chemie.uni-hamburg.de
> office: Grindelallee 117, room 250c
>
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Re: [gmx-users] Magic number error in XTC file

[Tsjerk Wassenaar]

Hi Gayathri,

For the XTC file you used only a selection of atoms to write out. The TRR
file always contains everything. With the conversion from TRR to XTC make
sure to write the same selection as is in the other XTC files.

Hope it helps,

Tsjerk

On Thu, Jul 28, 2016 at 7:36 AM, GAYATHRI S  wrote:

> Dear all,
>
> I had a run an MD simulation (GROMACS 4.6.6) which was abruptly stopped
> due to power failure. Then, I extended the simulation using the commands:
>
> $tpbconv -s production.tpr -o production_2.tpr -untill 5
>
> $mdrun -v -s production_2.tpr -deffnm production_2 -cpi production.cpt
>
> Then, when the simulation was complete, I renamed the output files of the
> first simulation as production_1. Next, I wanted to merge the trajectories
> of both the runs; hence, I used the following command:
>
> $trjcat -f production_1.xtc production_2.xtc -o production.xtc -overwrite
>
> Fatal Error: Magic number error in XTC file
>
> When I went through the mailing list archive, I found that this error is
> shown when the trajectory is corrupted.
> So, I used gmxcheck to find out which of the trajectories were corrupted.
> I discovered that production_1.trr did not show any error, but
> production_1.xtc showed the same error.
> Hence, I used trjconv to make a new production_1.xtc
>
> $trjconv -f production_1.trr -o production_1.xtc
>
> Again, I checked the new file for error using gmxcheck. When everything
> looked good, I tried the trjcat command again, only to get the following
> error
>
> Fatal error: Different numbers of atoms (584885/9944) in the files.
>
> Please suggest how to resolve the issue.
>
> Thank you.
>
> Regards,
> Gayathri.
>
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Re: [gmx-users] Cutting simulatio box

[Tsjerk Wassenaar]

Hi Faezeh,

It helps if you begin with stating your objective and context, rather than
asking for the solution to what you think is the critical issue in what you
think is the solution of what you think your problem is. If you ask for
water in a slab, you get an answer for water in a slab. Apparently you want
a specific water molecule. Then you ask for a 'phase', which usually
involves many particles, but it appears that it's that same single
molecule? That changes matters quite a bit, as whatever you're going to
look at is going to be pretty noise.

What is your objective?

Cheers,

Tsjerk

On Mon, Jul 18, 2016 at 1:10 PM, Faezeh Pousaneh <fpoosa...@gmail.com>
wrote:

> Hi Tsjerk,
>
> That option seemed complicated in my case, as my previous discussion with
> Mark (titled: g_select, only 'one' water within z>=10 and z<=10.1). Since I
> need the energy between 'single' molecule at specific 'z' of the box
> indicating the phases .
>
> So I think my given way is easier, but not sure if the reruns goes like the
> original simulations?
>
>
> Best regards
>
>
> On Mon, Jul 18, 2016 at 12:57 PM, Tsjerk Wassenaar <tsje...@gmail.com>
> wrote:
>
> > Hi Faezeh,
> >
> > You could use gmx select to make groups for the two phases and then
> perform
> > a rerun with these new groups as energy_grps. That would give you the
> > within and between group energies.
> >
> > Hope it helps,
> >
> > Tsjerk
> >
> > On Jul 18, 2016 12:49 PM, "Faezeh Pousaneh" <fpoosa...@gmail.com> wrote:
> >
> > Hi,
> >
> > I have a Phase-separation in my simulation result. I need to find energy
> > between molecules at each phase. Can I cut the box into small boxes, each
> > having one phase, and then by extension the run (with similar setting as
> > original) obtain the energies at each phase?
> >
> > Thank you!
> > Best regards
> > --
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Re: [gmx-users] Cutting simulatio box

[Tsjerk Wassenaar]

Hi Faezeh,

You could use gmx select to make groups for the two phases and then perform
a rerun with these new groups as energy_grps. That would give you the
within and between group energies.

Hope it helps,

Tsjerk

On Jul 18, 2016 12:49 PM, "Faezeh Pousaneh"  wrote:

Hi,

I have a Phase-separation in my simulation result. I need to find energy
between molecules at each phase. Can I cut the box into small boxes, each
having one phase, and then by extension the run (with similar setting as
original) obtain the energies at each phase?

Thank you!
Best regards
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Re: [gmx-users] Facing poblem in enegy minimization step

[Tsjerk Wassenaar]

Hi Swagata,

That's when the potential energy remains high and/or the maximum force is
still large.

Cheers,

Tsjerk

On Sat, Jul 16, 2016, 12:27 Swagata Patra <swagatal...@gmail.com> wrote:

> Thank you very much Tsjerk.
>
> Actually I searched in google and somewhere i read that it might be because
> either the topology is bad or the starting structure has clashes that
> cannot be adequately addressed using EM or because of improper
> parametrization.
>
>
> On Sat, Jul 16, 2016 at 3:43 PM, Tsjerk Wassenaar <tsje...@gmail.com>
> wrote:
>
> > Hi Swagata,
> >
> > That's not a problem. You should be fine running a simulation, given the
> > potential energy of the system. Check the archives for more elaborate
> > comments on this matter. And please check the archives/google before
> > posting questions. We like breaking our heads over new, tough issues, and
> > don't really fancy chewing on old matters, which come up on a monthly
> > basis.
> >
> > Cheers,
> >
> > Tsjerk
> >
> > On Jul 16, 2016 12:08 PM, "Swagata Patra" <swagatal...@gmail.com> wrote:
> >
> > > Hello evryone,
> > >
> > > I am tying to do simulation of a protein-ligand complex. But in energy
> > > minimization step I am facing the following problem:
> > >
> > >
> > > Stepsize too small, or no change in energy.
> > > Converged to machine precision,
> > > but not to the requested precision Fmax < 1
> > > You might need to increase your constraint accuracy, or turn
> > > off constraints alltogether (set constraints = none in mdp file)
> > >
> > > writing lowest energy coordinates.
> > >
> > > Steepest Descents converged to machine precision in 37686 steps,
> > > but did not reach the requested Fmax < 1.
> > > Potential Energy  = -1.8866049133e+06
> > > Maximum force =  1.60313450715092e+02 on atom 1628
> > > Norm of force =  1.38085169243203e+00
> > >
> > > i prepared the ligand topology file using ATB. There I was getting an
> > > warning like : "This molecule contains non-standard atom types not
> > included
> > > in the standard GROMOS 53A6 and 54A7 forcefield. To use these atom
> types
> > > the internal GROMACS parameter files must be updated. These can be
> > > downloaded using the link below. So I donloaded the filee and also
> modify
> > > it in topology file.
> > >
> > > Please help me to overcome the problem.
> > > I am attaching the topology file.
> > >
> > > --
> > > Swagata Patra
> > > M.Tech (Biotech)
> > > JRF
> > > IIT Guwahati
> > >
> > > --
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> > > posting!
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>
>
>
> --
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> M.Tech (Biotech)
> JRF
> IIT Guwahati
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Re: [gmx-users] Facing poblem in enegy minimization step

[Tsjerk Wassenaar]

Hi Swagata,

That's not a problem. You should be fine running a simulation, given the
potential energy of the system. Check the archives for more elaborate
comments on this matter. And please check the archives/google before
posting questions. We like breaking our heads over new, tough issues, and
don't really fancy chewing on old matters, which come up on a monthly basis.

Cheers,

Tsjerk

On Jul 16, 2016 12:08 PM, "Swagata Patra"  wrote:

> Hello evryone,
>
> I am tying to do simulation of a protein-ligand complex. But in energy
> minimization step I am facing the following problem:
>
>
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 1
> You might need to increase your constraint accuracy, or turn
> off constraints alltogether (set constraints = none in mdp file)
>
> writing lowest energy coordinates.
>
> Steepest Descents converged to machine precision in 37686 steps,
> but did not reach the requested Fmax < 1.
> Potential Energy  = -1.8866049133e+06
> Maximum force =  1.60313450715092e+02 on atom 1628
> Norm of force =  1.38085169243203e+00
>
> i prepared the ligand topology file using ATB. There I was getting an
> warning like : "This molecule contains non-standard atom types not included
> in the standard GROMOS 53A6 and 54A7 forcefield. To use these atom types
> the internal GROMACS parameter files must be updated. These can be
> downloaded using the link below. So I donloaded the filee and also modify
> it in topology file.
>
> Please help me to overcome the problem.
> I am attaching the topology file.
>
> --
> Swagata Patra
> M.Tech (Biotech)
> JRF
> IIT Guwahati
>
> --
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Re: [gmx-users] System blowing up in final MD run

[Tsjerk Wassenaar]

Hi Deep,

What force field? What system? How many cores? Did you try running on one?
What error? Did pdb2gmx or grompp give any warnings?

Cheers,

Tsjerk

On Wed, Jul 13, 2016 at 5:44 AM, Deep Bhattacharya 
wrote:

> Hello,
> My system is blowing up for the protein carbohydrate solvent complex. I
> have attached the mdp file below. The NPT and NVT were in good accordance
> to tutorial listed by Justin. 'Please help me solve the issue.
> title   = CD44  complex MD simulation
> ; Run parameters
> integrator  = md; leap-frog integrator
> nsteps  = 1000; 0.001 * 100 = 1 ps (10 ns)
> dt  = 0.001 ; 1 fs
> ; Output control
> nstxout = 5 ; suppress .trr output
> nstvout = 5 ; suppress .trr output
> nstenergy   = 5; save energies every 1000.0 ps
> nstlog  = 5  ; update log file every 1000.0 ps
> nstxtcout = 5
> xtc_precision = 1000
> energygrps  = Protein LIG SOL
> ; Bond parameters
> continuation= yes   ; first dynamics run
> constraint_algorithm = lincs; holonomic constraints
> constraints = all-bonds ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter  = 1 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
> ; Neighborsearching
> ns_type = grid  ; search neighboring grid cells
> nstlist = 1;
> rcoulomb= 0.81
> rvdw= 0.81
> coulombtype = Cut-off   ; Particle Mesh Ewald for long-
> vdwtype= cut-off
> rlistlong  = 1.4
> epsilon-rf = 61
> rlist  = 0.8
> ; Temperature coupling is on
> tcoupl = nose-hoover; modified Berendsen thermostat
> tc-grps   =Protein_LIG Water_and_ions   ; two coupling groups - more
> accurate
> tau_t = 2.0  2.0; time constant, in ps
> ref_t = 300  300; reference temperature, one for each group, in K
> ; Pressure coupling is on
> pcoupl= Parrinello-Rahman; Pressure coupling on in NPT
> pcoupltype= isotropic; uniform scaling of box vectors
> tau_p= 6.0; time constant, in ps
> ref_p= 1.0; reference pressure, in bar
> compressibility = 4.5e-5; isothermal compressibility of
> water, bar^-1
> refcoord_scaling= com
> ; Periodic boundary conditions
> pbc = xyz   ; 3-D PBC
> ; Dispersion correction
> DispCorr= EnerPres  ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel = no; assign velocities from Maxwell distribution
>
>
> Steepest Descents converged to Fmax < 1000 in 573 steps
> Potential Energy  = -7.58370311664555e+05
> Maximum force =  9.53896348096555e+02 on atom 1163
> Norm of force =  2.44608995242254e+01
>
>
> *Deep S Bhattacharya*
>
> *Graduate Research Assistant*
>
> Mohs Biomedical Imaging & Nanotechnology Group
>
> Pharmaceutical Sciences
>
> *University of Nebraska Medical Center*
>
> 4018 Eppley Science Hall  |  Omaha, NE 68198-6805
>
> office 402.559.4349  | cell 402.906.1640
>
> deep.bhattacha...@unmc.edu.deep.bhattacharya...@gmail.com
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Re: [PyMOL] ray command

[Tsjerk Wassenaar]

Hi Mohsen,

So raytracing is indeed not available in the educational version. I find
this a bit strange, as I regarded the educational version the
least-changed-with-respect-to-the-original (say 0.99), which did have
raytracing available. Also, I like students to give me reports with pretty
pictures, and would argue that 'educational' should also allow some basic
raytracing.

Alternatives are:

- getting an academic license
- compile from source (or get from a repository)
- export the scene and ray trace in a different program.

Hope it helps,

Tsjerk

On Tue, Jul 12, 2016 at 10:16 AM, Mohsen Chitsaz <
mohsen.chit...@flinders.edu.au> wrote:

> Hi Pymol users,
>
>
>
> The “ray command” is not working in my Educational version of Pymol. It
> seems that educational version does not allow to use this command.
>
>
>
> Does anyone have a solution for this please?
>
>
>
> Your reply is very much appreciated.
>
>
>
> Cheers
>
> Mohsen
>
>
> --
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Re: [PyMOL] ray command

[Tsjerk Wassenaar]

Hi Mohsen,

What happens? What error do you get?

Best,

Tsjerk
On Jul 12, 2016 10:46 AM, "Mohsen Chitsaz" 
wrote:

Hi Pymol users,



The “ray command” is not working in my Educational version of Pymol. It
seems that educational version does not allow to use this command.



Does anyone have a solution for this please?



Your reply is very much appreciated.



Cheers

Mohsen

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Re: [gmx-users] Position restraints for water during EM

[Tsjerk Wassenaar]

Hi Gregory,

There is no default position restraint during EM. Of course, one wouldn't
expect them to move much and one would expect the local energy minimum to
be rather close to the initial position, if you used an equilibrated water
box to set up the system.

Cheers,

Tsjerk
On Jul 8, 2016 08:38, "Gregory Poon"  wrote:

> Hello all:
>
> I would like to know where it is specified that waters are
> position-restrained during energy minimization.  I can see that there is a
> #ifdef block for restraining the water, but I don't know where it is
> actually called.  The .mdp files I use for EM (which I adapted from
> tutorials) do not make DEFINE statements, and I also don't see any DEFINE
> statements for DPOSRES_WATER in the mdout.mdp file.
>
> Thanks in advance for pointing me in the right direction.
>
> Gregory
>
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Re: [gmx-users] PCA and gmx analyze

[Tsjerk Wassenaar]

Hi Suniba,

Don't look at the cosine content. It doesn't convey anything useful. If you
want to know more, I've posted more lengthy remarks about it before.

