Re: [gmx-users] SARS-CoV-2 main protease with ligand from acpype, but converting to vsites?

[Erik Marklund]

Hi Bjorn (and others interested in virtual sites for non-protein molecules),

We have an article in press where we describe our new tool Mkvsites, which is a 
great help when you want virtual sites for a new residue, ligand, etc. I will 
announce the article once it is available, but I might as well provide the tool 
already now: https://github.com/ErikMarklund/mkvsites

In short: Use topinspect.py to identify any atomtypes and interactions in your 
itp/top file that need to be added to the force field (not needed for some 
things, like nucleic acids already present in the force field, but for which no 
vsite parameters exist). topinspect.py optionally produces an rtp file, which 
is very helpful because it enables you to use pdb2gmx to place all dummy masses 
etc at a later stage. Then use Mkvsites.py to generate the required vsite 
parameters, including angle constraints for -OH groups. Put that in your force 
field, then prepare your system with pdb2gmx etc like you would for a vanilla 
protein system.

Look at the examples provided and get in touch if you need help. I am sure 
there are things we can do to improve the usability, so input is welcome. We 
have NOT automated the actual modification of force field files, since we have 
noticed that some of the input we have used for testing need human 
interpretation (e.g. to decide element type for new atom types). While we could 
implement some logic for that, it is difficult to foresee all possible flavours 
of input, and that strategy risk causing silent errors in the simulations.

Kind regards,
Erik
__
Erik Marklund, PhD, Associate Professor of Biochemistry
Associate Senior Lecturer in Computational Biochemistry
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4562
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 27 Mar 2020, at 17:14, Bjorn Wesen 
mailto:bjorn.we...@gmail.com>> wrote:

Hi list, I have a working sim of the solvated SARS-CoV-2 main protease
dimer from

https://www.rcsb.org/structure/6Y84

using amber99sb-ildn and pdb2gmx-generated vsites for speed, and wanted to
proceed by adding some of the various proposed inhibitor ligands to the sim
for further workflow testing, for example, this one:
"COCCOc1cc(C(=O)N=c2[nH][nH]c(C)c2-c2ccc(Cl)cc2)ccn1".

So I made a pdb of this and generated a .gro and .itp through one of the
online Acpype servers (the one at http://bio2byte.be/acpype ), but there is
no option to generate gmx vsites for getting rid of the hydrogen
bond-angles so I simply assume the result will blow up when running with
the longer timesteps the rest of the sim now uses.

I found a 5 year old post on this list with the same problem, with this
advice from Justin:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-October/101732.html


"At present, the simplest way forward is to take the information you have
in your
ligand topology from acpype and create an .rtp entry, then allow pdb2gmx to
process the whole thing and build the virtual sites on the ligand."

I was wondering, is this still the recommended method? I'm not
super-knowledgeable in the details of how to port something from the ITP to
the RTP formats. Should I just give up on doing it this way or is it an
"opportunity to learn the details" ;) Or is there a better way. Maybe some
other gmx tool to build the vsites for a ligand without having to go all
the way by creating the rtp stuff.

Also, yes, I could simply give up the vsites and run everything slower.
This is the fallback. Maybe some of these ligands simply won't work well
with these constructions at any rate.

Regards
/Bjorn
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Re: [gmx-users] Force field for urea and urea-TMAO mixture

[Erik Marklund]

Dear Ishrat,

I recommend this article and references therein for TMAO + urea parameters: 
http://dx.doi.org/10.1021/jacs.7b11695.

Kind regards,
Erik
__
Erik Marklund, PhD, Associate Professor of Biochemistry
Associate Senior Lecturer in Computational Biochemistry
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4562
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 5 Mar 2020, at 10:05, Alessandra Villa 
mailto:alessandra.villa.bio...@gmail.com>> 
wrote:

Hi,
The urea model of Lorna Smith (
https://pubs.acs.org/doi/abs/10.1021/jp030534x
) should be compatible with  GROMOS force field.
Best regards
Alessandra

On Wed, Mar 4, 2020 at 7:00 AM ISHRAT JAHAN  wrote:

Dear all,
I want to do MD simulation of protein in urea and urea-TMAO mixture. Can
you suggest me which force field would be better for urea and urea tmao
mixture? Is Kast-2016 TMAO model is compatible with gromos54a5 force field
as I have done the simulation of protein with this force field. Any
suggestions regarding this will be highly appreciated.
Thank you
Regards


--
Ishrat Jahan
Research Scholar
Department Of Chemistry
A.M.U Aligarh
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[gmx-users] Fourier dihedrals

[Erik Marklund]

Dear all,

I am looking in the manual at how the Fourier dihedrals are defined, and there 
appears to be a discrepancy between section 5.5 and the table of topology 
directives in 5.14. 5.5 shows an equation with four coefficients (F1, F2, F3, 
F4), whereas the table shows 5 coefficients for the Fourier-type dihedrals 
(C1,C2,C3,C4,C5). How does gromacs actually handle this? With 4 or 5 parameters?

Kind regards,
Erik
__
Erik Marklund, PhD, Associate Professor of Biochemistry
Associate Senior Lecturer in Computational Biochemistry
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4562
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>









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Re: [gmx-users] Tpr version check

[Erik Marklund]

Hi,

Thanks Mark. See https://redmine.gromacs.org/issues/2924.

Kind regards,
Erik
__
Erik Marklund, PhD, Associate Professor of Biochemistry
Associate Senior Lecturer in Computational Biochemistry
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4562
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 11 Apr 2019, at 08:42, Mark Abraham 
mailto:mark.j.abra...@gmail.com>> wrote:

Hi,

The old behavior of a graceful rejection of the file with a new version
number is still expected.

The most likely explanation for your observations is that they old version
of gmx is linking somehow to newer versions of things (which also shouldn't
happen ...), and the chimera can't work.
If you can share a tpr on Redmine we can see if there is an issue we can
fix.

Mark

On Wed., 10 Apr. 2019, 23:05 Erik Marklund, 
mailto:erik.markl...@kemi.uu.se>>
wrote:

Hi users,

I accidentally used an older version (2016.3) to run trjconv on some
trajectories. Some conversions worked, seemingly depending on pbc options
etc, whereas others stopped with the following output:

Back Off! I just backed up mol.xtc to ./#mol.xtc.1#
->  frame  0 time0.000
---
Program: gmx trjconv, version 2016.3
Source file: src/gromacs/pbcutil/pbc.cpp (line 94)

Fatal error:
Unknown ePBC=1051770189 in ePBC2npbcdim

Call me a hopeless nostalgic, but I remember a time when such mistakes
rendered an error saying that I am using an older version of gmx than the
version used to generate the tpr file. Is that not a thing anymore, and
this is the expected behaviour? Seems problematic if gmx tools try to read
nonsense data (from the viewpoint of the gromacs version used).

Kind regards,
Erik
______
Erik Marklund, PhD, Associate Professor of Biochemistry
Associate Senior Lecturer in Computational Biochemistry
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4562
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se><mailto:erik.markl...@kemi.uu.se>









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[gmx-users] Tpr version check

[Erik Marklund]

Hi users,

I accidentally used an older version (2016.3) to run trjconv on some 
trajectories. Some conversions worked, seemingly depending on pbc options etc, 
whereas others stopped with the following output:

Back Off! I just backed up mol.xtc to ./#mol.xtc.1#
 ->  frame  0 time0.000
---
Program: gmx trjconv, version 2016.3
Source file: src/gromacs/pbcutil/pbc.cpp (line 94)

Fatal error:
Unknown ePBC=1051770189 in ePBC2npbcdim

Call me a hopeless nostalgic, but I remember a time when such mistakes rendered 
an error saying that I am using an older version of gmx than the version used 
to generate the tpr file. Is that not a thing anymore, and this is the expected 
behaviour? Seems problematic if gmx tools try to read nonsense data (from the 
viewpoint of the gromacs version used).

Kind regards,
Erik
__
Erik Marklund, PhD, Associate Professor of Biochemistry
Associate Senior Lecturer in Computational Biochemistry
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4562
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>









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Re: [gmx-users] NVT equilibration in vacuum

[Erik Marklund]

Additionally, be aware of the tumbling ice cube effect and set comm-mode to 
angular to avoid it.

Kind regards,
Erik
__
Erik Marklund, PhD, Associate Professor  of Biochemistry
Associate Senior Lecturer in Computational Biochemistry
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4562
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 27 Mar 2019, at 00:53, Justin Lemkul 
mailto:jalem...@vt.edu>> wrote:



On 3/26/19 5:43 PM, Neena Susan Eappen wrote:
Hello gromacs users,

I am using gromacs to simulate a peptide in vacuum. I was wondering for the NVT 
equilibration step, are there any particular parameters to be changed for 
vacuum conditions as there is no position restraining on solvent molecules?

Preparing a vacuum system is not like a condensed-phase system. To do a 
simulation in vacuum, turn off PBC and set all cutoffs to zero (rlist, rvdw, 
rcoulomb).

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

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http://www.thelemkullab.com

==

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Re: [gmx-users] Different models of TMAO

[Erik Marklund]

Dear Dilip,

Perhaps you are aware of these publications 
http://dx.doi.org/10.1021/jacs.7b11695, 
https://doi.org/10.1103/PhysRevLett.119.108102.

Unless someone provides parameter files for you, you will need to learn how the 
gromacs topology and force field files work. That is a good thing to know 
long-term anyway if you plan on doing MD in the future.

Kind regards,
Erik
__
Erik Marklund, PhD, Associate Professor  of Biochemistry
Associate Senior Lecturer in Computational Biochemistry
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4562
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 20 Mar 2019, at 16:24, Dilip.H.N 
mailto:cy16f01.di...@nitk.edu.in>> wrote:

Hello all,
I have run a simulation with TMAO using Charmm36 FF and i want to see
whether different models of TMAO ie., Kast, Netz and Garcia models do
solvate/behave in the same way.
So, can anybody share the relevant parameter files as .rtp, .itp etc., of
the above mentioned three different TMAO models required to run the
simulations...
How can i include the epsilon and LJ parameters in it...?

Any suggestions are appreciated.
Thank you.
---
With Best Regards,

Dilip.H.N
Ph.D. Student.

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Re: [gmx-users] Vanishing cofactors

[Erik Marklund]

Hm. Issue largely resolved itself. The chain labels disappear with 2019.1, 
which is why I might have misinterpreted the output pdb. Still an issue, but 
minor. Redmine issue updated.

Kind regards,
Erik

> On 20 Mar 2019, at 14:45, Erik Marklund  wrote:
> 
> Sorry. Wrong link. Here is the correct one
> http://redmine.gromacs.org/issues/2900
> ______
> Erik Marklund, PhD, Associate Professor  of Biochemistry
> Associate Senior Lecturer in Computational Biochemistry
> Department of Chemistry – BMC, Uppsala University
> +46 (0)18 471 4562
> erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>
> 
> On 20 Mar 2019, at 14:41, Erik Marklund 
> mailto:erik.markl...@kemi.uu.se>> wrote:
> 
> Dear dynamicists,
> 
> When I use a pdb file coming directly from pdb2gmx as input for editconf, my 
> protein’s two cofactor vanish mysteriously. This is using 2019.1. With 2016.3 
> I get no such issues. Is this a known issue? Has anyone experienced similar 
> problems?
> 
> I could not fine anything similar in redline, so I created an issue
> http://redmine.gromacs.org/projects/gromacs/issues/new?issue%5Btracker_id%5D=1<http://redmine.gromacs.org/projects/gromacs/issues/new?issue[tracker_id]=1>
> 
> Kind regards,
> Erik
> __
> Erik Marklund, PhD, Associate Professor  of Biochemistry
> Associate Senior Lecturer in Computational Biochemistry
> Department of Chemistry – BMC, Uppsala University
> +46 (0)18 471 4562
> erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>
> 
> 
> 
> 
> 
> 
> 
> 
> 
> När du har kontakt med oss på Uppsala universitet med e-post så innebär det 
> att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan 
> du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
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Re: [gmx-users] Vanishing cofactors

[Erik Marklund]

Sorry. Wrong link. Here is the correct one
http://redmine.gromacs.org/issues/2900
__
Erik Marklund, PhD, Associate Professor  of Biochemistry
Associate Senior Lecturer in Computational Biochemistry
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4562
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 20 Mar 2019, at 14:41, Erik Marklund 
mailto:erik.markl...@kemi.uu.se>> wrote:

Dear dynamicists,

When I use a pdb file coming directly from pdb2gmx as input for editconf, my 
protein’s two cofactor vanish mysteriously. This is using 2019.1. With 2016.3 I 
get no such issues. Is this a known issue? Has anyone experienced similar 
problems?

I could not fine anything similar in redline, so I created an issue
http://redmine.gromacs.org/projects/gromacs/issues/new?issue%5Btracker_id%5D=1<http://redmine.gromacs.org/projects/gromacs/issues/new?issue[tracker_id]=1>

Kind regards,
Erik
__
Erik Marklund, PhD, Associate Professor  of Biochemistry
Associate Senior Lecturer in Computational Biochemistry
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4562
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>









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[gmx-users] Vanishing cofactors

[Erik Marklund]

Dear dynamicists,

When I use a pdb file coming directly from pdb2gmx as input for editconf, my 
protein’s two cofactor vanish mysteriously. This is using 2019.1. With 2016.3 I 
get no such issues. Is this a known issue? Has anyone experienced similar 
problems?

I could not fine anything similar in redline, so I created an issue
http://redmine.gromacs.org/projects/gromacs/issues/new?issue%5Btracker_id%5D=1<http://redmine.gromacs.org/projects/gromacs/issues/new?issue[tracker_id]=1>

Kind regards,
Erik
__
Erik Marklund, PhD, Associate Professor  of Biochemistry
Associate Senior Lecturer in Computational Biochemistry
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4562
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>









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Re: [gmx-users] protein dna pulling

[Erik Marklund]

Hi,

Not necessarily. The COM still moves if one strand moves away. Your results 
however suggest that the DNA’s interaction with the protein is stronger than 
the interaction between strands. I will leave it up to you to decide whether 
that makes sense or not, or if there is something wrong with your setup.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4542
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 27 Aug 2018, at 20:11, abhisek Mondal 
mailto:abhisek.m...@gmail.com>> wrote:

Hi,
I have been trying to pull a double stranded DNA from protein's binding
surface. But I am facing an issue. After defining the pull vector when I
apply the pull force the DNA's one stand got pulled completely while other
strand partially remain attached (
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
).
Shouldn't the both strands be moving together (as the COM was determined
using residues from both strand of DNA) ?
Some suggestions in this regard would be highly appreciated.
Thank you.

--
Abhisek Mondal

*Senior Research Fellow*
*Protein Crystallography Group*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*
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Re: [gmx-users] Speed up simulations with GROMACS with virtual interaction sites

[Erik Marklund]

Hi,

We are working on a tool for automatic vsite parameter generation, which works 
with most force fields including CHARMM. Stay tuned.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 6 Apr 2018, at 13:11, Anthony Nash 
<anthony.n...@dpag.ox.ac.uk<mailto:anthony.n...@dpag.ox.ac.uk>> wrote:

Hi Stephane,

I hope it is useful. I am afraid I have very little charmm experience. I used 
the approach posted for an amber ff.   I hope someone can help with the charmm 
aspect.

Kind regards
Anthony Nash PhD MRSC
Department of Physiology, Anatomy, and Genetics
University of Oxford

From: 
gromacs.org_gmx-users-boun...@maillist.sys.kth.se<mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se>
 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se<mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se>]
 on behalf of ABEL Stephane [stephane.a...@cea.fr<mailto:stephane.a...@cea.fr>]
Sent: 06 April 2018 11:20
To: 
gromacs.org_gmx-users@maillist.sys.kth.se<mailto:gromacs.org_gmx-users@maillist.sys.kth.se>
Subject: [gmx-users] Speed up simulations with GROMACS with virtual 
interaction sites

Many thanks Anthony

I will read your post blog. I have another quick question: Does the approach 
work by defaults (w/o modifications) for other biomolecules such as surfactants 
or it is necessary to construct a virtual site table as we can found for 
protein in the charmm*.ff distribution ?

Stéphane



--

Message: 3
Date: Fri, 6 Apr 2018 09:33:46 +
From: Anthony Nash 
<anthony.n...@dpag.ox.ac.uk<mailto:anthony.n...@dpag.ox.ac.uk>>
To: "gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org>" 
<gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org>>
Subject: Re: [gmx-users] Speed up simulations with GROMACS with
   virtual interaction sites
Message-ID:
   
<84462751076e544cbb9e12bcca3e2d49389...@mbx12.ad.oak.ox.ac.uk<mailto:84462751076e544cbb9e12bcca3e2d49389...@mbx12.ad.oak.ox.ac.uk>>
Content-Type: text/plain; charset="iso-8859-1"


Hi,

I tried something like this about a year ago and I put an instructional blog 
post together. Warning: it was pulled together from a paper I found and not my 
own efforts although I did get it to work. Any questions I might not be able to 
respond, I'm on vacation!

https://distributedscience.wordpress.com/2017/06/19/speeding-up-md-simulations-in-explicit-solvent/

Kind regards
Anthony Nash PhD MRSC
Department of Physiology, Anatomy, and Genetics
University of Oxford

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of ABEL Stephane 
[stephane.a...@cea.fr]
Sent: 06 April 2018 08:51
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Speed up simulations with GROMACS with virtual 
interaction sites

Hi gmx users,

I know that it is possible to speed up  the simulations by a factor 2 (by using 
a larger timestep) in GROMACS with virtual interaction sites. By I do not find 
a clear procedure on the web in particular if I use CHARMM. Do you have any 
pointers or procedures and examples of mdp files to share with me

Thanks

St?phane

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End of gromacs.org_gmx-users Digest, Vol 168, Issue 24
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Re: [gmx-users] Regarding calculation of Hydrogen-Bond

[Erik Marklund]

A shortcut would be to only look at the C-O distance, which can be done with 
gmx hbond without modification.

Kind regards,
Erik

> On 13 Mar 2018, at 15:01, Jeremy T First <jeremy_fi...@utexas.edu> wrote:
> 
> Hi Dilip,
> 
> There is quite a bit of literature, especially recently, that considers the
> alpha carbon as a hydrogen bond donor. How well this is represented in your
> simulation will depend on your force field.
> 
> You will likely need to develop your own gromacs tool to calculate this,
> but it should be quite easy. We recently wrote a tool that does something
> very similar, but you would need to edit it for your own purposes. If you
> are interested in using our code as a template, feel free to contact me off
> list.
> 
> Good luck!
> Jeremy
> 
> 
> 
> 
> Jeremy Todd First
> Webb Research Group
> University of Texas at Austin
> jeremy_fi...@utexas.edu
> (443) 243-1187
> 
> On Tue, Mar 13, 2018 at 7:25 AM, Erik Marklund <erik.markl...@kemi.uu.se>
> wrote:
> 
>> The point is that Calpha don’t form hydrogen bonds.
>> 
>> Erik
>> __
>> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
>> Department of Chemistry – BMC, Uppsala University
>> +46 (0)18 471 4539
>> erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>
>> 
>> On 13 Mar 2018, at 13:20, Dilip H N <cy16f01.di...@nitk.edu.in> cy16f01.di...@nitk.edu.in>> wrote:
>> 
>> Then how can i calculate the hydrogen bonding between C-alpha and Oxygen
>> atom of water molecules..??
>> What are the other possible ways..??
>> 
>> 
>> 
>> <https://mailtrack.io/> Sent with Mailtrack
>> <https://mailtrack.io?utm_source=gmail_medium=signature_campaign=
>> signaturevirality&<https://mailtrack.io/?utm_source=
>> gmail_medium=signature_campaign=signaturevirality&>>
>> 
>> On Tue, Mar 13, 2018 at 4:12 PM, Erik Marklund <erik.markl...@kemi.uu.se<
>> mailto:erik.markl...@kemi.uu.se>>
>> wrote:
>> 
>> Dear Dilip,
>> 
>> The Calpha is not considered a hbond donor.
>> 
>> Kind regards,
>> Erik
>> __
>> Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
>> Department of Chemistry – BMC, Uppsala University
>> +46 (0)18 471 4539
>> erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>> erik.markl...@kemi.uu.se>
>> 
>> On 13 Mar 2018, at 11:03, Dilip H N <cy16f01.di...@nitk.edu.in> cy16f01.di...@nitk.edu.in>> cy16f01.di...@nitk.edu.in<mailto:cy16f01.di...@nitk.edu.in>>> wrote:
>> 
>> Hello,
>> I want to calculate Hydrogen bonding between C-alpha of glycine and the
>> oxygen atom of water molecules.
>> So, i gave the command as:-
>> 
>> gmx hbond -f nptmd.trr -s nptmd.tpr -n CaOw.ndx -num abc.xvg
>> 
>> but i got the error as:
>> Calculating hydrogen bonds between OW (511 atoms) and CA (1 atoms)
>> Found 0 donors and 511 acceptors
>> No Donors found
>> ---
>> Program: gmx hbond, version 2016.2
>> Source file: src/gromacs/gmxana/gmx_hbond.cpp (line 2732)
>> Fatal error:
>> Nothing to be done
>> 
>> So, how can i solve this issue..?? Is there no any Hydrogen bonding between
>> this..?? (I think there is some hydrogen bonding present ...)
>> 
>> Any suggestions are appreciated.
>> 
>> Thank you.
>> 
>> --
>> With Best Regards,
>> 
>> DILIP.H.N
>> PhD Student
>> 
>> 
>> 
>> ‌
>> <https://mailtrack.io/> Sent with Mailtrack
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>> signaturevirality&>
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>> gromacs.org<http://gromacs.org/>>.
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Re: [gmx-users] Regarding calculation of Hydrogen-Bond