Cheers,

Tsjerk
On Jun 27, 2016 1:11 PM, "Sun Iba"  wrote:

> Hello Users and experts
>
> My system details:
> Force field: GROMOS 43a1
>
> Gromacs version: 5.0
>
> OS: Ubuntu 14.0
>
> Simulation time: 200 ns
>
> No. of eigenvectors and eigenvalues in gmx covar and gmx anaeig: 378
> Protein backbone was used for least square fit and covariance analysis. I
> am trying to monitor protein folding in the presence of a small molecule
> and interested in using first 2 PCs for FEL. Also, I am interested in
> assessing if the system is not converged. When I tried to analyze the
> cosine content of my eigenvectors with gmx analyze i get following results:
>
> Command line:
>   gmx analyze -f proj.xvg -ac autocorr.xvg -msd msd.xvg -cc coscont.xvg -av
> average.xvg -ee errest.xvg -b 10 -e 15
>
> Read 1 sets of 5001 points, dt = 10
>
>  std.
> dev.  relative deviation of
>   standard-
> cumulants from those of
> set  average deviation  sqrt(n-1)  a
> Gaussian distribition
>
> cum. 3   cum. 4
> SS1  -2.974823e+00   1.492213e-01   2.110308e-03   0.3810.401
>
>
>
> 2500, time=25000
>
>
> *Cosine content of set 1 with 0.5 periods: 1.14745e-05*
>
>
>
> Set   1:  err.est. 0.0155418  a 0.693315  tau1 12.3624  tau2 856.505
>
> Back Off! I just backed up autocorr.xvg to ./#autocorr.xvg.1#
>
> Can anyone help me with cosine content of set 1? I dont understand it.
> According to manual the cosine content should be closer to 1. Is that value
> (* 1.14745e-05) *considered to be closer to 1?
> .
>
> Thank You
> Suniba
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Re: [gmx-users] wrap only in XZ?

[Tsjerk Wassenaar]

Hi Albert,

Rotate the system 90 degrees and use PBC in xy only.

Cheers,

Tsjerk
On Jun 26, 2016 9:04 AM, "Albert"  wrote:

> Hello:
>
> I've got a membrane protein system and I would like the water and ions
> only wrap in XZ direction. Currently, they can also wrap at Z direction. I
> am just wondering how can we prevent them wrap at Z direction?
>
> Thank you very much.
>
> Albert
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Re: [gmx-users] least-squares fitting the second structure on the reference structure

[Tsjerk Wassenaar]

Hi Qasim,

If you fit a trajectory, with trjconv -fit rot+trans, then each frame is
fit onto the reference.

Hope it helps,

Tsjerk

On Tue, Jun 21, 2016 at 11:12 AM, Qasim Pars  wrote:

> Dear users,
>
> From GROMACS online manual:
> gmx confrms computes the root mean square deviation (RMSD) of two
> structures after least-squares fitting the second structure on the first
> one.
>
> My question is how GROMACS does least-squares fitting the second structure
> (each frame of trajectory) on the first one (reference structure)? It
> calculates the least-squares fitting of the second structure and the first
> one seperately?
>
> Thanks for your helps.
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Re: [gmx-users] Insufficient memory (128 GB) for ensemble entropy calculation with gmx covar/gmx anaeig

[Tsjerk Wassenaar]

Hi David,

And why the number of frames?

Cheers,

Tsjerk

On Tue, Jun 21, 2016 at 9:52 AM, David van der Spoel 
wrote:

> On 21/06/16 09:40, Qasim Pars wrote:
>
>> Dear David,
>>
>> Could you please more explain each term of the formula you said?
>>
>> Formula=The number of atoms (N * 3)^2 times number of frames times 4 bytes
>>
>> Why square the number of atoms?
>>
> Because we build a matrix of all degrees of freedom.
>
>>
>> Why 4 bytes?
>>
> The size of a floating point number. Unless you built gromacs in double
> precision.
>
>
>> Thanks in advance
>>
>> On 21 Jun 2016, at 09:39, David van der Spoel 
>>> wrote:
>>>
>>> On 21/06/16 08:11, Billy Williams-Noonan wrote:
   Sorry, the original post provides an example of the -dt flag with
 100ps
 intervals.

>>> You can calculate how much space you need by number of atoms (N * 3)^2
>>> times number of frames times 4 bytes.
>>>
>>> Do you select just your biomolecule?
>>>
>>>
 On 21 June 2016 at 16:10, Billy Williams-Noonan <
 billy.williams-noo...@monash.edu> wrote:

 Thank you for your reply. :)
>
>   My main problem is with gmx covar which does not have a -skip flag.
> As
> you can see from the OP I have tried the -dt flag with 250ps
> intervals.  It
> still crashes due to insufficient memory.  It also crasses with 5000ps
> intervals, giving me just 20ps of frames to work with for the whole
> ensemble.
>
> Billy
>
> On 21 June 2016 at 16:00, David van der Spoel 
> wrote:
>
> On 21/06/16 07:34, Billy Williams-Noonan wrote:
>>>
>>> Hi Gromacs Users,
>>>
>>>   I am running g_mmpbsa.py to calculate the binding enthalpy of a
>>> cyclic
>>> peptide in a drug target.  At the same time I am trying to generate
>>> ensemble estimates for entropy for the protein, ligand and complex.
>>> By
>>> using these two variables I aim to get an idea of the Gibbs free
>>> energy
>>> of
>>> binding.
>>>
>>>   My system for the complex and the protein is some 50,000 atoms
>>> large,
>>> with just over 3000 atoms belonging to the proteins, and the rest of
>>> the
>>> system is water and ions, to make up a physiological concentration of
>>> NaCl.  These are approximate estimates and not exact numbers.  gmx
>>> covar
>>> seems to keep crashing every time I try to use it to generate
>>> eigenvectors
>>> for the system.  These are the commands I am using:
>>>
>>>
>>> "  gmx covar -f md.xtc -s md.tpr -v md.eigenvec.trr -av average.pdb
>>> -ascii
>>> covar -xpm covar -xpma covara -l covar -o md.eigenval.xvg -dt 100
>>> -pbc
>>> yes
>>> << EOF
>>> 0
>>> 0
>>> EOF  "
>>>
>>> and:
>>>
>>> "  gmx anaeig -v md.eigenvec.trr -f md.xtc -s md.tpr -entropy -temp
>>> 300 >
>>> out.entropy.schlitter  "
>>>
>>>
>>>   I have tried this on a local machine with 16GB of RAM and on a
>>> cluster
>>> using one core and a node's worth of RAM (128GB).  I do not have
>>> access
>>> to
>>> more RAM than this.  Any ideas on how I can stop my calculation from
>>> crashing due to insufficient memory?
>>>
>> Use the -skip or -dt flags.
>>
>>
>>   Kind regards,
>>>
>>>   Billy
>>>
>>
>> --
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Re: [gmx-users] SOLVED: Re: helixorient, jacobi iteration or junk output...?

[Tsjerk Wassenaar]

Hi Phil,

Did you write all atoms to the trajectory or only a group? Does the
reference structure match the trajectory? The Jacobi error usually occurs
when there is a mismatch, and the route via a PDB file is consistent with
that.

Cheers,

Tsjerk

On Sat, Jun 18, 2016 at 3:25 AM, Phil Dude  wrote:

> Hi,
>
> OK after some messing around, it appears the bug is in the use of.xtc as
> input.
>
>
> I dumped the C-alpha atoms as a .pdb (using trjconv) and then the .ndx
> selection is "0 0". Seems to complete without crashing or the jacobi error.
>
> Now, we need to fix the .xvg format to be something useful. Everyone
> reporting they just get a line, is the format being slightly off, and
> the data being perhaps more complex than is easy to import without some
> work?
>
> Cheers
>
> P.
>
> On 06/17/2016 05:58 PM, Phil Dude wrote:
> > Hi,
> >
> > I am trying to use helixorient to analyse my trajectories, using gromacs
> > 5.0.2
> >
> > It appears to fail on:
> >
> > Program gmx, VERSION 5.0.2
> > Source code file:
> > /build/gromacs-dDhxvD/gromacs-5.0.2/src/gromacs/linearalgebra/nrjac.c,
> > line: 163
> >
> >
> > If I allow it to process more than one frame. I have tried to reduce my
> > data set and index files to contain SOLEY a single helix and the index
> > file just the C-alpha atoms.
> >
> > Is this tool in active development?
> >
> > Is there specific way in which the tool is supposed to be used?
> >
> > I seem to have run out of ideas!
> >
> > Regards
> >
> > PHiL
> >
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Re: [gmx-users] Calculating Eccentricity

[Tsjerk Wassenaar]

Hi Sanket,

You probably want the clustering routine of trjconv. And then calculate the
principal axes of the micelle. The instantaneous value does not mean much,
but a an average non-zero eccentricity would suggest with a greater extent
than without peptide would suggest an effect. Note that you do need the
control experiment, because the eccentricity cannot have a mean value of
zero in a dynamic system.

Cheers,

Tsjerk


On Wed, Jun 15, 2016 at 8:28 AM, Sanket Ghawali 
wrote:

> Dear gmx user
>
> I am performing a MD simulation of peptides in sds for 100ns. After the
> completion of my production I am unable to remove the periodic boundary
> condition.
> I wanted to Calculate the eccentricity of the SDS micelle after 100ns, does
> the periodic boundary condition affect my eccentricity result ?
> Is it necessary first to remove the pbc effect and then calculate
> Eccentricity.
> Also does the high eccentricity value obtained after 100ns tell me that the
> micelle is distorted and the peptide has some activity?
>
> Thank you.
> Sanket
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Re: [gmx-users] to neutralize the system

[Tsjerk Wassenaar]

Hi Qasim,

Not only should you neutralize the system, but you should add additional
ions too. The behaviour of charged side chains which can find a partner ion
from solution is different from those that can't. You won't see any
problems, but the results will be affected. Not coming across any problems
is not good quality assurance in simulations.

Cheers,

Tsjerk
On Jun 15, 2016 00:01, "Qasim Pars"  wrote:

Dear gmx users,

I am confused on below questions:

1) Is it necessary to neutralize a protein without ligand?  Does the PME
method work with a charged protein correctly?

2) I have done lots of MD simulations at a charged complex structure
(protein+ligand) with the PME method using GROMACS. I haven't come across
with any problems because of the charge of the system. It means that the
PME method works at a charged complex system properly. In spite of that, do
you think that I need to neutralize a charged complex system?

Can anyone comment on above questions?

Cheers,

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Re: [gmx-users] Is charmm GUI ideal for membrane building

[Tsjerk Wassenaar]

Hi Sotirios,

What membrane and what time scale are you talking about? Complex membranes
may take microseconds to equilibrate.

Cheers,

Tsjerk
On Jun 13, 2016 09:30, "Sotirios Dionysios I. Papadatos" <
si.papada...@edu.cut.ac.cy> wrote:

> I might be wrong here, but energy is supposed to converge. Maybe you want
> to verify something else?
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Tsjerk
> Wassenaar <tsje...@gmail.com>
> Sent: Monday, June 13, 2016 7:44:03 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Is charmm GUI ideal for membrane building
>
> Hi Amit,
>
> What membrane and what time scale are you talking about? Complex membranes
> may take microseconds to equilibrate.
>
> Cheers,
>
> Tsjerk
> On Jun 13, 2016 06:13, <amitbe...@chemeng.iisc.ernet.in> wrote:
>
> > Hello everyone,
> > I built a lipid membrane in Charmm-GUI and tried to equilibrate it in
> > GROMACS 5.1.2. But the total energy goes on decreasing. Is it normal or
> > should I try building the membrane by other methods.
> >
> > Thanks in advance,
> >
> > Amit Behera
> >
> > --
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Re: [gmx-users] Is charmm GUI ideal for membrane building

[Tsjerk Wassenaar]

Hi Amit,

What membrane and what time scale are you talking about? Complex membranes
may take microseconds to equilibrate.

Cheers,

Tsjerk
On Jun 13, 2016 06:13,  wrote:

> Hello everyone,
> I built a lipid membrane in Charmm-GUI and tried to equilibrate it in
> GROMACS 5.1.2. But the total energy goes on decreasing. Is it normal or
> should I try building the membrane by other methods.
>
> Thanks in advance,
>
> Amit Behera
>
> --
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> dangerous content by MailScanner, and is
> believed to be clean.
>
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Re: [gmx-users] How many times should I do Umbrella Sampling

[Tsjerk Wassenaar]

Hi Agnivo,

In addition to the remarks of Andre, if you can show that another US run on
the same system gives pretty much the same result, then you can present
that as proof of the robustness, and it is futile to do three more,
especially if you have convergence and sufficient overlap. You can
highlight the regions where the difference is largest, and can probably
argue why a difference of X in those regions will not invalidate your
conclusions.

Another possibility is to construct the PMF using the first 50%, 60%, 70%,
80%, 90%, and 100% of the simulations. Then you can show how the profile
converges and how longer simulations wouldn't help (provided they
wouldn't). That is sort of the same as extending, and I think it's better
than repeating.

Cheers,

Tsjerk
On Jun 9, 2016 4:15 AM, "André Farias de Moura"  wrote:

> Hi Agnivo,
>
> good overlap of histograms and a smooth pmf cannot be taken as evidences of
> convergence. Some people would extend the simulations to prove that pmf
> does not change appreciably with further sampling, while other people (as
> your reviewer) would do extra independent pmf profiles to prove that all
> profiles agree within a certain precision (and then the best profile would
> be the average, preferably the Jarzynski average of those profiles). I
> prefer the later, though I think that it is a matter of taste, as long as
> you are able to demonstrate that a thorough sampling has been reached. How
> many extra replicas you should do is something you should validate for your
> system (5 replica is somewhat arbitrary).
>
> Maybe you might want to take a look at our papers dealing with that:
>
> J. Phys. Chem. B, 2013, 117 (24), pp 7324–7334
> Phys. Chem. Chem. Phys., 2015,17, 3820-3831
>
> I hope it helps.
>
> Andre
>
>
> On Wed, Jun 8, 2016 at 8:38 PM, Agnivo Gosai 
> wrote:
>
> > Hello Users
> >
> > I did one umbrella sampling on a trajectory generated by a pulling
> > simulation. There were 45 windows in my US and the PMF curve converged
> with
> > good overlap of histograms.
> >
> > However the reviewer is asking for 5 US simulations from 5 pulling sims
> on
> > the same system and wants the average free energy from those 5 sims. I
> was
> > assuming that the bootstrap calculation takes care of the averages.
> >
> > If there is a proper explanation / reply for the reviewer please share.
> >
> > I am unsure as it takes a long time to do one US sim. I did another one
> for
> > the same system but for a different pulling simulation and the result is
> > almost identical. I think as my pulling code is same I am getting more or
> > less same result.
> >
> >
> > Thanks & Regards
> > Agnivo Gosai
> > Grad Student, Iowa State University.
> > --
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>
>
>
> --
> _
>
> Prof. Dr. André Farias de Moura
> Department of Chemistry
> Federal University of São Carlos
> São Carlos - Brazil
> phone: +55-16-3351-8090
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Re: [gmx-users] Saving time of the coordinates for conformational entropy

[Tsjerk Wassenaar]

Hi Qasim,

The RMSD is not good for assessing convergence, especially if it goes above
0.5 nm.

Cheers,

Tsjerk


On Wed, Jun 8, 2016 at 8:48 PM, Qasim Pars  wrote:

> Dear users,
>
> I have simulated a protein with simulation time of 200 ns and saving the
> coordinates at every 40 ps. Conformational entropy (~4500 kJ/mol K)
> obtained by Quasiharmonic approach using gmx covar and gmx anaeig tools is
> not consistent with literature (~2500 kJ/mol K). Whereas, the RMSD results
> show that system has reached the convergence.
> Do you think that the problem is the long saving time (every 40 ps) of
> coordinates? Maybe I should redo the simulation with saving the coordinates
> at every 10 ps to capture all conformatinal states of protein during the
> simulation? I am not sure that the saving the coordinates at every 10 ps
> will be enough to get the conformational entropy consisted with literature?
>
> Thanks for any suggestions.
>
>
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Re: [gmx-users] PCA problems

[Tsjerk Wassenaar]

Hey :)



>  That usually gives a fitted ensemble that more closely retains the
> original RMSD values between all pairs of structures.
>

This should read: ... a fitted ensemble of which the sum of the traces of
all pairwise inner product matrices is closer to minimal.
The pairwise RMSDs (and their sum) remain what they are.

Cheers,

Tsjerk

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Re: [gmx-users] PCA problems

[Tsjerk Wassenaar]

Hi James,

That's silly! Ambiguous means that the same structure can have multiple
solutions in a fit. The fit to a single reference structure (with more than
three atoms) is never ambiguous. Can never, by definition!

Now if you have two reference structures at hand, and they have (quite)
different structures, then fitting on one may give a different ensemble
from fitting on the other. The fit is not consistent, and the inconsistency
is worse for flexible molecules. Different ensembles will mean different
correlations, thus giving different principal components.

Progressive fitting does not solve the problem. In fact, progressive
fitting _is_ ambiguous. Let's say we have a series of conformations ABCAC.
Then we  fit C once to B, which was fitted to A, and later we have C fitted
to A, which was fitted to the previous C. Note that in practice the
situation will be much worse as we can approach a certain configuration
from many sides. Using B as reference will yield a fit that is different
from using A as reference, so the structure C will have two different
orientations in the resulting ensemble. Hence, the fit is ambiguous.

For structured proteins, the difference will not matter much. However, in
long trajectories there may be an added contribution (drift) of the
orientation.

Hope it helps,

Tsjerk

On Wed, Jun 8, 2016 at 5:33 PM,  wrote:

> Thanks Tsjerk,
>
> Isn't the progressive fit supposed to rotate everything back into the same
> orientation without having to worry about inferring that orientation from
> a reference structure that doesn't align well? Each configuration should
> in theory align well to its predecessor all the way back to the starting
> structure (which is what I'd usually take as a reference anyway).
>
> The original note I was thinking of says as follows:
>
> '''Before a PCA, all structures should be superimposed onto a common
> reference
> structure. This can be problematic for very flexible systems such as
> peptides,
> where the fit may be ambiguous, leading to artificial structural
> transitions. In
> certain cases, such problems may be alleviated by using a progressive fit,
> where
> each structure is superimposed onto the previous one. It is also important
> to note
> that when results of different PCAs are to be compared with each other,
> then
> each individual PCA should be based on the same reference structure used
> for
> superposition.'''
>
> Please could you explain further what it is I have misunderstood.
>
> Also would you say a progressive fit is a bad idea for more structured
> proteins?
>
> Many thanks
> James
>
> > Hi James,
> >
> > 'Spurious alignment' is the dependence of the resulting ensemble on the
> > reference structure. Unfortunately, that's not solved by a progressive
> > fit.
> > Rather, in a progressive fit, the same configuration can have multiple
> > orientations, based on the previous structures, which is also problematic
> > when you're trying to understand spatial correlations between atoms
> within
> > their reference frame.
> >
> > Cheers,
> >
> > Tsjerk
> >
> > On Wed, Jun 8, 2016 at 9:27 AM,  wrote:
> >
> >> Dear Teresa,
> >>
> >> That sounds like a periodic boundary issue to me. It could be fixed by
> >> using a tpr instead of a gro as the gmx covar manual says "All
> >> structures
> >> are fitted to the structure in the structure file. When this is not a
> >> run
> >> input file periodicity will not be taken into account." Alternatively if
> >> you don't have a tpr you could use gmx trjconv first with -pbc whole or
> >> -pbc nojump.
> >>
> >> I also remember reading (I think it was in the Hayward and de Groot
> >> review
> >> 2008) that fitting peptides to a reference structure can cause spurious
> >> alignments. I don't know if this is also related to what you're seeing
> >> but
> >> it might be worth using gmx trjconv again with-fit progressive then use
> >> -nofit in gmx covar.
> >>
> >> Best wishes
> >> James
> >>
> >> > Dear GROMACS community
> >> >
> >> > I am trying to complete a PCA analysis of my peptide adsorbed to a
> >> > surface. However when I use :
> >> >
> >> > gmx covar -s trajectory.gro  -f md_golp_vacuo.xtc
> >> >
> >> > and select the protein for both the least squares fit and covariance
> >> > calculation, followed by
> >> >
> >> >
> >> > gmx anaeig -s trajectory.gro -f md_golp_vacuo.trr -filt filter1.gro
> >> > -first 1 -last 1 -skip 100
> >> >
> >> > and I select the peptide for the least squares and covariance
> >> > calculation
> >> >
> >> > My peptide is now broken up into pieces. Is this right?
> >> >
> >> >
> >> >
> >> > Best
> >> > Teresa
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Re: [gmx-users] RMSD question

[Tsjerk Wassenaar]

Hi Teresa,

You probably want to try clustering, and then check the percentage of
bound/unbound structures in the clusters you get. Just the RMSD won't tell
you much.

Cheers,

Tsjerk

On Wed, Jun 8, 2016 at 11:30 AM, ingram  wrote:

> Dear GROMACS community,
>
> I am trying to identify the number of unique peptide structures on the
> surface of a slab. If I simply calculate the RMSD between the protein atoms
> in each frame of the trajectory this tells me nothing about how these
> structures compare on the surface as the constraint of the surface will not
> be taken into account. Can anyone suggest what I should use as a reference
> structure and what I structures I should compare when calculating the RMSD
>
>
> BEst
>
> Teresa
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Re: [gmx-users] PCA problems

[Tsjerk Wassenaar]

Hi James,

'Spurious alignment' is the dependence of the resulting ensemble on the
reference structure. Unfortunately, that's not solved by a progressive fit.
Rather, in a progressive fit, the same configuration can have multiple
orientations, based on the previous structures, which is also problematic
when you're trying to understand spatial correlations between atoms within
their reference frame.

Cheers,

Tsjerk

On Wed, Jun 8, 2016 at 9:27 AM,  wrote:

> Dear Teresa,
>
> That sounds like a periodic boundary issue to me. It could be fixed by
> using a tpr instead of a gro as the gmx covar manual says "All structures
> are fitted to the structure in the structure file. When this is not a run
> input file periodicity will not be taken into account." Alternatively if
> you don't have a tpr you could use gmx trjconv first with -pbc whole or
> -pbc nojump.
>
> I also remember reading (I think it was in the Hayward and de Groot review
> 2008) that fitting peptides to a reference structure can cause spurious
> alignments. I don't know if this is also related to what you're seeing but
> it might be worth using gmx trjconv again with-fit progressive then use
> -nofit in gmx covar.
>
> Best wishes
> James
>
> > Dear GROMACS community
> >
> > I am trying to complete a PCA analysis of my peptide adsorbed to a
> > surface. However when I use :
> >
> > gmx covar -s trajectory.gro  -f md_golp_vacuo.xtc
> >
> > and select the protein for both the least squares fit and covariance
> > calculation, followed by
> >
> >
> > gmx anaeig -s trajectory.gro -f md_golp_vacuo.trr -filt filter1.gro
> > -first 1 -last 1 -skip 100
> >
> > and I select the peptide for the least squares and covariance
> > calculation
> >
> > My peptide is now broken up into pieces. Is this right?
> >
> >
> >
> > Best
> > Teresa
> > --
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Re: [gmx-users] PCA problems

[Tsjerk Wassenaar]

Hi Teresa,

No, the peptide should not be broken. Did you remove jumps over PBC?
The peptide will probably be severely distorted by filtering, though.

Cheers,

Tsjerk


On Wed, Jun 8, 2016 at 8:49 AM, ingram  wrote:

> Dear GROMACS community
>
> I am trying to complete a PCA analysis of my peptide adsorbed to a
> surface. However when I use :
>
> gmx covar -s trajectory.gro  -f md_golp_vacuo.xtc
>
> and select the protein for both the least squares fit and covariance
> calculation, followed by
>
>
> gmx anaeig -s trajectory.gro -f md_golp_vacuo.trr -filt filter1.gro -first
> 1 -last 1 -skip 100
>
> and I select the peptide for the least squares and covariance calculation
>
> My peptide is now broken up into pieces. Is this right?
>
>
>
> Best
> Teresa
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Re: [gmx-users] Simulating a protein dimer

[Tsjerk Wassenaar]

Hey :)

There's a suggested workflow on the Gromacs site:

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Cheers,

Tsjerk
On Jun 7, 2016 11:50 PM,  wrote:

> I solved the problem by using an em.tpr with pbc nojump for my dimers. pbc
> whole takes the monomers as whole units and does as you described. pbc
> nojump starting from md.tpr like I'd normally do didn't work because
> partial boundary crossings had happened before the production md.
>
> > I encountered similar problem after simulating a pentameric model of
> > protein. It was solved by applying pbc whole in gmx trjconv.
> >
> > Sent from my iPhone
> >
> >> On 07-Jun-2016, at 7:49 pm, Biplab Ghosh 
> wrote:
> >>
> >> Dear Gromacs Users,
> >>
> >> I am trying to simulate a protein dimer using Gromacs-5.1.2. Gromacs
> >> completed successfully
> >> but when analysing the trajectories, the monomers are flying apart and
> >> coming back again!
> >>
> >> I used the following Gromacs commands/options:
> >>
> >> gmx trjconv -s protein-md.tpr -f protein-md.xtc  -pbc mol -center -ur
> >> compact -o protein-md-center.xtc
> >>
> >> gmx trjconv -s protein-md.tpr -f  protein-md-center.xtc -fit rot+trans
> >> -o
> >> protein-md-center-fit.xtc
> >>
> >> gmx trjconv -s protein-processed.gro -f protein-md-center-fit.xtc -o
> >> protein-movie.pdb -tu ns -dt 1
> >>
> >>
> >> I would really appreciate any help on this.
> >>
> >> Regards,
> >> Biplab.
> >>
> >> --
> >> "Simplicity in life allows you to focus on what's important"
> >> --
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Re: [gmx-users] projection on the first two eigenvectors obtained from the concatenated trajectories

[Tsjerk Wassenaar]

Hi Qasim,

Didn't see the plot :) Now I did, and it's not strange. It's a dimer? I
think that the one/two ligand cases may be quite similar, but they look
different, because they're mirrored. You can imagine a line through the
center of wt and the joint center of the other two and see what I mean.
Also, the first and second eigenvectors as you got them are still mixed.
The difference between the wt/ligand case can be best described by that
line between the centers as I just sketched.

I found the tutorial of Lindsay Smith on PCA quite good. Google knows where
it is.

Cheers,

Tsjerk
On Jun 8, 2016 2:04 AM, "Qasim Pars" <qasimp...@gmail.com> wrote:

> Dear Tsjerk,
>
> Then my plot is not strange?
> You said that "The overall mean of any set of projections lies at the
> origin". Could you please suggest me any material that explains what you
> said? I couldn't find anything about that on google.
>
> Cheers,
>
> On 7 June 2016 at 15:15, Tsjerk Wassenaar <tsje...@gmail.com> wrote:
>
> > Hi Qasim,
> >
> > What makes you think that they should start at 0,0 ?
> > The overall mean of any set of projections lies at the origin.
> > PCA is a pretty powerful and advanced technique, that requires quite a
> bit
> > of thinking in the preparation, the execution and the interpretation.
> > Please do read plenty of tutorial material dealing with it, not only from
> > the perspective of simulations, but also from the linear algebra view.
> >
> > Cheers,
> >
> > Tsjerk
> >
> > On Tue, Jun 7, 2016 at 2:09 PM, Qasim Pars <qasimp...@gmail.com> wrote:
> >
> > > Dear gmx users,
> > >
> > > I have simulated three systems. The projection of each individual
> > > trajectory on the first two eigenvectors obtained from the concatenated
> > > trajectory is strange because each projection should start at (0,0)
> > points
> > > or near (0,0). Please have a look at the plot
> > > https://www.dropbox.com/s/3jrlkdwbv4csccq/pca.png?dl=0
> > >
> > > Why the projections do not start at (0,0) points or near (0,0)? Can
> > anyone
> > > of you tell me where I might have made a mistake?
> > >
> > > In order to remove jumps across the box of each trajectory I used the
> gmx
> > > trjconv -pbc nojump. The other commands are below:
> > >
> > > trjcat -f wt.xtc one-ligand.xtc two-ligands.xtc -o merged.xtc -cat
> > >
> > > gmx covar -f merged.xtc -s wt.pdb
> > >
> > > gmx anaeig -f wt.xtc -s wt.pdb -v eigenvec.trr -2d wt.xvg -first 1
> -last
> > 2
> > > gmx anaeig -f one-ligand.xtc -s wt.pdb -v eigenvec.trr -2d
> one-ligand.xvg
> > > -first 1 -last 2
> > > gmx anaeig -f two-ligands.xtc -s wt.pdb -v eigenvec.trr -2d
> > two-ligands.xvg
> > > -first 1 -last 2
> > >
> > > Cheers,
> > >
> > > --
> > > Qasim Pars
> > > --
> > > Gromacs Users mailing list
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> > >
> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
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>
>
>
> --
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Re: [gmx-users] DPPC-DOTAP Mixed Lipid Bilayer

[Tsjerk Wassenaar]

Hi Nidhin,

It looks like you have a version of insane that still builds oleyl with
five beads. It should be four as 'CDCC' like you did for building the
topology. So you also need to remove the C5 beads and shift the D to
position two. Then you should be set to make/simulate your bilayers.