[Erik Marklund]

The point is that Calpha don’t form hydrogen bonds.

Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 13 Mar 2018, at 13:20, Dilip H N 
<cy16f01.di...@nitk.edu.in<mailto:cy16f01.di...@nitk.edu.in>> wrote:

Then how can i calculate the hydrogen bonding between C-alpha and Oxygen
atom of water molecules..??
What are the other possible ways..??



<https://mailtrack.io/> Sent with Mailtrack
<https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality;<https://mailtrack.io/?utm_source=gmail_medium=signature_campaign=signaturevirality;>>

On Tue, Mar 13, 2018 at 4:12 PM, Erik Marklund 
<erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>>
wrote:

Dear Dilip,

The Calpha is not considered a hbond donor.

Kind regards,
Erik
______
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se><mailto:erik.markl...@kemi.uu.se>

On 13 Mar 2018, at 11:03, Dilip H N 
<cy16f01.di...@nitk.edu.in<mailto:cy16f01.di...@nitk.edu.in>mailto:cy16f01.di...@nitk.edu.in>>> wrote:

Hello,
I want to calculate Hydrogen bonding between C-alpha of glycine and the
oxygen atom of water molecules.
So, i gave the command as:-

gmx hbond -f nptmd.trr -s nptmd.tpr -n CaOw.ndx -num abc.xvg

but i got the error as:
Calculating hydrogen bonds between OW (511 atoms) and CA (1 atoms)
Found 0 donors and 511 acceptors
No Donors found
---
Program: gmx hbond, version 2016.2
Source file: src/gromacs/gmxana/gmx_hbond.cpp (line 2732)
Fatal error:
Nothing to be done

So, how can i solve this issue..?? Is there no any Hydrogen bonding between
this..?? (I think there is some hydrogen bonding present ...)

Any suggestions are appreciated.

Thank you.

--
With Best Regards,

DILIP.H.N
PhD Student



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With Best Regards,

DILIP.H.N
Ph.D Student
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Re: [gmx-users] Regarding calculation of Hydrogen-Bond

[Erik Marklund]

Dear Dilip,

The Calpha is not considered a hbond donor.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 13 Mar 2018, at 11:03, Dilip H N 
<cy16f01.di...@nitk.edu.in<mailto:cy16f01.di...@nitk.edu.in>> wrote:

Hello,
I want to calculate Hydrogen bonding between C-alpha of glycine and the
oxygen atom of water molecules.
So, i gave the command as:-

gmx hbond -f nptmd.trr -s nptmd.tpr -n CaOw.ndx -num abc.xvg

but i got the error as:
Calculating hydrogen bonds between OW (511 atoms) and CA (1 atoms)
Found 0 donors and 511 acceptors
No Donors found
---
Program: gmx hbond, version 2016.2
Source file: src/gromacs/gmxana/gmx_hbond.cpp (line 2732)
Fatal error:
Nothing to be done

So, how can i solve this issue..?? Is there no any Hydrogen bonding between
this..?? (I think there is some hydrogen bonding present ...)

Any suggestions are appreciated.

Thank you.

--
With Best Regards,

DILIP.H.N
PhD Student



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Re: [gmx-users] Calculation of potential of mean force between sodium and chloride ion pair in water using replica exchange umbrella sampling in gromacs

[Erik Marklund]

Hi,

Just out of curiosity, what is the point of REMD for such a simple system? Is 
the enhanced sampling really worth the overhead?

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 9 Mar 2018, at 18:43, Marc Hoemberger 
<hoemb...@brandeis.edu<mailto:hoemb...@brandeis.edu>> wrote:

You could compile Gromacs with PLUMED (http://www.plumed.org/)  and use
that to run your umbrella sampling with replica exchange.

-Marc

On Thu, Mar 8, 2018 at 11:32 AM, Mayank Dixit 
<dixit.maya...@gmail.com<mailto:dixit.maya...@gmail.com>>
wrote:

Dear Gromacs Users,
I would like to calculate the potential of mean force between sodium and
chloride ion pair in water using replica exchange umbrella sampling method
in gromacs. Please let me know the details of replica exchange umbrella
sampling in gromacs.

Thanks and kind regards
Mayank

​


*Dr. Mayank  Dixit *
Post-doctoral fellow
Department of Chemistry
The city college of New York
Marshak Science Building
160 convent avenue 138th street.
New York, NY-10031
Cell no: 16465894905
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--
Marc Hoemberger
Ph.D. Candidate, Biochemistry and Biophysics,
Laboratory of Dorothee Kern
MS-009, 415 South St.
Brandeis University
Waltham, MA, 02453
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Re: [gmx-users] Potential energy coming out to be zero but not negative

[Erik Marklund]

Dear Shayantani,

The output you quote show a negative potential energy. Is that not for the run 
you refer to?

(With regards to “Hello Sir”, may I suggest a more gender inclusive greeting.)

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 23 Feb 2018, at 19:32, SHYANTANI MAITI 
<shyantani.ma...@gmail.com<mailto:shyantani.ma...@gmail.com>> wrote:

Hello Sir,

When I go for energy minimization for a protein complex containing 3
proteins, I obtain potential energy being minimized upto zero from
positive. The potential energy is not becoming negative even after running
for many steps as viewed in potential.xvg obtained after energy
minimzation.

Energy  Average   Err.Est.   RMSD  Tot-Drift

---
Potential-6.06412e+061.2e+06 5.5e+07 -7.26522e+06
(kJ/mol)

Is the energy minimization considerable for further equilibration or do I
need to obtain only negative energy and after that only should I start my
equilibration? Does the value of potential energy  obtained after
minimization need to be  negative in all cases? Can I continue my
equilibration with this result?

Thanking you

--
Best regards,
*Shyantani Maiti*
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Re: [gmx-users] Why the '5-Helix' randomly displayed in the scount.xvg after running do_dssp?

[Erik Marklund]

Dear Cheng,

Gromacs is open source. Implement this at your own will. If there is a 
sufficient interest in such a feature it might even have a place in the 
official release at some point.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 22 Feb 2018, at 18:19, ZHANG Cheng 
<272699...@qq.com<mailto:272699...@qq.com>> wrote:

Dear Gromacs,
The scount.xvg file was obtained after running


echo 1 | gmx do_dssp -f md_0_1_noPBC.xtc -s md_0_1.tpr -ssdump ssdump.dat -map 
ss.map -o ss.xpm -sc scount.xvg -a area.xpm -ta totarea.xvg -aa averarea.xvg 
-tu ns


The secondary structures listed are:
'Structure','Coil','B-Sheet','B-Bridge','Bend','Turn','A-Helix','3-Helix','5-Helix'


I ran the command for different proteins. It surprised me that the last 
'5-Helix' randomly displayed in the scount.xvg. Maybe some proteins did not 
have the '5-Helix', but why not just show them as 0? Can this be improved?


Because I am using a script to read the scount.xvg files, so I want all the 
files have the same format.


Thank you.


Yours sincerely
Cheng
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Re: [gmx-users] gmx hbond

[Erik Marklund]

Hi Negar,

Correct, the -dist option doesn’t do what you want it to. I cannot come up with 
a recipe for how to do this, but I suspect multiple rounds of gmx select and 
gmx hbond might do the trick.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 5 Feb 2018, at 15:49, negar habibzadeh 
<negar...@gmail.com<mailto:negar...@gmail.com>> wrote:

Hi

I want to calculate *number of hydrogen bond* by *distance from center of
bilayer*.
i use gmx hbonds -dist but it doesn't give me the proper 
result.is<http://result.is> it true?
which options should i implement to get the best result?

best regads
-negar
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Re: [gmx-users] how to set hetrodimer for MD Simulation

[Erik Marklund]

Dear Rana,

a) We are not (necessarily) Amber users. This is a gromacs mailing list.

b) If the separate structures are correctly positioned relative to each other, 
you basically just need to cut-and-paste the ATOM records from one pdb file 
into the other one.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 22 Nov 2017, at 22:15, Rana Rehan Khalid 
<rrkha...@umich.edu<mailto:rrkha...@umich.edu>> wrote:

Dear Amber users

My protein system consist of two subunit chains alpha and beta each chain
consist four domains. I predicted the structure of both subunit chains now
i want to combine both structure  subunits models, How i can combine them
in one pdb file.  so that i can run the simulation on complete structure.
Kindly guide me.