Cheers,

Tsjerk
On Jun 8, 2016 6:47 AM, "Nidhin Thomas"  wrote:

> Hi Dr. Wassenaar,
>
> I have edited insane.py using the following command.
>
> "DOTAP": (moltype, " -   -   -   -   -  NC3 GL1 GL2 C1A C2A D3A C4A C5A
> -  C1B C2B D3B C4B C5B  - “),
>
> I replaced NC3 of DOPC with ‘-‘ and PO4 of DOPC with NC3 as you suggested.
> Then I used insane.py to create the mixed bilayer of DPPC-DOTAP.
>
> I also created the .itp file for DOTAP using lipid-martini-itp.py code.
>
> I used the command given below to create the .itp file.
>
> python lipid-martini-itp.py -o martini_v2.0_DOTAP_01.itp -alname DOTAP
> -alhead 'C' -allink 'G G' -altail 'CDCC CDCC’
>
> Is this the correct method to create the bilayer and .itp file? Is there
> anything more that I should do?
>
> Thanks a lot for helping me to create the bilayer.
>
> Regards,
>
> Nidhin Thomas
> University of Houston
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Re: [gmx-users] DPPC-DOTAP Mixed Lipid Bilayer

[Tsjerk Wassenaar]

Hi Nidhin,

As I understand, it would simply mean copying the line of DOPC, change the
name to DOPAT, replace NC3 by a dash (-) and replace PO4 with NC3.

Cheers,

Tsjerk
On Jun 7, 2016 6:21 PM, "Nidhin Thomas" <nidhin.thomas0...@gmail.com> wrote:

> Hi Dr. Wassenaar,
>
> Thanks a lot for offering help to create DPPC-DOTAP bilayer model.
>
> I have gone through the research paper on insane method.
>
> I understand that I may be able to create DOTAP template by taking the
> fatty acids and linkers from DOPC lipid template and link them with NC3
> head group.
>
> But I don’t know whether this is correct or how to execute this in
> insane.py.
>
> Could you please guid me through the process of creating the template?
>
> Thanks,
>
> Nidhin Thomas
> University of Houston
>
>
> > On Jun 7, 2016, at 12:51 AM,
> gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote:
> >
> > Send gromacs.org_gmx-users mailing list submissions to
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> > To subscribe or unsubscribe via the World Wide Web, visit
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> >
> > 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: Position restrain of of different chain in fibril
> >  structure (Md. Imrul Reza Shishir)
> >   2. cannot output all the structures of one cluster (Zhenyu Meng)
> >   3. Re: Non-bonded energy (ABANTIKA PAL)
> >   4. Re: gmx gangle selections help (Teemu Murtola)
> >   5. Re: DPPC-DOTAP Mixed Lipid Bilayer (Tsjerk Wassenaar)
> >   6. How to fix the ends of the protein? (Seera Suryanarayana)
> >
> >
> > --
> >
> > Message: 1
> > Date: Tue, 7 Jun 2016 12:32:14 +0900
> > From: "Md. Imrul Reza Shishir" <imrul.reza.shis...@gmail.com>
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] Position restrain of of different chain in
> >   fibril  structure
> > Message-ID:
> >   

Re: [gmx-users] Dodecahedron Box size and Appropriate number of SOL molecules

[Tsjerk Wassenaar]

Hi Apramita,

No restrictions. You're in charge. To get a correct density, you'll need to
equilibrate with pressure coupling.

Cheers,

Tsjerk



On Tue, Jun 7, 2016 at 1:08 PM, Apramita Chand 
wrote:

> Hey,
>  Thanks a lot Tsjerk for your advice regarding box size. You've mentioned
> that we could take a box size which lets us add a bit more water than
> needed and we could delete some molecules. So can I use genbox to add water
> and then delete any number of water molecules to reach my target solvent
> number? I'm using a box size of say 2.9 and I want a box of peptide,5 urea
> and 494 water molecules. genbox adds 566 water molecules. Do I have to
> simply delete the extra water molecules and that would be okay after
> equilibration?
> So there is basically no restriction that only a fixed  number of water
> molecules  should be present in a particular box,right?
>
>
> Regards,
> Apramita Chand
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Re: [gmx-users] projection on the first two eigenvectors obtained from the concatenated trajectories

[Tsjerk Wassenaar]

Hi Qasim,

What makes you think that they should start at 0,0 ?
The overall mean of any set of projections lies at the origin.
PCA is a pretty powerful and advanced technique, that requires quite a bit
of thinking in the preparation, the execution and the interpretation.
Please do read plenty of tutorial material dealing with it, not only from
the perspective of simulations, but also from the linear algebra view.

Cheers,

Tsjerk

On Tue, Jun 7, 2016 at 2:09 PM, Qasim Pars  wrote:

> Dear gmx users,
>
> I have simulated three systems. The projection of each individual
> trajectory on the first two eigenvectors obtained from the concatenated
> trajectory is strange because each projection should start at (0,0) points
> or near (0,0). Please have a look at the plot
> https://www.dropbox.com/s/3jrlkdwbv4csccq/pca.png?dl=0
>
> Why the projections do not start at (0,0) points or near (0,0)? Can anyone
> of you tell me where I might have made a mistake?
>
> In order to remove jumps across the box of each trajectory I used the gmx
> trjconv -pbc nojump. The other commands are below:
>
> trjcat -f wt.xtc one-ligand.xtc two-ligands.xtc -o merged.xtc -cat
>
> gmx covar -f merged.xtc -s wt.pdb
>
> gmx anaeig -f wt.xtc -s wt.pdb -v eigenvec.trr -2d wt.xvg -first 1 -last 2
> gmx anaeig -f one-ligand.xtc -s wt.pdb -v eigenvec.trr -2d one-ligand.xvg
> -first 1 -last 2
> gmx anaeig -f two-ligands.xtc -s wt.pdb -v eigenvec.trr -2d two-ligands.xvg
> -first 1 -last 2
>
> Cheers,
>
> --
> Qasim Pars
> --
> Gromacs Users mailing list
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>



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Re: [gmx-users] Fwd: Dodecahedron Box size and Appropriate number of SOL molecules

[Tsjerk Wassenaar]

Hi Apramita,

First of all, your box diameter should be the length of the peptide plus 2,
with a minimum of 2.8. Otherwise, the peptide will be able to interact
directly with its periodic image.

The solvent is typically added by overlaying a box of pre-equilibrated
solvent and deleting all molecules that are outside the target box or
overlap with those present in the target box. If you want control over the
amount of water added, the easiest way is to take a box size which gives a
bit more water than you need, and delete a number of molecules. The
equilibration steps will make things right for you.

There are no precautions or problems with rhombic dodecahedron boxes.
They're the best for many purposes.

Cheers,

Tsjerk


On Tue, Jun 7, 2016 at 8:20 AM, Apramita Chand 
wrote:

> Dear Experts,
>  I am trying to simulate a peptide in urea-water mixture in GROMOS53a6 ff.
> Since rvdW=1.4 in this case, any box length less than ~2.8 gives errors
> like
> ERROR 1 [file topol.top, line 133]:
>   ERROR: The cut-off length is longer than half the shortest box vector or
>   longer than the smallest box diagonal element. Increase the box size or
>   decrease rvdw.
>  Hence I've to choose a box size of 2.9angstroms and above.
> I'm trying to ascertain the number of water molecules that are needed to
> solvate the system.
> Say I've to solvate a box of my peptide and 5 urea molecules...I can't just
> go ahead with whatever number of solvent molecules I have in mind,can
> I?-maxsol and -nmol options wouldn't give the optimum number of water
> molecules actually needed to solvate the box.
> So,is the number of SOL molecules which are added by genbox completely
> acceptable? Is it calculated on the basis of volume or something else? Any
> particular rules or formulae as to how many molecules can fit inside the
> rhombic dodecahedron ?
>
> I would also like some advice on what precautions are to be taken or any
> special changes in parameters that need to be done when handling
> dodecahedron boxes.
>
>
> Regards,
> Apramita Chand
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Re: [gmx-users] DPPC-DOTAP Mixed Lipid Bilayer

[Tsjerk Wassenaar]

Hi Nidhin,

Insane allows you to build lipids from the command line. Alternatively,
it's pretty easy to add DOTAP to insane, using the templates inside. If you
feel you need a hand with that, let me know.

Cheers,

Tsjerk
On Jun 7, 2016 12:21 AM, "Nidhin Thomas" 
wrote:

> Hi GROMACS Users,
>
> I would like to create a mixed bilayer of DPPC and DOTAP lipids for
> research. I usually use charm-gui or insane.py to create a mixed bilayer.
> But I could not find DOTAP listed in either of these lists. When I searched
> online, I got a mixed bilayer system for DMPC & DPPC lipids and the
> parameter file for DOTAP lipid from
> http://www.softsimu.net/downloads.shtml.
>
> My objective is to create mixed lipid bilayer system with various
> percentage of DOTAP lipids. In addition, I have to create a bilayer with
> one DOTAP in each layer and remaining DPPC lipids. Can anyone please guide
> me to create these lipid bilayers? It would be great if someone could
> explain, how to create these mixed bilayers from scratch.
>
> Thanks a lot everyone!,
>
> Nidhin Thomas
> University of Houston
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Re: [gmx-users] error installing trj_cavity with gromacs

[Tsjerk Wassenaar]

Hi Williams,

It looks like you didn't set the Gromacs include directory. What
command/procedure did you use to compile?

Cheers,

Tsjerk
On Jun 3, 2016 21:25, "Williams Miranda" 
wrote:

> Dear GROMACS users
> I use gromacs 4.6.5, then, I downloaded trj_cavity v1.1 for installation.
> But I am getting this error:
>
>
> src/AtomReaderGromacs.cpp:13:19: fatal error: xtcio.h: No such file or
> directory
>
>
> Actually, the AtomReaderGromacs.cpp includes the following files:
>
> include "xtcio.h"
> include "trajana.h"
> include "statutil.h"
> include "typedefs.h"
> include "smalloc.h"
> include "copyrite.h"
> include "tpxio.h"
> include "names.h"
> include "gmx_random.h"
> include "gmx_ana.h"
> include "filenm.h"
> include "macros.h"
> include "pbc.h"
> include "vec.h"
> include "xvgr.h"
> include "pdb2top.h"
>
> However, only typedefs.h is found in my GROMACS library. What could I do
> to fix this problem?
> Regards
>
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Re: [gmx-users] allosteric effect

[Tsjerk Wassenaar]

Hi Qasim,

Do you assume MWC or KNF like allostery, and conformational based, dynamics
based or mixed?

Cheers,

Tsjerk

On Fri, Jun 3, 2016 at 2:54 AM, Qasim Pars  wrote:

> Dear gmx users,
>
> The protein I have simulated over 200 ns with GROMACS is dimer and shows
> positive allostery. Based on experimental data, the second ligand of
> protein has greater binding affinity than the first ligand. I would like to
> prove the positive allosteric effect of protein by some analyses. But I
> really don't know which analyses helps me to investigate/look into the
> allosteric effect. Could you please suggest me some useful analyses to
> investigate the allosteric effect (except for RMSD, RMSF)? I have
> simulations for singly liganded, doubly liganded and apo state.
>
> Thanks a lot, in advance.
> --
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Re: [gmx-users] Cross correlation map of residues

[Tsjerk Wassenaar]

Hi Qasim,

The plot you refer to is the result of NMA on C-alpha only. So g_covar
-xpma using only C-alpha atoms should come close. You might also want to
try the g_correlation tool mentioned earlier on the list, but again with a
selection of only C-alpha atoms.

Cheers,

Tsjerk

On Fri, Jun 3, 2016 at 1:50 AM, Qasim Pars  wrote:

> Dear gmx users,
>
> I need to get the cross correlation map of all residues belonging to a
> protein (like this figure
> http://thegrantlab.org/bio3d/vignettes/Bio3D_nma/figures/ex1C-dccmplot.png
> ).
> Is there any tool to get such a plot with GROMACS?
>
> By the way, gmx covar -xpma gives the cross correlation for each atom pair
> but it is not what I want.
>
> Any suggestions will be appreciated.
>
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Re: [gmx-users] protonation of histidines

[Tsjerk Wassenaar]

Hi Irem,

pdb2gmx checks the hydrogen bonding network and decides which form of His
fits best.

Cheers,

Tsjerk
On Jun 2, 2016 17:20, "Irem Altan"  wrote:

> Hi,
>
> When I process a .pdb structure using pdb2gmx, how does Gromacs add
> hydrogens to the histidine residues? I see that in the processed structure,
> some histidines have their NE2 atom protonated, while some have ND1
> protonated. How does Gromacs decide which nitrogen to protonate?
>
> Best,
> Irem
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Re: [PyMOL] post-processing of pdb ensemble

[Tsjerk Wassenaar]

Hi James,

This should do:

for i in range(65:78): cmd.alter("bound_combined and chain
%s"%chr(i+1),'chain="%s"'%chr(i))

Cheers,

Tsjerk


On Wed, May 25, 2016 at 5:00 PM, James Starlight 
wrote:

> More precisely I would like to know how to script in pymol the
> following alteration fo the chains for the multi-chain pdb
>
>
> PyMOL>alter (bound_combined and chain B), chain="A"
>  Alter: modified 5157 atoms.
> PyMOL>alter (bound_combined and chain C), chain="B"
>  Alter: modified 2285 atoms.
> PyMOL>alter (bound_combined and chain D), chain="C"
>  Alter: modified 2778 atoms.
> PyMOL>alter (bound_combined and chain E), chain="D"
>  Alter: modified 1560 atoms.
> PyMOL>alter (bound_combined and chain F), chain="E"
>  Alter: modified 1114 atoms.
> PyMOL>alter (bound_combined and chain G), chain="F"
>  Alter: modified 950 atoms.
> PyMOL>alter (bound_combined and chain H), chain="G"
>  Alter: modified 895 atoms.
> PyMOL>alter (bound_combined and chain I), chain="H"
>  Alter: modified 843 atoms.
> PyMOL>alter (bound_combined and chain J), chain="I"
>  Alter: modified 806 atoms.
> PyMOL>alter (bound_combined and chain K), chain="J"
>  Alter: modified 574 atoms.
> PyMOL>alter (bound_combined and chain L), chain="K"
>  Alter: modified 501 atoms.
> PyMOL>alter (bound_combined and chain M), chain="L"
>  Alter: modified 511 atoms.
> PyMOL>alter (bound_combined and chain N), chain="M"
>  Alter: modified 433 atoms.
>
>
> So each step we rename chain i to the i-1 name within given model :)
>
> Thanks!
>
> J.
>
> 2016-05-23 19:11 GMT+02:00 James Starlight :
> > Dear Pymol users!
> >
> > After some post-processing of MD simulation I have extracted from the
> > traejctory several snapshots as individual pdbs which I need to
> > 1-  to re-assign information regarding chain letters (which was lost
> > after some operations on pdbs)  for all of those structures assuming
> > that within each of these pdbs residues are ordered correctly e.g from
> > (1-104 which
> > should be chain A) than from 1-100 (it should be chain B), than 1-70
> > (in should be chain C) etc.
> >
> > 2- superimpose and combine all of the pdbs within one model in nmr-like
> format.
> >
> > Thanks for help!
> >
> > James
>
>
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Re: [gmx-users] Using pdb2gmx with martini (coarse-grained) model to assign termini charges

[Tsjerk Wassenaar]

Hi Sourav,

For Martini there's the conversion script martinize, which has an option
-nt to suppress putting charges on termini.

This is not really a Gromacs question, and it's better to post Martini
related questions on the forum at http://cgmartini.nl

Cheers,

Tsjerk
On May 24, 2016 23:35, "Justin Lemkul"  wrote:

>
>
> On 5/24/16 5:33 PM, Sourav Ray wrote:
>
>> Hello
>>
>> Thanks for your answer, I presume pdb2gmx needs some force-field
>> definitions to work, anyway, can I assign charges selectively to certain
>> atom  number? Let me know if it is feasible, I searched the forums but
>> couldn't find anything specific.
>>
>>
> Try some MARTINI tutorials; IIRC topology generation is not typically done
> via pdb2gmx.
>
> -Justin
>
> Regards
>> Sourav
>>
>> On Wed, May 25, 2016 at 2:48 AM, Mark Abraham 
>> wrote:
>>
>> Hi,
>>>
>>> If you've already arranged your own termini, then you can choose "None"
>>> from the options pdb2gmx presents.
>>>
>>> Mark
>>>
>>> On Tue, May 24, 2016 at 11:15 PM Sourav Ray 
>>> wrote:
>>>
>>> Hello

 I am trying to put selective charges on the termini, I am getting stuck

>>> at
>>>
 the initial stage where I am supposed to mention the force-field needed.

>>> As
>>>
 martini termini differ from conventional ones, I am unable to bypass
 NH3+
 or COO- termini options at the start and end respectively as there is no
 appropriate force-field option present there. Please let me know if

>>> anyone
>>>
 has a workaround.

 Regards
 Sourav
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>
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Re: [gmx-users] find out tpx version of tpr

[Tsjerk Wassenaar]

Hey :)

If you just have the .tpr and you don't want to use Gromacs' tools, you can
use python:

python -c 'import struct; print
"".join(struct.unpack(100*"c",open("YOUR-TPR-HERE").read(100)))'

(Python 2, mind you).

Cheers,

Tsjerk

On Mon, May 23, 2016 at 11:33 AM, Mark Abraham 
wrote:

> Hi,
>
> Mdrun reports it to the log file, or likely gmx dump and gmx check also do
> so.
>
> Mark
>
> On Mon, 23 May 2016 11:12 Sabine Reisser  wrote:
>
> > Hello,
> >
> > how can I find out the tpx version of a tpr file?
> >
> > Cheers
> > Sabine
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Re: [gmx-users] g_cluster analysis

[Tsjerk Wassenaar]

Hi Sapna,

How should we know how many clusters you should have?

A cutoff of 0.2 is quite tight, and will give many clusters. Whether that's
what you want/need or whether that's meaningful/helpful for your goals is
something you should consider. We don't know what you're trying or doing.

Cheers,

Tsjerk

On Mon, May 23, 2016 at 9:03 AM, SAPNA BORAH  wrote:

> Dear all,
>
> I am trying to use g_cluster protocol to get representative snapshots of
> the simulations. I have concatenated 9 set of simulations and run g_cluster
> for the same. The result shows a total of 198 clusters.
>
> Is this correct?
>
> Following is the command I have used:
>
> g_cluster -s models.gro -f concatenated.xtc -dm rmsd-matrix.xpm -o
> clusters.xpm -sz cluster_size.xvg -clid cluster-id-over-time.xvg -cl
> all_clusters.pdb -cutoff 0.2 -method gromos
>
> Thanks in advance.
>
> Regards,
> Sapna.
>
> Sapna Mayuri Borah
> c/o Dr. A. N. Jha
> Research student
> Tezpur University,
> India
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Re: [gmx-users] WARNING no output error while dumping structures with trjconv from MD.trr

[Tsjerk Wassenaar]

Oh, you don't want to dump one frame! You want the frames beyond 25 ns. So
don't use -dump at all. You'll only get one frame though, using a spacing
of 1 ns.

Cheers,

Tsjerk
On May 21, 2016 13:53, "Tsjerk Wassenaar" <tsje...@gmail.com> wrote:

> Hi Antara,
>
> You indicate you want the frame at 27ns (-dump 27000), but that's not in
> the trajectory. The suggestion is to ask for a frame that is in, like -dump
> 25290
>
> Cheers,
>
> Tsjerk
> On May 21, 2016 13:09, "Antara mazumdar" <antara.mazum...@igib.in> wrote:
>
> Dear gromacs users,
>
>I was trying to dump structures from MD.trr using trjconv. The MD.trr
> has 0ns to 382ns of data. (i checked the MD.log file also).  However, when
> i try to dump structures beyond 25ns, with the following command :
> *gmx trjconv mpi -f MD.trr -dump 27000.000 -dt 1000 -s MD.tpr -b 2.000*
>
>
> *it gives the following error :WARNING no output, last frame read at
> t=25290*
>
> I have also tried to check with gmxcheck but it only runs till 20ns.
>
> trjconv and or gmxcheck did not give any error with MD.xtc which was
> generated during the simulation.
>
> I require the MD.trr as i  need velocity and force information for my
> analysis.
>
> Kindly suggest something!!
> Kind Regards,
> Antara
>
> --
> Junior research fellow(project)
> Systems biology group
> CSIR-Institute of Genomics & Integrative Biology
> South Campus
> New Delhi -  110020
> M : +91-9717970040
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Re: [gmx-users] WARNING no output error while dumping structures with trjconv from MD.trr

[Tsjerk Wassenaar]

Hi Antara,

You indicate you want the frame at 27ns (-dump 27000), but that's not in
the trajectory. The suggestion is to ask for a frame that is in, like -dump
25290

Cheers,

Tsjerk
On May 21, 2016 13:09, "Antara mazumdar"  wrote:

Dear gromacs users,

   I was trying to dump structures from MD.trr using trjconv. The MD.trr
has 0ns to 382ns of data. (i checked the MD.log file also).  However, when
i try to dump structures beyond 25ns, with the following command :
*gmx trjconv mpi -f MD.trr -dump 27000.000 -dt 1000 -s MD.tpr -b 2.000*


*it gives the following error :WARNING no output, last frame read at
t=25290*

I have also tried to check with gmxcheck but it only runs till 20ns.

trjconv and or gmxcheck did not give any error with MD.xtc which was
generated during the simulation.

I require the MD.trr as i  need velocity and force information for my
analysis.

Kindly suggest something!!
Kind Regards,
Antara

--
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M : +91-9717970040
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Re: [PyMOL] a special phenomenon on using pymol

[Tsjerk Wassenaar]

Hi Smith,

You probably hit the  key. Or you clicked the down triangle in the
lower right menu.

Cheers,

Tsjerk

On Fri, May 20, 2016 at 7:56 AM, Smith Liu  wrote:

> Dear All,
>
> Today as every day I do, I align 2 pdb files by pymol. After a moment, I
> find the aligned 2 molecules start to rock back and forth continuously in
> the pymol window (from about 45 degree to -45 degree). Today I never used
> the rotate or rock command.
>
> Will you please explain why this phenomenon can occur?
>
> Smith
>
>
> --
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> bring their own devices (BYOD) to work are irked by the imposition of MDM
> restrictions. Mobile Device Manager Plus allows you to control only the
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Re: [gmx-users] simulation_time[Nikita Bora]

[Tsjerk Wassenaar]

Hi Nikita,

It's not like there's a range to take a minimum from. It's this with this
force field and that with another. Any deviation will alter the behaviour
of the force field, and you'll have to show that the result is valid,
either by running tests, or by referring to a paper that has results from
such tests. The most suitable value is probably the one used by groups that
have direct ties to the developing group(s).


Hope it helps,


Tsjerk



On May 20, 2016 07:20, "Ms. Nikita Bora"  wrote:

> Thanks Tsjerk
>
> That was really a good explanation. And it helped me out a lot.
> Still,I would like to know what are the standard values for these
> parameters as somewhere rvdw=1 and somewhere rvdw=1.4 is used.
>
> As earlier it was mentioned that with different force field different
> value is used so is there any link where i can get to know the minimum cut
> off values for these parameters and which value should be used for which
> force field or condition
>
> thanks
> Nikita
>
>
>
>   Original Message 
> > Subject: Re: simulation_time
> > From:"Ms. Nikita Bora" 
> > Date:Mon, May 16, 2016 9:42 am
> > To:  nik...@tezu.ernet.in
> >
> --
> >
> > Respected Sir,
> >
> > Thanks for the reply. I would further like to know that according to this
> > tutorial
> > (
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/07_equil2.html
> )
> > the rvdw=rcoulomb=1 is used for the protein while according to this
> > tutorial
> > (
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/07_equil2.html
> )
> > rvdw=rcoulomb=1.4 is used. why a different value for the simple protein
> > and protein-ligand complex is used??
> >
>
> Different force fields, different settings.
>
> -Justin
>
> >
>
>
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Re: [gmx-users] Help required for calculation of protein coverage % wrt time

[Tsjerk Wassenaar]

Hi Antara,

You can also simply calculate the ratio of buried surface area to total
surface area, which you can both get with gmx sasa

Cheers,

Tsjerk

On Thu, May 19, 2016 at 3:10 PM, Sarath Chandra <
sarathchandrada...@gmail.com> wrote:

> You can use g_contacts tool which will give you list of residues which are
> in contact with the membrane and their frequencies. You might have to write
> an overhead script to convert the residues in contact to %Protein in
> contact
>
> http://www.sciencedirect.com/science/article/pii/S0010465513002464
>
> Regards,
>
> Sarath
>
> --
> Sarath Chandra Dantu, PhD, ELS
> Room No. 606, New BSBE Building
> Department of Biosciences and Bioengineering
> Indian Institute of Technology Bombay
> Powai Mumbai, 400-076, India
>
>
> On 19 May 2016 at 18:35, Antara mazumdar  wrote:
>
> > Dear gromacs users,
> >
> > I have a peripheral membrane protein which I have simulated using Charmm
> 36
> > in a mixed lipids bilayer. I want to calculate the percentage of protein
> in
> > contact with membrane wrt time. I already have residue wise distances
> from
> > membrane calculated.
> >
> > Can anyone suggest me how to go about it after this?
> >
> > Antara Mazumdar
> >
> > ISCB SC RSG-India
> >
> > Core Committee Member
> > --
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> >
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Re: [gmx-users] simulation_time

[Tsjerk Wassenaar]

Hi Nikita,

That's actually a good question, and I think it hasn't been phrased like
this before. I rephrase it slightly again, so it says "which parameters
should be considered part of a force field?"

The first thing that springs to mind is not really a parameter, but a vital
part of the force field: the solvent model. pdb2gmx has a list of water
models of choice for each force field, although some force fields have
several water models, which were then developed to match, but possibly
tailored to specific goals.

The simulation parameters are those related to (non)bonded interactions,
temperature and pressure coupling, of which the latter two are less
critical. However, things like the coupling constants (tau_t/tau_p) may
affect the properties of the system, and for sure force fields have limited
temperature and pressure ranges within which the physics is acceptable.

The trickiest are the non-bonded interactions, where care always needs to
be taken, as these are intimately linked to core parameters of the force
field: the partial charges on atoms and the non-bonded parameters. In
particular, consider the following settings integral part of the force
field:

coulombtype
coulomb-modifier
rcoulomb
rcoulomb-switch
epsilon-r
epsilon-rf

vdwtype
vdw-modifier
rvdw
rvdw-switch
DispCorr

---

Hope it helps,

Tsjerk









On Wed, May 18, 2016 at 9:20 AM, Ms. Nikita Bora 
wrote:

> Thank you sir for the reply...
>
> a few queries are still there
>
> 1) what are the parameters that change according to force fields??
> 2) and what are the minimum cut offs for the parameters that changes
> according to force fields or is there any link where the information can
> be retrieved.
>
>
> ___
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Re: [gmx-users] Production run error

[Tsjerk Wassenaar]

Hi Sanket,

The problem is that a charge group moved too far between two domain
decomposition steps.