Regards
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Re: [gmx-users] autocorrelation function and residence time

[Erik Marklund]

Dear Tsaneem,

Negative values don’t signify lack of correlation, but anticorrelation. Also, 
by omitting negative values you introduce a slight bias in your fit towards 
longer half-life.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 22 Sep 2017, at 06:18, Tasneem Kausar 
<tasneemkausa...@gmail.com<mailto:tasneemkausa...@gmail.com>> wrote:

Thank you for reply

I read the references and I know that one of the columns of g_hbond output
is without subtraction
and the value ranges between 0 to 1. The only help I need is that can I
fit the curve of the first column (which has negative value) and neglect
the range of curve of negative part while fitting to get the exponential
parameters of the curve. This seems to me reasonable only for getting
information parameter as negative ACF value mean no correlation parameter.

Any help will be appreciated.

Thanks in Advance.

On Thu, Sep 21, 2017 at 2:54 PM, Erik Marklund 
<erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>>
wrote:

Dear Tasneem,

Quite often ACF calculations involve subtraction of the average signal,
and this normally renders some negative values in the ACF. It’s been a bit
too long since I dealt with the gmx hbond code, but I suspect that is what
is going on here. I suggest reading the references that gmx hbond mentions,
where the four quantities in the output are defined.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se><mailto:erik.markl...@kemi.uu.se>

On 21 Sep 2017, at 11:12, Tasneem Kausar 
<tasneemkausa...@gmail.com<mailto:tasneemkausa...@gmail.com><
mailto:tasneemkausa...@gmail.com>> wrote:

Still waiting for suggestions.

On Wed, Sep 20, 2017 at 9:42 AM, Tasneem Kausar 
<tasneemkausa...@gmail.com<mailto:tasneemkausa...@gmail.com>
<mailto:tasneemkausa...@gmail.com>>
wrote:

Dear all

I want to calculate residence time of interface water molecules at protein
interface. I am using Gromacs-4.6.4.
I am using using following command
g_hbond -s protein.tpr -f protein.xtc -b 2000 -n proein.ndx -ac
protein_ac.xvg -contact
In the index file there are protein interface residues and  8 water
molecule that are present at the protein interface. I have selected protein
interface and 8 water for calculation. In the output of autocorrelation
there are four y axis columns. I came through reply of Erik. He mentioned
the effect of periodic boundary condition on the output. In my case first y
axis has several negative values. I want to do an exponential fit with
function y=exp(-(x/t)^n) to obtain value of t and b. Can we skip the
negative values of the output file? If yes what is the reason to do that.
If I am wrong please suggest me to do the right way to obtain residence
time.


Thanks in Advance

Tasneem Kausar



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Re: [gmx-users] autocorrelation function and residence time

[Erik Marklund]

Dear Tasneem,

Quite often ACF calculations involve subtraction of the average signal, and 
this normally renders some negative values in the ACF. It’s been a bit too long 
since I dealt with the gmx hbond code, but I suspect that is what is going on 
here. I suggest reading the references that gmx hbond mentions, where the four 
quantities in the output are defined.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 21 Sep 2017, at 11:12, Tasneem Kausar 
<tasneemkausa...@gmail.com<mailto:tasneemkausa...@gmail.com>> wrote:

Still waiting for suggestions.

On Wed, Sep 20, 2017 at 9:42 AM, Tasneem Kausar 
<tasneemkausa...@gmail.com<mailto:tasneemkausa...@gmail.com>>
wrote:

Dear all

I want to calculate residence time of interface water molecules at protein
interface. I am using Gromacs-4.6.4.
I am using using following command
g_hbond -s protein.tpr -f protein.xtc -b 2000 -n proein.ndx -ac
protein_ac.xvg -contact
In the index file there are protein interface residues and  8 water
molecule that are present at the protein interface. I have selected protein
interface and 8 water for calculation. In the output of autocorrelation
there are four y axis columns. I came through reply of Erik. He mentioned
the effect of periodic boundary condition on the output. In my case first y
axis has several negative values. I want to do an exponential fit with
function y=exp(-(x/t)^n) to obtain value of t and b. Can we skip the
negative values of the output file? If yes what is the reason to do that.
If I am wrong please suggest me to do the right way to obtain residence
time.


Thanks in Advance

Tasneem Kausar



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Re: [gmx-users] Regarding calculation of Lennard-Jones potential

[Erik Marklund]

Dear Dilip,

The LJ parameters are present in the topology file and the force-field files 
included within. So no need to calculate anything, just to locate them in said 
files.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 18 Sep 2017, at 05:42, Dilip H N 
<cy16f01.di...@nitk.edu.in<mailto:cy16f01.di...@nitk.edu.in>> wrote:

Hello,
I have a simulation mixture of aminoacid (eg., glycine) with water and
cosolvent. I want to calculate Lennard-Jones Parameters of the all atom
types. How can i calculate it...??

Can it be done with commands, or any other method..??
Any suggestions are appreciated...

Thank you..

--
With Best Regards,

DILIP.H.N
Ph.D Student



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Re: [gmx-users] regarding hydrogen bond correlation function for Cdd for TIP4P/2005 water model

[Erik Marklund]

Dear Abhinav,

This is a bit tricky. We implemented the geminate recombination model some time 
ago, but have taken it our of the gmx hbond tool because it complicates the 
code quite a lot.

That said, if you want to use that old code you first need to "pbc-unwrap” your 
trajectory using trjconv -nojump. Try that and see if you get more reasonable 
output.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 13 Sep 2017, at 06:16, Abhinav Srivastava (P14CHM002) 
<srivastav...@iitj.ac.in<mailto:srivastav...@iitj.ac.in>> wrote:

Dear Gromacs Users,

Kindly consider this as my query mail as in the last mail, subject line was
not complete. I apologize for the same .
I am trying to calculate hydrogen bond correlation function Cdd(t) for bulk
water (TIP4P/2005 water) using reversible geminate recombination as
mentioned in
Markovitch et al., J. Chem. Phys.,129,084505(2008).

Following is the command which I have used :

g_hbond -f NVT.xtc -s NVT.tpr -n bulk-water.ndx -b 0 -e 100 -P 1 -temp 308
-geminate dd -ac Cdd-bulk-water.xvg

I have simulated two systems viz. smaller system consisting of 851 water
molecules and a bigger system consisting of 1944 water molecules. I am not
able to get t^-3/2 scaling in hydrogen bond correlation function for Cdd
case in both these systems. It would be nice if you can please help me.
Thanks in advance.

--
*Abhinav Srivastava*
*Research Scholar*
Indian Institute of Technology, Jodhpur
Rajasthan
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Re: [gmx-users] Difference in hydrogen bond lifetimes with and without pbc

[Erik Marklund]

Dear Apramita,

What version are you using? There might have been some PBC-related bugs that 
were fixed if memory serves me right.

Kind regards
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 29 Aug 2017, at 15:26, Apramita Chand 
<apramita.ch...@gmail.com<mailto:apramita.ch...@gmail.com>> wrote:

Dear Eric and other Gromacs users,
Thanks for clarifying about how different timescale of trajectories can
affect lifetimes
But the case with and without pbc have same length of trajectories (100 ns).
Then why the difference in lifetimes ( 1793ps with pbc and 2345 without pbc)
Which can be regarded as more accurate?

Yours sincerely,
Apramita
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Re: [gmx-users] Difference in Hydrogen Bond Lifetimes on truncating trajectory and also on using pbc

[Erik Marklund]

Dear Apramita,

Right. Still, the same still applies with regards to the -666.

It could be a matter of statistics, why you get sensible values for the longer 
trajectory chunk. Also, note that the trajectory length limits the possible 
timescales that the model can tease out. If I understand correctly, your 
trajectories with and without pic have different length, so I’m not surprised 
that the kinetic constants that you get out are different.

Kind regards,
Erik

__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 29 Aug 2017, at 14:02, Apramita Chand 
<apramita.ch...@gmail.com<mailto:apramita.ch...@gmail.com>> wrote:

Dear Eric,
Its actually the DG(kj/mol) value  which is -666. The time is coming to
be-126 ps. But the g_hbond is failing to fit the kinetic model to the data
for the last 60ns as you have implied. Any reasons why this could have
happened, while for the entire trajectory, I am getting positive values?
But for the entire trajectory, with and without pbc(1793ps and 2345ps
respectively) , I have two separate values for lifetime. Which one should I
take?

I would be appreciative of any suggestions

Looking forward to your help,

yours sincerely
Apramita

















*Message:( 2 Date: Tue, 29 Aug 2017 08:09:32 + From: Erik Marklund
<erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> 
<erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>>> To:
"gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org> 
<gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org>>" 
<gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org>
<gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org>>> Subject: Re: [gmx-users] 
Difference in Hydrogen
Bond Lifetimes on truncating trajectory and also on using pbc
Message-ID: 
<e2a33c50-036b-4dc7-9f79-bc136147f...@kemi.uu.se<mailto:e2a33c50-036b-4dc7-9f79-bc136147f...@kemi.uu.se>
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text/plain; charset="utf-8" Dear Apramita, IIRC, the time is set to.-666
when gmx hbond fails to fit the kinetic model to the data. Not the most
informative way of indicating an error perhaps. Kind regards, Erik
__*



* Erik Marklund, PhD, Marie Sk?odowska Curie INCA Fellow
Department of Chemistry ? BMC, Uppsala University +46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> 
<erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>><*

*mailto:erik.markl...@kemi.uu.se 
<erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>>> On 29 Aug
2017, at 07:20, Apramita Chand 
<apramita.ch...@gmail.com<mailto:apramita.ch...@gmail.com>
<apramita.ch...@gmail.com<mailto:apramita.ch...@gmail.com>><*



















*mailto:apramita.ch...@gmail.com 
<apramita.ch...@gmail.com<mailto:apramita.ch...@gmail.com>>>> wrote: Dear
All, I've carried out a 100ns simulation of protein in water and want to
calculate hydrogen bond (forward) lifetime between Protein-Water.
Initially, I thought it would be better to analyse hydrogen bonds in last
60ns of simulation, so I truncated the trajectory using g_trjconv using -b
4 -e 10 as options. The results came as *ACF
10628/10628Normalization for c(t) = 0.0621737 for gh(t) = 2.07246e-06Back
Off! I just backed up hbac1.xvg to ./#hbac1.xvg.1#Hydrogen bond
thermodynamics at T = 300 KFitting parameters chi^2 = 2.8733Q =
 0-*


























*-Type Rate (1/ps) Time (ps)  DG (kJ/mol)
Chi^2Forward-0.008 -126.851-666.000  2.8733* (This came for
both with and without pbc). I also tried to do it from the g_hbond command
itself by giving starting time as 40ns and ending as 100ns, but again it
came negative lifetime. Next, I tried g_trjconv with application of -pbc
mol -ur compact options on untruncated(100ns) trajectory. The results came
as: *ACF 11303/11303Normalization for c(t) = 0.0615891 for gh(t) =
1.23179e-06Back Off! I just backed up hbac1.xvg to ./#hbac1.xvg.2#Hydrogen
bond thermodynamics at T = 300 KFitting parameters chi^2 =3.03095Q =
 0-*




















*-Type Rate (1/ps) Time (ps)  DG (kJ/mol)
Chi^2Forward 0.001 1793.775  23.259 3.03095* When I tried
the same with the original unconverted trajectory(without g_trjconv
,without pbc options), I got a lifetime of *2345.890ps*. *My question is
,1) why do the truncated trajectories give negative values for my
simulation?* *2)If I take the whole 100ns for analysis of hydrogen bond
lifetime, wh

Re: [gmx-users] gmx analyze Luzar analysis

[Erik Marklund]

Dear Valerio,

Have a glance at the paper by Luzar and Chandler.

Btw: your data doesn’t fit with the kinetic model very well, hence the -666 for 
the integral.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 29 Aug 2017, at 13:52, Valerio Ferrario 
<valerio.ferra...@gmail.com<mailto:valerio.ferra...@gmail.com>> wrote:

Dear all,

I am trying to obtain parameters for h-bonds. I used the tool gmx hbonds
with -ac option but resulted in segmentation fault. Therefore from the
normal gmx hbond output I used gmx analyze to obtain the autocorrelation
function. Therefore, using again gmx analyze with -luzar options and the
autorrelated xvg as input I want to calculate the hbonds parameters. I have
an output like this:

Hydrogen bond thermodynamics at T = 300 K
One-way 0.006156.395   17.174
Integral  -0.076- 13.220-666.000
Relaxation  1.0380.963 4.478

So my question is: what are the different values? I do not understand what
those values indicate since no "legend" is provide. I guess that 2 of the 3
values for relaxation might be k and k´ (rate constant for breaking and
reforming hbonds), but I am not sure... Can anyone help me in interpreting
those numbers?
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Re: [gmx-users] g_cluster

[Erik Marklund]

Dear Nikolai,

Group 1.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 24 Aug 2017, at 00:07, Smolin, Nikolai 
<nikolai.smo...@gmail.com<mailto:nikolai.smo...@gmail.com>> wrote:

Dear All,

I am using g_cluster. I am wondering what two groups used for?

group 1 for fit and RMSD calculation
group 2 for output

is g_cluster use RMSD values for clustering based on group 1 or group 2?


Any suggestions?

Thanks
Nikolai
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Re: [gmx-users] g_hbonds calculation on GPU

[Erik Marklund]

Dear Rraj,

Nope. No-one has made GPU support for gmx hbond (or any other analysis tool as 
far as I know).

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 9 Aug 2017, at 14:16, Rituraj Purohit 
<riturajpuro...@gmail.com<mailto:riturajpuro...@gmail.com>> wrote:

Hi Everyone,
I would like to run g_hbons calculation on GPU boards. I could only find
--nthreads option to fasten my calculations, Is it possible to use GPU
boards for this like mdrun.
reg
Rraj
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Re: [gmx-users] Regarding indexing to calculate hydrogen bond autocorrelation function

[Erik Marklund]

On 26 Jul 2017, at 19:04, Dilip H N 
> wrote:

but i dont have any OH or NH groups in glycine,water mixture...

Your water is packed with OH, and glycine has both NH and OH.

Kind regards,
Erik
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Re: [gmx-users] ForceField for Zn

[Erik Marklund]

…here: https://kamerlinlab.com/

On 24 Jul 2017, at 14:14, Erik Marklund 
<erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>> wrote:

Hi,

Metal ions are tricky, and Zn is particularly beasty. Check out Kammerlin’s 
work in this area.

Kind regards,
Erik
______
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se><mailto:erik.markl...@kemi.uu.se>

On 24 Jul 2017, at 13:24, Anjali Patel 
<anjalipatel60...@gmail.com<mailto:anjalipatel60...@gmail.com><mailto:anjalipatel60...@gmail.com>>
 wrote:

Hello to all

In my pdb structure their are two ion of Zn; Can anyone suggest which
forcefield is appropriate for that.


With regards
Anjali Patel
Research Scholar
Department of Physics
The M S University of Baroda, Vadodara-390002
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Re: [gmx-users] ForceField for Zn

[Erik Marklund]

Hi,

Metal ions are tricky, and Zn is particularly beasty. Check out Kammerlin’s 
work in this area.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 24 Jul 2017, at 13:24, Anjali Patel 
<anjalipatel60...@gmail.com<mailto:anjalipatel60...@gmail.com>> wrote:

Hello to all

In my pdb structure their are two ion of Zn; Can anyone suggest which
forcefield is appropriate for that.


With regards
Anjali Patel
Research Scholar
Department of Physics
The M S University of Baroda, Vadodara-390002
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Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

[Erik Marklund]

Hi Mark,

Exactly. But we want to phrase it such that it is legible in the legend if the 
file is plotted.

Erik

On 1 Jun 2017, at 16:51, Mark Abraham 
<mark.j.abra...@gmail.com<mailto:mark.j.abra...@gmail.com>> wrote:

Hi,

"Pairs within 0.35" has misled David, Justin and I, and doubtless others...
without clarification, it is normal to assume that if a hydrogen bond is
"pairs within 0.35 nm and a suitable angle," then "pairs within 0.35" would
be a superset of the former. But the field is actually "pairs within 0.35
that do not satisfy the angle requirement."

Mark

On Thu, Jun 1, 2017 at 3:47 PM Erik Marklund 
<erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>>
wrote:

Yes. The sets have no overlap. But for some reason putting that in a short
description seems difficult :-)

On 1 Jun 2017, at 15:31, Mark Abraham 
<mark.j.abra...@gmail.com<mailto:mark.j.abra...@gmail.com>> wrote:

Hi,

I still don't understand your description. Is the third column
*additional*
pairs within 0.35 that do not satisfy the angle criterion?

Mark

On Sat, May 27, 2017 at 4:36 PM Erik Marklund 
<erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>>
wrote:



On 26 May 2017, at 22:12, David van der Spoel 
<sp...@xray.bmc.uu.se<mailto:sp...@xray.bmc.uu.se>
<mailto:sp...@xray.bmc.uu.se>> wrote:

On 26/05/17 22:05, Erik Marklund wrote:
“Pairs within 0.35 nm”. They also don’t fulfil the angle criterion,
which
is why they are sometimes fewer than the hbonds.

Therefore I would assume they are more instead.


They sometimes are, but not necessarily. I pointed it out because
sometimes people ask if g_hbond is buggy when they see that there are
occasionally lower numbers in the third column, assuming that it
contains
all pairs within 3.5 Å regardless of angle which should more numeorus
than
the pairs that also fullfil the angle criterion. That’s not the meaning
of
the third column however.

Kind regards,
Erik

On 26 May 2017, at 19:38, Adarsh V. K. 
<adarsh_p13008...@nitc.ac.in<mailto:adarsh_p13008...@nitc.ac.in>
<mailto:adarsh_p13008...@nitc.ac.in>> wrote:

Dear all,

The 'gmx hbond' command returns a *.xvg file... viz. " hbnum.xvg "

I would like to edit the file before viewing in 'Xmgrace'

I opened the hbnum.xvg using 'gedit'. It shows following details (see
below)

Can you please tell me what is there in the third column of the file?

-
# gmx hbond is part of G R O M A C S:
#
# GROtesk MACabre and Sinister
#
@title "Hydrogen Bonds"
@xaxis  label "Time (ps)"
@yaxis  label "Number"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Hydrogen bonds"
@ s1 legend "Pairs within 0.35 nm"
 02   7
10   2   5
20   4   3
30   3   2
40   3   3
50   5   1
60   3   6
70   3   6
80   2   3
90   5   1
   100  3   3
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--
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Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205
<018-471%2042%2005> <018-471%2042%2005>
.
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Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

[Erik Marklund]

Yes. The sets have no overlap. But for some reason putting that in a short 
description seems difficult :-)

> On 1 Jun 2017, at 15:31, Mark Abraham <mark.j.abra...@gmail.com> wrote:
> 
> Hi,
> 
> I still don't understand your description. Is the third column *additional*
> pairs within 0.35 that do not satisfy the angle criterion?
> 
> Mark
> 
> On Sat, May 27, 2017 at 4:36 PM Erik Marklund <erik.markl...@kemi.uu.se>
> wrote:
> 
>> 
>> 
>> On 26 May 2017, at 22:12, David van der Spoel <sp...@xray.bmc.uu.se
>> <mailto:sp...@xray.bmc.uu.se>> wrote:
>> 
>> On 26/05/17 22:05, Erik Marklund wrote:
>> “Pairs within 0.35 nm”. They also don’t fulfil the angle criterion, which
>> is why they are sometimes fewer than the hbonds.
>> 
>> Therefore I would assume they are more instead.
>> 
>> 
>> They sometimes are, but not necessarily. I pointed it out because
>> sometimes people ask if g_hbond is buggy when they see that there are
>> occasionally lower numbers in the third column, assuming that it contains
>> all pairs within 3.5 Å regardless of angle which should more numeorus  than
>> the pairs that also fullfil the angle criterion. That’s not the meaning of
>> the third column however.
>> 
>> Kind regards,
>> Erik
>> 
>> On 26 May 2017, at 19:38, Adarsh V. K. <adarsh_p13008...@nitc.ac.in
>> <mailto:adarsh_p13008...@nitc.ac.in>> wrote:
>> 
>> Dear all,
>> 
>> The 'gmx hbond' command returns a *.xvg file... viz. " hbnum.xvg "
>> 
>> I would like to edit the file before viewing in 'Xmgrace'
>> 
>> I opened the hbnum.xvg using 'gedit'. It shows following details (see
>> below)
>> 
>> Can you please tell me what is there in the third column of the file?
>> 
>> -
>> # gmx hbond is part of G R O M A C S:
>> #
>> # GROtesk MACabre and Sinister
>> #
>> @title "Hydrogen Bonds"
>> @xaxis  label "Time (ps)"
>> @yaxis  label "Number"
>> @TYPE xy
>> @ view 0.15, 0.15, 0.75, 0.85
>> @ legend on
>> @ legend box on
>> @ legend loctype view
>> @ legend 0.78, 0.8
>> @ legend length 2
>> @ s0 legend "Hydrogen bonds"
>> @ s1 legend "Pairs within 0.35 nm"
>>   02   7
>>  10   2   5
>>  20   4   3
>>  30   3   2
>>  40   3   3
>>  50   5   1
>>  60   3   6
>>  70   3   6
>>  80   2   3
>>  90   5   1
>> 100  3   3
>> --
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>> 
>> 
>> 
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Head of Department, Cell & Molecular Biology, Uppsala University.
>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205 <018-471%2042%2005>
>> .
>> http://www.icm.uu.se<http://www.icm.uu.se/>
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Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

[Erik Marklund]

Hi Mark,

Thinking out loud: “Non-Hbonding pairs within 3.5 Å”.