Seriously, we can't say more than that, unless you tell us more about the
system and how you got to the point where you are.

Cheers,

Tsjerk
On May 18, 2016 8:44 AM, "Sanket Ghawali"  wrote:

> *Dear all,
> I'm performing a production run for a 100ns simulation. It runs well
> upto 88 ns, but stops after that. Giving an error message.*
>
> Program mdrun_mpi, VERSION 4.6.5
> Source code file: /root/data/gromacs-4.6.5/src/mdlib/domdec.c, line: 4412
>
> Fatal error:
> A charge group moved too far between two domain decomposition steps
> This usually means that your system is not well equilibrated
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> "Come on boys, Let's push it hard" (P.J. Harvey)
>
> Error on node 25, will try to stop all the nodes
> Halting parallel program mdrun_mpi on CPU 25 out of 48
>
> ---
> Program mdrun_mpi, VERSION 4.6.5
> Source code file: /root/data/gromacs-4.6.5/src/mdlib/domdec.c, line: 4412
>
> Fatal error:
> A charge group moved too far between two domain decomposition steps
> This usually means that your system is not well equilibrated
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> "Come on boys, Let's push it hard" (P.J. Harvey)
>
> Error on node 37, will try to stop all the nodes
> Halting parallel program mdrun_mpi on CPU 37 out of 48
>
> gcq#339: "Come on boys, Let's push it hard" (P.J. Harvey)
>
>
> gcq#339: "Come on boys, Let's push it hard" (P.J. Harvey)
>
>
> ---
> Program mdrun_mpi, VERSION 4.6.5
> Source code file: /root/data/gromacs-4.6.5/src/mdlib/domdec.c, line: 4412
>
> Fatal error:
> A charge group moved too far between two domain decomposition steps
> This usually means that your system is not well equilibrated
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> "Come on boys, Let's push it hard" (P.J. Harvey)
>
> Error on node 38, will try to stop all the nodes
> Halting parallel program mdrun_mpi on CPU 38 out of 48
>
> gcq#339: "Come on boys, Let's push it hard" (P.J. Harvey)
>
> --
> MPI_ABORT was invoked on rank 38 in communicator MPI_COMM_WORLD
> with errorcode -1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --
> [compute-0-2.local][[20037,1],46][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv]
> mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
> [compute-0-2.local][[20037,1],26][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv]
> mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
> [compute-0-1.local][[20037,1],13][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv]
> mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
> [compute-0-1.local][[20037,1],33][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv]
> mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
> [compute-0-1.local][[20037,1],45][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv]
> mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
> [bicamp.bicnirrh.res.in:13287] 2 more processes have sent help message
> help-mpi-api.txt / mpi-abort
> [bicamp.bicnirrh.res.in:13287] Set MCA parameter
> "orte_base_help_aggregate" to 0 to see all help / error messages
> [compute-0-0.local][[20037,1],24][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv]
> mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
> [compute-0-0.local][[20037,1],36][btl_tcp_frag.c:215:mca_btl_tcp_frag_recv]
> mca_btl_tcp_frag_recv: readv failed: Connection reset by peer (104)
> --
> mpirun has exited due to process rank 38 with PID 5651 on
> node compute-0-2 exiting improperly. There are two reasons this could
> occur:
>
> 1. this process did not call "init" before exiting, but others in
> the job did. This can cause a job to hang indefinitely while it waits
> for all processes to call "init". By rule, if one process calls "init",
> then ALL processes must call "init" prior to termination.
>
> 2. this process called "init", but exited without calling "finalize".
> By rule, all processes that call "init" MUST call "finalize" prior to
> exiting or it will be considered an "abnormal 

Re: [gmx-users] Calculating Distance

[Tsjerk Wassenaar]

Hi Sanket,

You can use 'gmx traj' to write the COM over time.

Cheers,

Tsjerk

On Wed, May 18, 2016 at 7:09 AM, Sanket Ghawali 
wrote:

> Thank you Justin. I am sorry, I didn't make my query specific.
>
> g_dist calculates distance between COMS of 2 groups with reference to time.
> I want to monitor the change in the COM of the peptide with respect to the
> initial position (COM) of the peptide at 0ns and not between COM of 2
> different groups with reference to time.
>
> Please help me with "how to fix the reference position for distance
> calculation"
>
> Greatly appreciate your help and do let me know if I need to explain the
> query further
>
> With regards,
>
> Sanket.
> --
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Re: [gmx-users] Removing periodic boundary condition

[Tsjerk Wassenaar]

Hi Sanket,

Can you check the structure in the tpr file (editconf -f .tpr -o
.gro/.pdb)? If that is good, then -pbc nojump should work. For the second
pass, you shouldn't need -pbc mol then.

Cheers,

Tsjerk
On May 16, 2016 9:06 AM, "Sanket Ghawali"  wrote:

> Dear, gmx-users,
>
> Hello everyone,
> I'm simulating a peptide in an SDS micelle. The simulation was
> performed for 100ns
> When I view the trajectory in VMD, a portion of the SDS micelle moves
> to the right and goes into the next box. Of course, because of
> periodic boundary conditions. I tried using trjconv to see if I could
> suppress the periodic boundary conditions for the purpose of
> visualization. I've used all the different -pbc options none of them
> helped.
>
> options i have used
>
> trjconv -f .trr -s .tpr -o nojump.trr -pbc nojump
>
> used the above created nojump.trr in the below command
>
> trjconv -f nojump.trr -s .tpr -n .ndx -o .trr -b 0 -e 10 -ur
> compact -pbc mol -center
>
> Selected Protein as centering group and system as output group
>
>
> Any suggestions on how to go about doing this?
>
> Thanks,
>
> Sanket
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Re: [gmx-users] PCA and FEL

[Tsjerk Wassenaar]

Hi Suniba,

No, you will get the stability of configuration in the order parameters you
choose. But you don't know how much conformational freedom you have at each
point. Low RMSD will mean stable, but a fixed point at high RMSD does not.
Also note that the Rg is sort of part of the RMSD, which can be written as
Rg(A)+Rg(B)-2S(A,B), where S is the similarity. So these order parameters
will be correlated.

Cheers,

Tsjerk

On Sun, May 15, 2016 at 8:13 AM, sun <sun.i...@gmail.com> wrote:

> Thank you very much Sir. I get you. Is it good enough to probe the
> stability of complex by projecting any two variables with free energy? like
> RMSD and Rg?
>
>
> Sent from my iPhone
>
> > On 15-May-2016, at 10:51 am, Tsjerk Wassenaar <tsje...@gmail.com> wrote:
> >
> > Hi Suniba,
> >
> > No, with gmx anaeig you can select -2d, which does a 2D projection onto
> the
> > selected eigenvectors. Alternatively, you can combine any two projections
> > onto eigenvectors, which you get using the option -proj. The quickest way
> > to do that is something like:
> >
> > paste <(grep -v '^[@#]'  proj1.xvg) <(proj2.xvg) | awk '{print $2, $4}' >
> > combined.xvg
> >
> > You will loose the labels, but that should be fine.
> >
> > You can combine other variables in a similar manner.
> >
> > Hope it helps,
> >
> > Tsjerk
> >
> >> On Sun, May 15, 2016 at 5:33 AM, sun <sun.i...@gmail.com> wrote:
> >>
> >> Hello everyone
> >> I am using Gromacs 5.0 for protein-ligand MD. I want to do FEL analysis
> >> for the stability of my pro-lig complex.   In a 2015 paper, The group
> >> calculated two principal component, PC1 and PC2 and then prepared an.xvg
> >> file to be used as input for g_sham. My question is, when we use
> g_anaeig;
> >> we get eigenvec.xvg. from -comp flag. Now how shall one select two
> >> principal components from that data? I am sorry if my question is wrong
> but
> >> please help me.
> >>
> >> My second question is, can we use any two parameters like rmsd and Rg
> for
> >> input in g_sham to probe the stability of complex? Is that valid?
> >>
> >> With Regards
> >> Suniba
> >>
> >> Sent from my iPhone
> >> --
> >> 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.
> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > --
> > 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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> >
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> send a mail to gmx-users-requ...@gromacs.org.
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>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>



-- 
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-- 
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Re: [gmx-users] PCA and FEL

[Tsjerk Wassenaar]

Hi Suniba,

No, with gmx anaeig you can select -2d, which does a 2D projection onto the
selected eigenvectors. Alternatively, you can combine any two projections
onto eigenvectors, which you get using the option -proj. The quickest way
to do that is something like:

paste <(grep -v '^[@#]'  proj1.xvg) <(proj2.xvg) | awk '{print $2, $4}' >
combined.xvg

You will loose the labels, but that should be fine.

You can combine other variables in a similar manner.

Hope it helps,

Tsjerk

On Sun, May 15, 2016 at 5:33 AM, sun  wrote:

> Hello everyone
> I am using Gromacs 5.0 for protein-ligand MD. I want to do FEL analysis
> for the stability of my pro-lig complex.   In a 2015 paper, The group
> calculated two principal component, PC1 and PC2 and then prepared an.xvg
> file to be used as input for g_sham. My question is, when we use g_anaeig;
> we get eigenvec.xvg. from -comp flag. Now how shall one select two
> principal components from that data? I am sorry if my question is wrong but
> please help me.
>
> My second question is, can we use any two parameters like rmsd and Rg for
> input in g_sham to probe the stability of complex? Is that valid?
>
> With Regards
> Suniba
>
> Sent from my iPhone
> --
> 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.
>



-- 
Tsjerk A. Wassenaar, Ph.D.
-- 
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* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [PyMOL] How to export secondary structure information from aPDBusing PyMol?

[Tsjerk Wassenaar]

Hi Zhang Chen,

Yes, Pymol only recognizes Helix (3-,alpha,pi), Sheet and Loop (including
turns and such).

Best,

Tsjerk
On May 14, 2016 13:55, "ZHANG Cheng" <272699...@qq.com> wrote:

> Dear Dr Tsjerk,
> Thank you very much. Now it works!
>
> There are only L, S, H
>
> So,
> L: loop
> S: beta-strand
> H: alpha-helix
>
> Is that right?
>
> Thank you.
>
> Cheng
>
>
> -- Original --
> *From: * "Tsjerk Wassenaar";<tsje...@gmail.com>;
> *Date: * Sat, May 14, 2016 07:49 PM
> *To: * "ZHANG Cheng"<272699...@qq.com>;
> *Cc: * "pymol-users"<pymol-users@lists.sourceforge.net>;
> *Subject: * Re: [PyMOL] How to export secondary structure information
> from aPDBusing PyMol?
>
> Hi Zhang Chen,
>
> Oh, I guess that the %d should be %s then. Sorry.
>
> Cheers,
>
> Tsjerk
> On May 14, 2016 13:45, "ZHANG Cheng" <272699...@qq.com> wrote:
>
>> Dear Dr Tsjerk,
>> Thank you very much!.
>>
>> For example, I have a structure of "protein.pdb". I tried but seems not
>> work:
>>
>> PyMOL>open("ss.dat","w").writelines(["Residue %d: %s\n"%(a.resi,a.ss) for
>> a in cmd.get_model("protein"+" and n. ca").atom])
>> Traceback (most recent call last):
>>   File "D:\Program Files (x86)\PyMOL\PyMOL/modules\pymol\parser.py", line
>> 464, in parse
>> exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
>>   File "", line 1, in 
>> TypeError: int argument required
>>
>> Can I ask how to modify that?
>>
>> Thank you!
>>
>>
>> -- Original --
>> *From: * "Tsjerk Wassenaar";<tsje...@gmail.com>;
>> *Date: * Sat, May 14, 2016 05:24 AM
>> *To: * "ZHANG Cheng"<272699...@qq.com>;
>> *Cc: * "pymol-users"<pymol-users@lists.sourceforge.net>;
>> *Subject: * Re: [PyMOL] How to export secondary structure information
>> from a PDBusing PyMol?
>>
>> Hi Zhang Cheng,
>>
>> If you replace SELECTION with a proper selection statement (with quotes),
>> then something like:
>>
>> open("ss.dat","w").writelines( ["Residue %d: %s\n"%(a.resi,a.ss) for a in
>> cmd.get_model(SELECTION+" and n. ca").atom] )
>>
>> It will write the results to a file called ss.dat. Do mind all
>> parentheses/brackets.
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>> On Fri, May 13, 2016 at 10:30 PM, ZHANG Cheng <272699...@qq.com> wrote:
>>
>>> Dear PyMol friends,
>>> I would like to export the secondary structure of individual residues
>>> from a PDB. Can I ask if I can use PyMol to do that?
>>>
>>> I would like something like this:
>>>
>>> Residue 1: alpha-helix
>>> Residue 2: beta-sheet
>>> ..
>>>
>>>
>>>
>>> I think "http://webclu.bio.wzw.tum.de/cgi-bin/stride/stridecgi.py; can
>>> also do that. However, I found that one residue is loop in Pymol but is
>>> indicated as "strand" in the website. So I wonder if Pymol can output the 
>>> secondary
>>> structure of individual residues from a PDB?
>>>
>>> Thank you.
>>>
>>>
>>> --
>>> Mobile security can be enabling, not merely restricting. Employees who
>>> bring their own devices (BYOD) to work are irked by the imposition of MDM
>>> restrictions. Mobile Device Manager Plus allows you to control only the
>>> apps on BYO-devices by containerizing them, leaving personal data
>>> untouched!
>>> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
>>> ___
>>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>>
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>>
--
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
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Re: [PyMOL] How to export secondary structure information from a PDBusing PyMol?

[Tsjerk Wassenaar]

Hi Zhang Chen,

Oh, I guess that the %d should be %s then. Sorry.

Cheers,

Tsjerk
On May 14, 2016 13:45, "ZHANG Cheng" <272699...@qq.com> wrote:

> Dear Dr Tsjerk,
> Thank you very much!.
>
> For example, I have a structure of "protein.pdb". I tried but seems not
> work:
>
> PyMOL>open("ss.dat","w").writelines(["Residue %d: %s\n"%(a.resi,a.ss) for
> a in cmd.get_model("protein"+" and n. ca").atom])
> Traceback (most recent call last):
>   File "D:\Program Files (x86)\PyMOL\PyMOL/modules\pymol\parser.py", line
> 464, in parse
> exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
>   File "", line 1, in 
> TypeError: int argument required
>
> Can I ask how to modify that?
>
> Thank you!
>
>
> -- Original --
> *From: * "Tsjerk Wassenaar";<tsje...@gmail.com>;
> *Date: * Sat, May 14, 2016 05:24 AM
> *To: * "ZHANG Cheng"<272699...@qq.com>;
> *Cc: * "pymol-users"<pymol-users@lists.sourceforge.net>;
> *Subject: * Re: [PyMOL] How to export secondary structure information
> from a PDBusing PyMol?
>
> Hi Zhang Cheng,
>
> If you replace SELECTION with a proper selection statement (with quotes),
> then something like:
>
> open("ss.dat","w").writelines( ["Residue %d: %s\n"%(a.resi,a.ss) for a in
> cmd.get_model(SELECTION+" and n. ca").atom] )
>
> It will write the results to a file called ss.dat. Do mind all
> parentheses/brackets.
>
> Hope it helps,
>
> Tsjerk
>
> On Fri, May 13, 2016 at 10:30 PM, ZHANG Cheng <272699...@qq.com> wrote:
>
>> Dear PyMol friends,
>> I would like to export the secondary structure of individual residues
>> from a PDB. Can I ask if I can use PyMol to do that?
>>
>> I would like something like this:
>>
>> Residue 1: alpha-helix
>> Residue 2: beta-sheet
>> ..
>>
>>
>>
>> I think "http://webclu.bio.wzw.tum.de/cgi-bin/stride/stridecgi.py; can
>> also do that. However, I found that one residue is loop in Pymol but is
>> indicated as "strand" in the website. So I wonder if Pymol can output the 
>> secondary
>> structure of individual residues from a PDB?
>>
>> Thank you.
>>
>>
>> --
>> Mobile security can be enabling, not merely restricting. Employees who
>> bring their own devices (BYOD) to work are irked by the imposition of MDM
>> restrictions. Mobile Device Manager Plus allows you to control only the
>> apps on BYO-devices by containerizing them, leaving personal data
>> untouched!
>> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
>> ___
>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>
--
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
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Re: [gmx-users] (no subject)

[Tsjerk Wassenaar]

Hi Upasana,

What is your goal, your research objective? 'opening it for docking
purpose' is way too vague for us to help you, other then suggesting that
you are probably not choosing an optimal approach.

Cheers,

Tsjerk
On May 14, 2016 07:04, "Upasana Ray"  wrote:

> Dear  user,
>
>  I have generated my final protein.pdb file by using trjconv command from
> .xtc file. The size of my pdb file is 0.98 GB, so whenever I am opening it
> for docking purpose my computer is freezing. Now how can I reduce my pdb
> file size  from GB to MB for using it properly. please help me to deal
>  with this problem.
> --
> 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.
>
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Re: [PyMOL] How to export secondary structure information from a PDB using PyMol?

[Tsjerk Wassenaar]

Hi Zhang Cheng,

If you replace SELECTION with a proper selection statement (with quotes),
then something like:

open("ss.dat","w").writelines( ["Residue %d: %s\n"%(a.resi,a.ss) for a in
cmd.get_model(SELECTION+" and n. ca").atom] )

It will write the results to a file called ss.dat. Do mind all
parentheses/brackets.

Hope it helps,

Tsjerk

On Fri, May 13, 2016 at 10:30 PM, ZHANG Cheng <272699...@qq.com> wrote:

> Dear PyMol friends,
> I would like to export the secondary structure of individual residues from
> a PDB. Can I ask if I can use PyMol to do that?
>
> I would like something like this:
>
> Residue 1: alpha-helix
> Residue 2: beta-sheet
> ..
>
>
>
> I think "http://webclu.bio.wzw.tum.de/cgi-bin/stride/stridecgi.py; can
> also do that. However, I found that one residue is loop in Pymol but is
> indicated as "strand" in the website. So I wonder if Pymol can output the 
> secondary
> structure of individual residues from a PDB?
>
> Thank you.
>
>
> --
> Mobile security can be enabling, not merely restricting. Employees who
> bring their own devices (BYOD) to work are irked by the imposition of MDM
> restrictions. Mobile Device Manager Plus allows you to control only the
> apps on BYO-devices by containerizing them, leaving personal data
> untouched!
> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>



-- 
Tsjerk A. Wassenaar, Ph.D.
--
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
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Re: [gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein

[Tsjerk Wassenaar]

Hi Antara,

What commands did you use? At least make sure you add -rdd 1.6 to the
command line of mdrun, because the default value is too small for coarse
grain simulations.

Cheers,

Tsjerk

On Fri, May 13, 2016 at 8:12 PM, Antara mazumdar 
wrote:

> Dear users,
>
> I am trying to run a coarse grained simulation of a membrane protein in a
> mixed lipid billayer using martini model 2.2. I have already performed all
> the equilibration steps successfully on my desktop with GROMACS 5.1.0.
> However, when i try to execute its production run in parallel(having
> gromacs 5.1 version installed)  it complains of LINCS warning and
> terminates at step 0. But on the contrary, it runs on the desktop
> successfully. Kindly suggest something and please let me know if any more
> information is required from my side.
>
>
> Thanks!!
>
> Kind Regards,
> Antara
>
> --
> Junior research fellow(project)
> Systems biology group
> CSIR-Institute of Genomics & Integrative Biology
> South Campus
> New Delhi -  110020
> M : +91-9717970040
> --
>
>
>
> On Fri, May 13, 2016 at 11:11 PM, Antara mazumdar  >
> wrote:
>
> > Dear gromacs users,
> >
> > I am trying to run a coarse grained simulation of a membrane protein in a
> > mixed lipid billayer using martini model. I have already performed all
> the
> > equilibration steps successfully on my desktop. However, when i try to
> > execute its production run in parallel it complains of LINCS warning and
> > terminates at step 0. But on the contrary, it runs on the desktop
> > successfully. Kindly suggest something and please let me know if any more
> > information is required from my side.
> >
> >
> > Thanks!!
> >
> >
> >
> > Kind Regards,
> > Antara
> >
> > --
> > Junior research fellow(project)
> > Systems biology group
> > CSIR-Institute of Genomics & Integrative Biology
> > South Campus
> > New Delhi -  110020
> > M : +91-9717970040
> > --
> >
> >
> >
> --
> 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.
>



-- 
Tsjerk A. Wassenaar, Ph.D.
-- 
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Re: [PyMOL] Contact map visualizer

[Tsjerk Wassenaar]

Hi James,

You can convert the .xpm file to .png/.jpg using tools like convert
(imagemagick) and Gimp. Convert doesn't always get the Gromacs .xpm right,
but it's an easy one to try.

Cheers,

Tsjerk
On May 11, 2016 2:40 PM, "James Starlight"  wrote:

> Dear Pymol users!
>
> I am in charge with the analysis of protein-protein association during
> long molecular dynamic simulation. In particularly I am interesting to
> find residues on one of the protein which are crustal for the binding
> interface established during Md.
> For that purpose I am trying to use Contact map visualizer plugin to
> map contact maps produced by gromacs onto the 3D structure via Pymol.
> The problem that on the stage of loading of the contact map Pymol
> proposed me to load only png or jpg files (not xpm produced by
> g_mdmat). How it's possible to solve the issue? Any other suggestions
> regarding my topic?
>
> Thanks!
>
> James
>
>
> --
> Mobile security can be enabling, not merely restricting. Employees who
> bring their own devices (BYOD) to work are irked by the imposition of MDM
> restrictions. Mobile Device Manager Plus allows you to control only the
> apps on BYO-devices by containerizing them, leaving personal data
> untouched!
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> ___
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
--
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Re: [PyMOL] Bash scripting and pymol

[Tsjerk Wassenaar]

Hi,

You need

for i in ${pdb_array[@]}
do
...
done

Cheers,

Tsjerk
On Apr 27, 2016 4:44 PM, "James Starlight"  wrote:

> so As I tried to do it but it was not worked :-O)
>
> #pdbs list
> pdb_array=("1UBI" "1IGD" "1G33" "1CC7" "4LGJ" "5A2H")
> #where to save
> pdb_array_store=$template/pymol/
>
>
> # A simple FETCHER: download pdbs to the folder and pre-process them!
> #mkdir ${pdb_array_store}
> for i in `cat ${pdb_array}` ; do wget
> http://www.rcsb.org/pdb/files/${i}.pdb ${pdb_array_store}/${i}.pdb ;
> done
>
> result
> cat: 1UBI: No such file or directory
>
> 2016-04-27 12:29 GMT+02:00 James Starlight :
> > Please give me an example of the list of 3 pdbs instead of just cat $1 :)
> >  as well as proper syntax of how to save each pdb after fetching in
> > pymol using same command line
> > Forgot to mention important points:
> > 1) that list should be physically in my script like in python
> > 2) I use pymol because I will need to process each of the pdb- e,g to
> > remove from them ligands or water etc
> >
> > Thanks!
> >
> > 2016-04-27 12:18 GMT+02:00 James Starlight :
> >> Please give me an example of the list of 3 pdbs instead of cat $1  as
> >> well as how to save syntax of how to save each pdb
> >>
> >>
> >> Thanks!
> >>
> >> J
> >>
> >> 2016-04-27 12:09 GMT+02:00 Jordan Willis :
> >>> If you really want to use pymol, this works
> >>>
> >>> #!/bin/bash
> >>> #myscript.bash
> >>> for i in `cat $1` ; do pymol -d "fetch $i" -c ; done
> >>>
> >>>
> >>> Then on the command line
> chmod +x myscript.bash; ./myscript.bash mylist.txt
> >>>
> >>>
> >>> On Apr 27, 2016, at 2:55 AM, Jordan Willis 
> wrote:
> >>>
> >>> Must you use pymol?
> >>>
> >>>
> >>> Try directly from the PDB
> >>>
> >>> #!/bin/bash
> >>> #myscript.bash
> >>>
> >>> for i in `cat $1` ; do wget http://www.rcsb.org/pdb/files/${i}.pdb ;
> done
> >>>
> >>>
> >>>
> >>>
> >>> Then on the command line
> chmod +x myscript.bash; ./myscript.bash mylist.txt
> >>>
> >>>
> >>> J
> >>>
> >>> On Apr 27, 2016, at 2:41 AM, James Starlight 
> wrote:
> >>>
> >>> Dear Pymol users!
> >>>
> >>> I need to add a few strings to my simple bash script which will creat
> >>> a list of pdb files and than will call pymol without GUI from the
> >>> terminal to fetch all the pdbs and save it to the desired location.
> >>> For one pdb it should be smth like
> >>>
> >>> pdbs="1f88"
> >>>
> >>> pymol -c -q -d "fetch ${pdbs}; save $template/pymol/*.pdb " >
> >>> ${tmp}/pymol_${pdbs}.log
> >>>
> >>> will be thankful for the correction of this string as well as example
> >>> how it can be adapted for a list of pdbs in bash.
> >>>
> >>> Thanks!
> >>>
> >>> J
> >>>
> >>>
> --
> >>> Find and fix application performance issues faster with Applications
> Manager
> >>> Applications Manager provides deep performance insights into multiple
> tiers
> >>> of
> >>> your business applications. It resolves application problems quickly
> and
> >>> reduces your MTTR. Get your free trial!
> >>> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
> >>> ___
> >>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> >>> Archives:
> http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> >>>
> >>>
> >>>
>
>
> --
> Find and fix application performance issues faster with Applications
> Manager
> Applications Manager provides deep performance insights into multiple
> tiers of
> your business applications. It resolves application problems quickly and
> reduces your MTTR. Get your free trial!
> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
> ___
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
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Applications Manager provides deep performance insights into multiple tiers of
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Re: [gmx-users] Higher Density than Expected

[Tsjerk Wassenaar]

Hey :)

Salt water has a higher density than pure water anyway.

Cheers,

Tsjerk
On Apr 26, 2016 5:19 PM, "Christopher Schlicksup" 
wrote:

> Thanks Justin. I was expecting closer to 1000kg/m^3. My reading about the
> tip3p water model found approximately this value at 300K, and it is also
> the approximate experimental value. So I guess my question was whether
> 1025kg/m^3 was off enough to be a concern.
>
> I think you answered the question: that the system is too inhomogeneous to
> pay that close attention to the absolute density value. Thanks again.
>
>
>
> > Date: Mon, 25 Apr 2016 17:13:01 -0400
> > From: Justin Lemkul 
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] Higher Density than Expected
> > Message-ID: <571e885d.2030...@vt.edu>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> >
> >
> > On 4/25/16 5:09 PM, Christopher Schlicksup wrote:
> > > Hi, I am fairly new to simulation, and would like some input about
> > whether
> > > I have set up Gromacs correcly. I am using version 5.0.4 with the
> > > CHARMM36-Jun2015 force field and the TIP3P water model. I am
> simulating a
> > > 35kDa protein in a dodecahedron box (-d 1.6) with 150mM NaCl plus
> > > neutralizing ions.
> > >
> > > I do a 200ps NVT equilibration followed by a 500ps NPT equilibration
> > > followed by 230ps of production run where the protein is unrestrained.
> My
> > > observations so far are that the density is higher than I would expect
> > from
> > > reading literature. I would appreciate any insight into whether I have
> a
> > > problem, or if my density and pressure values look acceptable. Thanks
> in
> > > advance
> > >
> >
> > What value do you expect from the literature?  The density of such an
> > inhomogeneous system is rather useless.  Everything looks fine to me.
> >
> > -Justin
> >
> > > Here are my results from gmx energy:
> > >
> > > *Energy minimization*
> > >
> > > Energy  Average   Err.Est.   RMSD  Tot-Drift
> > >
> >
> ---
> > > Potential-1.93229e+06  2900077735.5-189748
> > > (kJ/mol)
> > >
> > >
> > > *NVT Equilibration 200ps*
> > >
> > > Energy  Average   Err.Est.   RMSD  Tot-Drift
> > >
> >
> ---
> > > Temperature   299.9  0.0992.59846   0.560458
> (K)
> > >
> > >
> > > *NPT Equilibration 500ps*
> > >
> > > Energy  Average   Err.Est.   RMSD  Tot-Drift
> > >
> >
> ---
> > > Pressure1.528921.781.007911.2974
> > (bar)
> > > Density 1024.74  0.0571.70907 -0.0499058
> > > (kg/m^3)
> > > Volume  1168.76  0.0651.96293  0.0505822
> > (nm^3)
> > >
> > >
> > > *Production Run 230ps*
> > >
> > > Energy  Average   Err.Est.   RMSD  Tot-Drift
> > >
> >
> ---
> > > Pressure   0.450022   0.6575.3012   0.157248
> > (bar)
> > > Density  1025.4  0.0481.39937  -0.209504
> > > (kg/m^3)
> > > Volume  1168.01  0.0551.59374   0.238338
> > (nm^3)
> > >
> >
> > --
> > ==
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalem...@outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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Re: [gmx-users] Standard volume of the simulation box

[Tsjerk Wassenaar]

Hi Sana,

There's no such thing as a standard volume. The key decision you have to
take is what distance there should be between periodic images, for which
the consensus view is that you need at least 2.0 nm. I typically use 2.25,
corresponding roughly to 9 layers of water, so the protein can stretch
without significant risk of direct interactions. That means setting up the
unit cell with a distance to the wall of 1.125 nm.