Kind regards,
Erik

> On 27 May 2017, at 17:56, Mark Abraham <mark.j.abra...@gmail.com> wrote:
> 
> Hi,
> 
> So what should we document in the help text as the meaning, so we don't
> keep having emails about this?
> 
> Mark
> 
> On Sat, May 27, 2017 at 4:36 PM Erik Marklund <erik.markl...@kemi.uu.se>
> wrote:
> 
>> 
>> 
>> On 26 May 2017, at 22:12, David van der Spoel <sp...@xray.bmc.uu.se
>> <mailto:sp...@xray.bmc.uu.se>> wrote:
>> 
>> On 26/05/17 22:05, Erik Marklund wrote:
>> “Pairs within 0.35 nm”. They also don’t fulfil the angle criterion, which
>> is why they are sometimes fewer than the hbonds.
>> 
>> Therefore I would assume they are more instead.
>> 
>> 
>> They sometimes are, but not necessarily. I pointed it out because
>> sometimes people ask if g_hbond is buggy when they see that there are
>> occasionally lower numbers in the third column, assuming that it contains
>> all pairs within 3.5 Å regardless of angle which should more numeorus  than
>> the pairs that also fullfil the angle criterion. That’s not the meaning of
>> the third column however.
>> 
>> Kind regards,
>> Erik
>> 
>> On 26 May 2017, at 19:38, Adarsh V. K. <adarsh_p13008...@nitc.ac.in
>> <mailto:adarsh_p13008...@nitc.ac.in>> wrote:
>> 
>> Dear all,
>> 
>> The 'gmx hbond' command returns a *.xvg file... viz. " hbnum.xvg "
>> 
>> I would like to edit the file before viewing in 'Xmgrace'
>> 
>> I opened the hbnum.xvg using 'gedit'. It shows following details (see
>> below)
>> 
>> Can you please tell me what is there in the third column of the file?
>> 
>> -
>> # gmx hbond is part of G R O M A C S:
>> #
>> # GROtesk MACabre and Sinister
>> #
>> @title "Hydrogen Bonds"
>> @xaxis  label "Time (ps)"
>> @yaxis  label "Number"
>> @TYPE xy
>> @ view 0.15, 0.15, 0.75, 0.85
>> @ legend on
>> @ legend box on
>> @ legend loctype view
>> @ legend 0.78, 0.8
>> @ legend length 2
>> @ s0 legend "Hydrogen bonds"
>> @ s1 legend "Pairs within 0.35 nm"
>>   02   7
>>  10   2   5
>>  20   4   3
>>  30   3   2
>>  40   3   3
>>  50   5   1
>>  60   3   6
>>  70   3   6
>>  80   2   3
>>  90   5   1
>> 100  3   3
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>> 
>> 
>> 
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>> Head of Department, Cell & Molecular Biology, Uppsala University.
>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205 <018-471%2042%2005>
>> .
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Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

[Erik Marklund]

On 26 May 2017, at 22:12, David van der Spoel 
<sp...@xray.bmc.uu.se<mailto:sp...@xray.bmc.uu.se>> wrote:

On 26/05/17 22:05, Erik Marklund wrote:
“Pairs within 0.35 nm”. They also don’t fulfil the angle criterion, which is 
why they are sometimes fewer than the hbonds.

Therefore I would assume they are more instead.


They sometimes are, but not necessarily. I pointed it out because sometimes 
people ask if g_hbond is buggy when they see that there are occasionally lower 
numbers in the third column, assuming that it contains all pairs within 3.5 Å 
regardless of angle which should more numeorus  than the pairs that also 
fullfil the angle criterion. That’s not the meaning of the third column however.

Kind regards,
Erik

On 26 May 2017, at 19:38, Adarsh V. K. 
<adarsh_p13008...@nitc.ac.in<mailto:adarsh_p13008...@nitc.ac.in>> wrote:

Dear all,

The 'gmx hbond' command returns a *.xvg file... viz. " hbnum.xvg "

I would like to edit the file before viewing in 'Xmgrace'

I opened the hbnum.xvg using 'gedit'. It shows following details (see below)

Can you please tell me what is there in the third column of the file?

-
# gmx hbond is part of G R O M A C S:
#
# GROtesk MACabre and Sinister
#
@title "Hydrogen Bonds"
@xaxis  label "Time (ps)"
@yaxis  label "Number"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Hydrogen bonds"
@ s1 legend "Pairs within 0.35 nm"
   02   7
  10   2   5
  20   4   3
  30   3   2
  40   3   3
  50   5   1
  60   3   6
  70   3   6
  80   2   3
  90   5   1
 100  3   3
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Re: [gmx-users] Third column of the " hbnum.xvg " file?...What is it meant for ?

[Erik Marklund]

“Pairs within 0.35 nm”. They also don’t fulfil the angle criterion, which is 
why they are sometimes fewer than the hbonds.

Kind regards,
Erik

> On 26 May 2017, at 19:38, Adarsh V. K.  wrote:
> 
> Dear all,
> 
> The 'gmx hbond' command returns a *.xvg file... viz. " hbnum.xvg "
> 
> I would like to edit the file before viewing in 'Xmgrace'
> 
> I opened the hbnum.xvg using 'gedit'. It shows following details (see below)
> 
> Can you please tell me what is there in the third column of the file?
> 
> -
> # gmx hbond is part of G R O M A C S:
> #
> # GROtesk MACabre and Sinister
> #
> @title "Hydrogen Bonds"
> @xaxis  label "Time (ps)"
> @yaxis  label "Number"
> @TYPE xy
> @ view 0.15, 0.15, 0.75, 0.85
> @ legend on
> @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "Hydrogen bonds"
> @ s1 legend "Pairs within 0.35 nm"
> 02   7
>10   2   5
>20   4   3
>30   3   2
>40   3   3
>50   5   1
>60   3   6
>70   3   6
>80   2   3
>90   5   1
>   100  3   3
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Re: [gmx-users] gmx hbond

[Erik Marklund]

Dear Moshen,

I doubt the difference in versions will cause any problems in this case.

The second column is ill-described. It contains the number of pairs within 0.3 
nm that don’t fulfil the angle criterion.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 14 Apr 2017, at 03:20, Mohsen Ramezanpour 
<ramezanpour.moh...@gmail.com<mailto:ramezanpour.moh...@gmail.com>> wrote:

Hi Gromacs users,

I have a question regarding the output file from g_hbond:

First:I have done my simulations with version 4.6.7 and doing the analysis
with version 2016.2
Will this cause any hidden problem in analysis? the analysis is working
fine but I am asking about the correctness of results because of this
change.


Second and the main question:

When I use this command:
gmx hbond -f md.xtc -n index.ndx -s  file.tpr -num hbond.xvg -g test.log -r
0.30

I get this:

...
@ s0 legend "Hydrogen bonds"
@ s1 legend "Pairs within 0.3 nm"
   400   0
*  40.1   1   0*
 40.2   1   3
 40.3   2   2
 40.4   0   2
 40.5   1   1
*  40.6   2   0*
...
the first column is time frame
the second is number of h-bonds
the third is "Pairs within 0.3 nm"


by -r 0.30 I wanted to change the cut-off for h-bond definition.
i.e. report a h-bond if and only if the D...A distance is less or equal to
0.30 ns, AND, the angle of H..D...A is less or equal than 35 (this angle is
default in 2016.2 version).

Regarding the highlighted lines:
How it is possible that the there is not any pair in this distance but we
still have hbond?
If they are not in this cut-off, thy should not be recognized as hbond
either.

I assume the pair means the D...A pair because I did NOT use -noda  option.

Also, it does not give any test.log file, and other problems :-)

Please let me know your opinion about this results.

Thanks in advance for your reply
Cheers
Mohsen


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Re: [gmx-users] Md simulation by Gromacs

[Erik Marklund]

Dear Maria,

Let’s keep this to the user list. I am first of all not a private tutor. 
Secondly, the answers you get (below) might be relevant for others.

> On 6 Apr 2017, at 16:04, maria khan <mariabiochemi...@gmail.com> wrote:
> 
> Good evening Dear sir Erik Marklund..
> 
> I am very Thankful for your attention ..Actually i even dont know the basics 
> and one of the NAMD expert user told me so that gromacs use united atom ff 
> thats why gromacs is fast and NAMD use all atom thats why it is slow.
> 

That is incorrect. Gromacs can do both all-atom and united-atom. Gromacs can 
also make use of virtual sites, which allows for a longer time step, hence more 
simulated ns per hour. You can also choose not to. And then there are on top of 
that a number of reasons why gromacs is really fast without cutting (important) 
corners.

> Now my problems are : is there any option for considering hydrogen atom  to 
> process its calculation in MD run as last time when i did simulation i 
> applied the command of ignoring hydrogen atom ,,secondly what is the 
> difference Between ignoring h- atoms and considering it in MD running.I mean 
> would it effect the result of calculation after MD run..and if there is 
> option for taking h- atom as part of amino acid then why there is an option 
> for ignoring it..
> 

Please be specific. Are you referring to pdb2gmx -ignh? That just tells pdb2gmx 
to derive hydrogen positions and occupancies based on hydrogen bonding patterns 
and force-field-related information. It doesn’t normally produce topologies 
without hydrogens, and the hydrogens are thus part of the subsequent 
simulations. See the user-list archives. I know this has been discussed before. 
And you can also inspect the output files to see what they contain.