Hope it helps,

Tsjerk

On Mon, Apr 25, 2016 at 5:27 AM, Sana Saeed 
wrote:

> hi
> how can i find the standard volume of the simulation box, that includes
> ligand, protein and water.
>
>  Sana Saeed Khan,
> Research Assistant
> Chemoinformatics Lab
> Graduate Student, MS bioinfo
> Department of Bioinformatics
> Soongsil University, Seoul, South Korea.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
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Re: [gmx-users] question about preferred values in itp files

[Tsjerk Wassenaar]

Hey,

In addition, for Q3, sure you can have a program build you acetonitrile
from the interactions. But what about cholesterol? Morphine? A protein? For
just a bit more complicated stuff, let alone the really complicated stuff,
you need to have coordinates to start with.

Cheers,

Tsjerk
On Apr 14, 2016 02:20, "Justin Lemkul"  wrote:

>
>
> On 4/13/16 1:53 PM, abhishek khetan wrote:
>
>> Dear gmx-users,
>>
>> I have the opls-aa forcefield file for acetonitrile. It looks something
>> like:
>>
>> ---
>>   [ moleculetype ]
>>   ; Namenrexcl
>>   ACN 3
>>
>>   [ atoms ]
>>   ;   nr   type  resnr residue  atom   cgnr charge   mass
>>1   opls_755  1ACN  C1  1  -0.0812.01100
>>2   opls_759  2ACN  H2  1   0.06 1.00800
>>3   opls_759  3ACN  H3  1   0.06 1.00800
>>4   opls_759  4ACN  H4  1   0.06 1.00800
>>5   opls_754  5ACN  C5  2   0.4612.01100
>>6   opls_753  6ACN  N6  3  -0.5614.00670
>>
>> ---
>>
>> My topol.top file looks like
>>
>> ---
>> #include "./oplsaa.ff/forcefield.itp"
>> #include "./oplsaa.ff/acn.itp"
>>
>> [ system ]
>> ; Name
>> ACN216
>>
>> [ molecules ]
>> ; Compound#mols
>> ACN  216
>>
>> ---
>>
>> And the forcefield.itp looks like
>>
>> ---
>> [ defaults ]
>> ; nbfunccomb-rulegen-pairsfudgeLJfudgeQQ
>> 13yes0.50.5
>>
>> #include "ffnonbonded.itp"
>> #include "ffbonded.itp"
>>
>> ---
>>
>> Needless to mention, that the ffbonded.itp and ffnonbonded.itp are the
>> standard files from the oplsaa.ff directory in which the opls_XYZ
>> [atomtypes]/[bondtypes]/[dihedraltypes] etc are defined.
>>
>> My questions now are these:
>>
>> 1. When the charge and mass are already mentioned in the ffbonded.itp and
>> ffnonbonded.itp files for each of the opls_XYZ entries, then why do we
>> specify it again in the acn.itp file? Which values are read in the
>> simulations? the one from ffnonbonded.itp or the ones from acn.itp ? In
>> acse the acn.itp values are preferred, does it mean that the epsilon and
>> sigma value are still read from the ffnonbonded.itp file ?
>>
>>
> Charges in ffnonbonded.itp are never used for anything.  Values specified
> in a topology always override those in ff(non)bonded.itp; this hierarchy is
> explained in the manual.
>
> 2. BIGGER QUESTION: When i look at the ffnonbonded and ffbonded files - the
>> bondtypes are specified in terms of the atom symbols from atomtpes,
>> instead
>> of the . The ffnonbonded and non bonded have entries like:
>>
>> 
>> [ atomtypes ]
>>   opls_001   C6  12.01100 0.500   A3.75000e-01
>> 4.39320e-01 ; SIG
>>   opls_017   C6  12.01100 0.700   A3.75000e-01
>> 4.39320e-01 ; SIG
>>   opls_026   C6  12.01100 0.265   A3.75000e-01
>> 4.60240e-01 ; SIG
>> ..
>> [ bondtypes ]
>>C C3  10.15220   265265.6   ; END
>>C CA  10.14900   334720.0   ; wlj 8/97
>>C CB  10.14190   374049.6   ; GUA
>>C CM  10.14440   343088.0   ; THY
>>C CS  10.14900   334720.0   ;
>> ..
>>
>> 
>>
>> As you see all the bondtypes involve C as one of the atom types - how does
>> gromacs know which atomtype to choose ?? there are multiple atomtypes
>> corresponding to the same symbol. Or are have the symbols been chosen in
>> such a way that when wither if opls 001/017/026 bonds with C3 then the
>> bond
>> distance
>>
>>
> The bonded parameter space is significantly smaller than the nonbonded
> parameter space.  The translations are in ffnonbonded.itp so grompp knows
> how to map bonded and nonbonded types.
>
> 3. EVEN BIGGER QUESTION: From what I understand, once I specify the
>> opls_XYZ type for a certain atom in a given molecule along with
>> [bonds]/[dihedrals]/etc in the acn.itp, it reads all specifications along
>> with the equilibrium bond distances, the angles and all that stuff from
>> the
>> 

Re: [gmx-users] very strange phenomenon for my production MD by gromacs

[Tsjerk Wassenaar]

right!

Cheers,

Tsjerk
On Apr 14, 2016 05:32, "Brett"  wrote:

> Dear All,
>
> If the issue in my production MD was caused by
> "Periodic_Boundary_Conditions", I can continue my production MD until it
> completed, and it will not affect my final results suppose I have it
> corrected by trjconv, right?
>
>
> Brett
>
>
>
>
>
>
>
>
>
>
>
> At 2016-04-13 22:37:34, "Justin Lemkul"  wrote:
> >
> >
> >On 4/13/16 10:30 AM, Brett wrote:
> >> Dear All,
> >>
> >>
> >> After energy minimization and equilibrations, I am now running a 50 ns
> >> production MD, for a protein of 6 identical subunits, with each subunit
> about
> >> 300 residues (from resi 120 to resi 420), and there were no breaks in
> any
> >> chain. Every day it runs about 1 ns, and every day I use the command
> trjconv
> >> to get a new PDB based on the md_0_1.trr file, for the comparison
> between the
> >> new pdb and the initial pdb.
> >>
> >>
> >> Today I got the PDB at 6 ns. However when I checked it my pymol, I find
> there
> >> is something very strange. Although the rmsd between the 6 ns md PDB
> and 0ns
> >> md PDB was about only 3.7, for chain B, residue 366-367 moved 180
> angstrom
> >> away from this residues neighbouring residues, and correspondingly make
> chain
> >> B has a break at residue 366-367!
> >>
> >>
> >> Will you please let me know what is wrong with my MD, and why 2 residues
> >> (resi 366-367) moved 180 angstrom away? Does this phenomenon often
> occur?
> >>
> >
> >
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
> >
> >-Justin
> >
> >--
> >==
> >
> >Justin A. Lemkul, Ph.D.
> >Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> >Department of Pharmaceutical Sciences
> >School of Pharmacy
> >Health Sciences Facility II, Room 629
> >University of Maryland, Baltimore
> >20 Penn St.
> >Baltimore, MD 21201
> >
> >jalem...@outerbanks.umaryland.edu | (410) 706-7441
> >http://mackerell.umaryland.edu/~jalemkul
> >
> >==
> >--
> >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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Re: [gmx-users] EM replicates

[Tsjerk Wassenaar]

Hi Gregory,

Yes, these steps are deterministic. Think of where the randomization should
come from. Sure, there is 'random' placement of ions in genion, but it has
a default seed, resulting in deterministic random numbers :)

Hope it helps,

Tsjerk
On Apr 9, 2016 00:33, "Gregory Poon"  wrote:

> Hello all!
>
> I am wondering if the solvate, genion, and energy minimization (using
> steepest descent) procedures are deterministic.  I have been performing
> replicate energy minimization of a duplex DNA structure, always starting
> from scratch (i.e., pdb2gmx) and using the same parameters in terms of
> force field, water choice, ion concentration/type etc. and getting
> convergent structures that are super-imposable.  My question is whether
> this is something that I would expect in any event, for any system (up to
> energy minimization, before dynamics simulation), or that I just happen to
> have a well-behaved system.
>
> Thanks in advance,
> Gregory
> --
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Re: [gmx-users] Partial density versus time

[Tsjerk Wassenaar]

Hi Faezeh,

According to your previous mail, what you want is...

> I am dealing with phase separation of a two-component system. At the end
of
> simulation the mixed system phase separate to two phases, one is rich in
> one component and the other phase is rich with the other component. So I
> want to see how each component  reachs those fractions by time?

... to see how the components phase separate.

In a maximally mixed state, the number of contacts between species A and B
in the mixture is maximal, while the number of contacts within the groups A
and B, respectively, are minimal. Vice-versa, in a completely phase
separated system, the number of contacts between groups is minimal (only
the interface), while the contacts within groups are maximized. So these
numbers should show you the time course and degree of phase separation,
which seems to be what you stated to want. Apparently, you do not want what
you said you wanted, but maybe we can give it another shot with a
description of what you really want then.

Best,

Tsjerk



On Thu, Apr 7, 2016 at 6:42 PM, Faezeh Pousaneh <fpoosa...@gmail.com> wrote:

> Dear Tsjerk, no that does not give what I want.
>
>
>
> Best regards
>
>
> On Thu, Apr 7, 2016 at 6:41 PM, Faezeh Pousaneh <fpoosa...@gmail.com>
> wrote:
>
> > Hi Negar,
> >
> > I tried your solution, but still it does not give the density (of each
> > component) versus time. It gives density versus distance for different
> > frames. This could be easily done by g_density with an .ndx file. I need
> to
> > have a plot of density-time for each of the components of the system.
> >
> > Please help...
> >
> >
> >
> >
> > Best regards
> >
> >
> > On Wed, Apr 6, 2016 at 7:13 PM, Tsjerk Wassenaar <tsje...@gmail.com>
> > wrote:
> >
> >> Hi Faezeh,
> >>
> >> You can count the number of contacts within and between groups to follow
> >> the process over time using gmx mindist.
> >>
> >> Hope it helps,
> >>
> >> Tsjerk
> >> On Apr 6, 2016 17:10, "Faezeh Pousaneh" <fpoosa...@gmail.com> wrote:
> >>
> >> > Hi Tsjerk,
> >> >
> >> > Thanks, but my question it is not that simple.
> >> > I am dealing with phase separation of a two-component system. At the
> >> end of
> >> > simulation the mixed system phase separate to two phases, one is rich
> in
> >> > one component and the other phase is rich with the other component.
> So I
> >> > want to see how each component  reachs those fractions by time?
> >> >
> >> >
> >> >
> >> > Best regards
> >> >
> >> >
> >> > On Wed, Apr 6, 2016 at 4:58 PM, Tsjerk Wassenaar <tsje...@gmail.com>
> >> > wrote:
> >> >
> >> > > Hi Faezeh,
> >> > >
> >> > > Using -b/-e flags you can get the density profile over a window of
> >> time
> >> > (or
> >> > > a single frame). Afterwards you can combine the results to have a
> >> density
> >> > > profile over time.
> >> > >
> >> > > Hope it helps,
> >> > >
> >> > > Tsjerk
> >> > >
> >> > > On Wed, Apr 6, 2016 at 4:29 PM, Faezeh Pousaneh <
> fpoosa...@gmail.com>
> >> > > wrote:
> >> > >
> >> > > > Hi,
> >> > > >
> >> > > > Is it possible to obtain partial density versus time in Gromacs?
> >> > > Precisely,
> >> > > > I have a system of two components which separate by time. I need
> the
> >> > > > evolution of density of each phase by time?
> >> > > >
> >> > > > thanks.
> >> > > > Best regards
> >> > > > --
> >> > > > 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] Partial density versus time

[Tsjerk Wassenaar]

Hi Faezeh,

You can count the number of contacts within and between groups to follow
the process over time using gmx mindist.

Hope it helps,

Tsjerk
On Apr 6, 2016 17:10, "Faezeh Pousaneh" <fpoosa...@gmail.com> wrote:

> Hi Tsjerk,
>
> Thanks, but my question it is not that simple.
> I am dealing with phase separation of a two-component system. At the end of
> simulation the mixed system phase separate to two phases, one is rich in
> one component and the other phase is rich with the other component. So I
> want to see how each component  reachs those fractions by time?
>
>
>
> Best regards
>
>
> On Wed, Apr 6, 2016 at 4:58 PM, Tsjerk Wassenaar <tsje...@gmail.com>
> wrote:
>
> > Hi Faezeh,
> >
> > Using -b/-e flags you can get the density profile over a window of time
> (or
> > a single frame). Afterwards you can combine the results to have a density
> > profile over time.
> >
> > Hope it helps,
> >
> > Tsjerk
> >
> > On Wed, Apr 6, 2016 at 4:29 PM, Faezeh Pousaneh <fpoosa...@gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > Is it possible to obtain partial density versus time in Gromacs?
> > Precisely,
> > > I have a system of two components which separate by time. I need the
> > > evolution of density of each phase by time?
> > >
> > > thanks.
> > > Best regards
> > > --
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> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > --
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