> Furthermore i dont know about forming parameters for my ligand thats is 
> alkaloid so im confuse how to form its parameter and if some one has 
> published its parameters then how i can find..i just need a stepwise protocol 
> for MD simulation,,most of the manuals are not understandable my majors are 
> pure biochemistry and mostly the explanations there are mathematica basedl.
> 

Well, parametrisation is not really for beginners. I also think others are more 
experienced in that area than I am.

> And yes i have studied the old version of manuals not updated one.
> 
> IF u have simplist form of manuals or any other stuff, kindly send me that i 
> very thankful. Last time u shared a paper of ur self but it was not my 
> research related.
> 

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Re: [gmx-users] Fast energy evaluation

[Erik Marklund]

Dear Andras,

Concatenate all structures into one trajectory and issue gmx mdrun -rerun. That 
will evaluate the energies for all conformations. You will of course need a tpr 
file too.

Kind regards,
Erik
__
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Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 6 Apr 2017, at 12:39, András Ferenc WACHA 
<wacha.and...@ttk.mta.hu<mailto:wacha.and...@ttk.mta.hu>> wrote:

Dear Gromacs Users,

does someone know a way to quickly evaluate the energy of a few structures?

In more detail:

I have several conformations of the same peptide, stored in PDB format.
In principle, they have the same topology. I want to optimize various
force field parameters, which involves the need to calculate the energy
multiple times, each time with different bond/angle/dihedral parameters.
Currently I use a single-step mdrun (integrator = steep) and
"gmx_energy" to extract the energy terms, but the overhead of calling
grompp, mdrun and energy in each case for each structure is too much. In
charmm you can write a script for this job: is there an equivalent in
gromacs without the overheads?

Thank you in advance.

Best regards,

András Wacha

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Re: [gmx-users] (no subject)

[Erik Marklund]

Dear Maria,

Are you confusing gromos and gromacs?

In the manual, under the Force fields heading: "GROMACS 2016 includes several 
force fields, and additional ones are available on the website. If you do not 
know which one to select we recommend GROMOS-96 for united-atom setups and 
OPLS-AA/L for all-atom parameters. That said, we describe the available options 
in some detail.”

(The comment about OPLS-AA/L is probably very old and in need of revision.)

Then follows subsections describing a range of supported force fields, most of 
which are all-atom. The phrase “united-atom” occurs only once in the manual, in 
the sentence quoted above. What made you think gromacs is united-atom only?

Kind regards,
Erik
__
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Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 5 Apr 2017, at 12:00, maria khan 
<mariabiochemi...@gmail.com<mailto:mariabiochemi...@gmail.com>> wrote:

Dear Erik..

I have studied the manuals of gromacs and from that i came to know that
gromacs use united atom ff thats why i asked and in manuals many things has
been explained by quantum basis,,which is not understandable for me.

How can i find ff parameters for my ligand of interest?? also if
ff parameters are not in published form then it means i will not be able to
use that ligand for MD run?? My ligand of interest is alkaloid. and i dont
know how can i make the parameters for it.

Thank you.
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Re: [gmx-users] Hydrogen bond occupancy

[Erik Marklund]

Dear Neha,

What fraction of the time the ligand hydrogen bonds to whatever it interacts 
with.

Kind regards,
Erik
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Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
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On 5 Apr 2017, at 10:00, Neha Gupta 
<nehaphysic...@gmail.com<mailto:nehaphysic...@gmail.com>> wrote:

Hi gromacs users,

What is meant by Hydrogen bond occupancy in protein ligand simulations?

What information do we extract from % of hydrogen bond occupancy?

Thanks,
Neha
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Re: [gmx-users] Charmm ff compatibility with Gromacs

[Erik Marklund]

Dear Maria,

Please see below.

Kind regards,
Erik

> On 5 Apr 2017, at 09:08, maria khan  wrote:
> 
> Hello Gromacs users..
> 
> Charmm 37 ff is for charmm and Namd which is all atom ff using codes,,and
> gromacs is united atom so how can its results will be reliable as these are
> different things??.My protein of interest is having DNA..
> 

This does not make sense. What do you mean by “using codes”? And while gromacs 
can do united atom, all-atom force fields are routinely used with gromacs.

> Secondly how can i find ff parameters for my ligand of interest?? also if
> ff parameters are not in published form then it means i will not be able to
> use that ligand for MD run??
> 
> Regards..
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Re: [gmx-users] vsites with CHARMM force fields

[Erik Marklund]

On 31 Mar 2017, at 10:51, Ramon Crehuet Simon 
<ramon.creh...@iqac.csic.es<mailto:ramon.creh...@iqac.csic.es>> wrote:

In that case, does it make sense to use virtual sites to allow 4fs time step? 
In other words, if vsites remove the fastest degrees of freedom, but we do not 
constrain bond distances, will a 4 fs time-step be stable?

No.

Kind regards,
Erik Marklund
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Re: [gmx-users] solvate with hexagonal box

[Erik Marklund]

Done! https://redmine.gromacs.org/issues/2148

On 28 Mar 2017, at 10:24, Erik Marklund 
<erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>> wrote:

Hi Mark,

Thanks. I will do so once my collaborators confirm that it’s ok that I upload 
the structure files.

Kind regards,
Erik
______
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se><mailto:erik.markl...@kemi.uu.se>

On 27 Mar 2017, at 20:20, Mark Abraham 
<mark.j.abra...@gmail.com<mailto:mark.j.abra...@gmail.com><mailto:mark.j.abra...@gmail.com>>
 wrote:

Hi,

Sounds like there is something worth improving, although I can't answer
your questions right now. Please open an issue on
https://redmine.gromacs.org and attach a tarball of suitable inputs for the
two(?) cases.

Mark

On Mon, 27 Mar 2017 13:54 Erik Marklund 
<erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se><mailto:erik.markl...@kemi.uu.se>>
 wrote:

Dear gmx-users,

We are trying to merge a box containing a peripheral membrane protein with
another box generated with memgen. Both boxes are hexagonal and exactly the
same size,Naively, we thought that gmx solvate -cp protein.gro -cs
membrane_and_water.gro would do the trick. Unfortunately, this causes gmx
solvate to crash:

Generating solvent configuration
Will generate new solvent configuration of 1x2x1 boxes
Solvent box contains 99373 atoms in 28208 residues
Removed 12253 solvent atoms due to solvent-solvent overlap
Removed 5122 solvent atoms due to solute-solvent overlap
Sorting configuration
Found 2 different molecule types:
 POPE (  52 atoms):   233 residues
  SOL (   3 atoms): 23294 residues
gmx(16892,0x7fffaa24f3c0) malloc: *** error for object 0x7fe36d0008f0:
pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
Abort trap: 6

So we then tried to remove the membrane, keeping only the water, and use
that system as the argument for -cs. Gmx solvate doesn’t crash now, but the
output file has strange gaps of some size in the water parts, which cannot
be explained by the removed lipids. Can gmx solvate not handle
non-orthogonal boxes as arguments for -cs?

The whole point in doing it this way was to avoid water molecules being
inserted in the membrane. Perhaps overkill, but I am quite surprised at how
bad things went with gmx solvate.

Kind regards,
Erik

__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se><mailto:erik.markl...@kemi.uu.se><mailto:erik.markl...@kemi.uu.se>

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Re: [gmx-users] Bond energy difference between CHARMM and GROMACS

[Erik Marklund]

Dear Yvon,

Are you sure you ‘re not constraining, say, H-bonds in one and not the other?

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 28 Mar 2017, at 07:55, Yvon Wong 
<wong.y...@gmail.com<mailto:wong.y...@gmail.com>> wrote:

I try to compare the energy in CHARMM and GROMACS.
After running 4 systems I found the dihedral energies are the same, but the
bond energies are different.
Can somebody help me to solve this problem?

(1)Only one residue: MET

Bond:

0.44*4.18   =   1.839 (CHARMM)  >  2.587 (GROMACS)   (different)
Dihedral:

3.687* 4.18 = 15.4116 (CHRAMM)  > 15.4448 (GROMACS)  (the same)

(2)Only one residue: GLY
BONDS:

 0.34243*4.18=  1.431  ===> 1.209


Dihedrals
1.77911*4.18 = 7.436  ===> 7.447

(3)5 -residue:  ASN GLY PHE TRP THR
BONS:

4.82777* 4.18=20.1800   >   22.58


DIHE:
37.82747*4.18 =  158.1188   >  158.504

(4)20- residue:  GLY LYS MET PHE SER TRP TYR VAL ALA ARG CYS VAL PRO
TRP MET SER SER LYS LYS MET
BONDS

17.48049 * 4.18 =73.068  ===>   78.64


DIHE

185.71* 4.18  =   776.26  ===>  777.32
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Re: [gmx-users] solvate with hexagonal box

[Erik Marklund]

Hi Mark,

Thanks. I will do so once my collaborators confirm that it’s ok that I upload 
the structure files.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 27 Mar 2017, at 20:20, Mark Abraham 
<mark.j.abra...@gmail.com<mailto:mark.j.abra...@gmail.com>> wrote:

Hi,

Sounds like there is something worth improving, although I can't answer
your questions right now. Please open an issue on
https://redmine.gromacs.org and attach a tarball of suitable inputs for the
two(?) cases.

Mark

On Mon, 27 Mar 2017 13:54 Erik Marklund 
<erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>> wrote:

Dear gmx-users,

We are trying to merge a box containing a peripheral membrane protein with
another box generated with memgen. Both boxes are hexagonal and exactly the
same size,Naively, we thought that gmx solvate -cp protein.gro -cs
membrane_and_water.gro would do the trick. Unfortunately, this causes gmx
solvate to crash:

Generating solvent configuration
Will generate new solvent configuration of 1x2x1 boxes
Solvent box contains 99373 atoms in 28208 residues
Removed 12253 solvent atoms due to solvent-solvent overlap
Removed 5122 solvent atoms due to solute-solvent overlap
Sorting configuration
Found 2 different molecule types:
  POPE (  52 atoms):   233 residues
   SOL (   3 atoms): 23294 residues
gmx(16892,0x7fffaa24f3c0) malloc: *** error for object 0x7fe36d0008f0:
pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
Abort trap: 6

So we then tried to remove the membrane, keeping only the water, and use
that system as the argument for -cs. Gmx solvate doesn’t crash now, but the
output file has strange gaps of some size in the water parts, which cannot
be explained by the removed lipids. Can gmx solvate not handle
non-orthogonal boxes as arguments for -cs?

The whole point in doing it this way was to avoid water molecules being
inserted in the membrane. Perhaps overkill, but I am quite surprised at how
bad things went with gmx solvate.

Kind regards,
Erik

__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se><mailto:erik.markl...@kemi.uu.se>

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[gmx-users] solvate with hexagonal box

[Erik Marklund]

Dear gmx-users,

We are trying to merge a box containing a peripheral membrane protein with 
another box generated with memgen. Both boxes are hexagonal and exactly the 
same size,Naively, we thought that gmx solvate -cp protein.gro -cs 
membrane_and_water.gro would do the trick. Unfortunately, this causes gmx 
solvate to crash:

Generating solvent configuration
Will generate new solvent configuration of 1x2x1 boxes
Solvent box contains 99373 atoms in 28208 residues
Removed 12253 solvent atoms due to solvent-solvent overlap
Removed 5122 solvent atoms due to solute-solvent overlap
Sorting configuration
Found 2 different molecule types:
   POPE (  52 atoms):   233 residues
SOL (   3 atoms): 23294 residues
gmx(16892,0x7fffaa24f3c0) malloc: *** error for object 0x7fe36d0008f0: pointer 
being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
Abort trap: 6

So we then tried to remove the membrane, keeping only the water, and use that 
system as the argument for -cs. Gmx solvate doesn’t crash now, but the output 
file has strange gaps of some size in the water parts, which cannot be 
explained by the removed lipids. Can gmx solvate not handle non-orthogonal 
boxes as arguments for -cs?

The whole point in doing it this way was to avoid water molecules being 
inserted in the membrane. Perhaps overkill, but I am quite surprised at how bad 
things went with gmx solvate.

Kind regards,
Erik

__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

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Re: [gmx-users] COMMAND IN HBOND

[Erik Marklund]

Dear Neha,

Gromacs doesn’t offer that much in terms of viewing. This sounds more like a 
PyMol/VMD/Other question.

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 24 Mar 2017, at 14:33, Neha Gupta 
<nehaphysic...@gmail.com<mailto:nehaphysic...@gmail.com>> wrote:

Hi gromacs users,

What is the command to view the residues of protein and atoms of ligand
involved in hydrogen bond?

Thanks,
Neha
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Re: [gmx-users] Failed to execute command: Try specifying your dssp version with the -ver option.

[Erik Marklund]

Dear Atila,

Have you confirmed that your dssp is working?

Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 28 Feb 2017, at 07:11, Andrew Bostick 
<andrew.bosti...@gmail.com<mailto:andrew.bosti...@gmail.com>> wrote:

Dear Gromacs users,

I did MD simulation of my peptide on Gromacs 5.1.3. I want to do do_dssp
analysis.

After using following command:

gmx_mpi do_dssp -f *.xtc -s *.tpr -n index.ndx -o -sc

Fatal error:
Failed to execute command: Try specifying your dssp version with the -ver
option.

According to the manuall for gmx do_dssp, I used following command:

gmx_mpi do_dssp -f *.xtc -s *.tpr -n index.ndx -o -sc -ver 2

But, again:

Fatal error:
Failed to execute command: Try specifying your dssp version with the -ver
option.

How to fix it?

Any help will highly be appreciated.

Best,
Atila
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Re: [gmx-users] run parameters

[Erik Marklund]

Dear Nikhil,

It depends, but generally no electrostatic cut-offs since there is no 
dielectric medium, making the effective range of electrostatics very long. And 
no pbc. If you are doing NVE with constraints you might want to increase 
lincs-iter and -order from their default values.

Kind regards,
__
Erik Marklund, PhD
Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC
Uppsala Universtity
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 10 Feb 2017, at 13:06, NIKHIL JOSHI 
<nikhil.joshi...@gmail.com<mailto:nikhil.joshi...@gmail.com>> wrote:

hii

What will be the best mdp file options for production run for polymer in
vacuum simulation.?
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Re: [gmx-users] Hydrogen bond problem

[Erik Marklund]

Dera Tasneem,

First thing to check is if you have read the -hbn or -hbm output upside down. 
This is a common mistake. Seriously.

Kind regards,
Erik
__
Erik Marklund, PhD
Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC
Uppsala Universtity
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 8 Feb 2017, at 06:06, Tasneem Kausar 
<tasneemkausa...@gmail.com<mailto:tasneemkausa...@gmail.com>> wrote:

Dear all

I am calculating hydrogen bond between protein and drug molecule using gmx
hbond tool. I am using default value for hydrogen bond radius.
Here is the command:
gmx hbond -f protein_drug.xtc -s protein+drug.tpr -hbn hbond.ndx -hbm
hbond.ndx
I am selecting group 1 and 13.
It shows many hydrogen bonds. Then I have calculated the percentage of
hydrogen bond using perl script. There are there hydrogen bonds that show a
significant existence. I wrote the snapshots of trajectories having all
three hydrogen bonds. In every snapshot, when visulaized with a
visulaization sofware such as chimera and LIGPLUS hydrogen bond of serin
does not exist though it shows hydrophobic interaction with drug molecule.
LIGPLUS gives a provision to show the missing hydrogen bond. When I have
plotted by taking consideration serin hydrogen bond, it shows a bond length
of 4.26 angstrom and like that in almost every extracted snapshot. In
existence map serin is showing 92% abundance of hydrogen bond. This problem
is occurring with serin only.

Why is this happening? Is there a cut off problem with the visualization
tools or something else?

Is there an method to write the hydrogen bond and there distance
simultaneously.

Thanks in Advance
Tasneem
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Re: [gmx-users] ignoring -h atoms

[Erik Marklund]

Dear Maria,

I’m not saying that it never makes a difference for the topology generation, 
but it depends on the quality of your input structure. Justin and I both gave 
examples of why you might want to use it. When you do, -ignh ignores the 
hydrogens in the input pdb and uses the rtp to model new ones. I don’t 
understand why you say that the “ff its ignore it”.

As for what is most reliable, that again depends on the quality of the input 
structure. Pdb2gmx -ignh normally does a good job.

Kind regards,
Erik

> On 8 Feb 2017, at 07:20, maria khan  wrote:
> 
> Dear ERIK..
> 
> """..No. -ignh ignores the hydrogen atoms in the input structure, but uses
> the rtp file(s) to generate new hydrogens. This is useful, for example,
> when some hydrogens are missing in the pdb file. The structure and topology
> will therefore contain hydrogens in the end also with -ignh."""..
> 
> 
> now i have confusion if the ff ist ignore it and then in rtp files consider
> it..so why it at ist it ignores..there is no need to do so.after all h-atom
> will be same if it is in input file or when later form by rtp file.
> 
> secondly what will be the consequences,,if in case it is ignored or not
> ignored..would it make difference to results in both cases.and if there
> would difference in results,,what kind of results are more reliable.???
> 
> regards..
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Re: [gmx-users] Ignoring H-atoms.

[Erik Marklund]

> On 7 Feb 2017, at 08:35, Amir Zeb  wrote:
> 
> Hello Maria,
> 
> f igoring h-atom command is applied ,,then forcefield will ignore all the
> added h-atoms
> 
> What I know about -ignh flag, it does not mean to remove the h-atoms,
> alternatively means that during the topology generation, the force field is
> considering the h-atoms as the light atoms and does not pay much attention
> to consider their parameters so accurately.

No. -ignh ignores the hydrogen atoms in the input structure, but uses the rtp 
file(s) to generate new hydrogens. This is useful, for example, when some 
hydrogens are missing in the pdb file. The structure and topology will 
therefore contain hydrogens in the end also with -ignh.

Kind regards,
Erik

> 
> it would be a vaccum simulation if
> the h-atom will be ignored
> 
> Also, in case of vacuum simulation, I think there is no water addition,
> while here we are gonna adding the water during the salvation step  of the
> procedure. So, I think you don't need to worry about it.
> 
> At the end, I would like to appraise in deep the explanation of other users.
> 
> Cheers!
> 
> Amir
> 
> On Mon, Feb 6, 2017 at 10:12 PM, maria khan 
> wrote:
> 
>> Dear Gromacs users,,
>> 
>> if igoring h-atom command is applied ,,then forcefield will ignore all the
>> added h-atoms,,,so my question is then it would be a vaccum simulation if
>> the h-atom will be ignored,,secondly the results will be also differnt then
>> when h-atoms are considered.
>> 
>> Regards..
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Re: [gmx-users] INDEX

[Erik Marklund]

Dear Subashini,

You forgot to provide trjconv with the index file you created. Try gmx trjconv 
-n your_index_file.ndx …

Kind regards,
Erik
__
Erik Marklund, PhD
Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC
Uppsala Universtity
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 6 Feb 2017, at 13:06, Subashini .K 
<subashi...@hotmail.com<mailto:subashi...@hotmail.com>> wrote:

Hi gromacs users,


I want to visualize the results of simulations using the command


gmx trjconv -s em.gro -f eq.xtc -e 1000.0 -o movie.pdb


Wish to see Protein and ligand simulations together in the pdb file.


But, when the command is given, we can either select protein group or ligand 
group


Before this was done,


The following commands were given

(1)  gmx make_ndx -f em.gro

In this step, group No 22 was created namely Protein-ligand

(2)genrestr -f em.gro -n index.ndx -fc 500 500 500

(3) gmx grompp -f nvt.mdp -c em.gro -p complex_GMX.top -n index.ndx -o nvt.tpr

(4) gmx mdrun -deffnm nvt


However, despite typing make_ndx 1|13 (Protein-ligand), it is not reflected in 
the movie.pdb file.


What to do?

Can someone help?


Thanks,

Subashini.K


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Re: [gmx-users] Installing DSSP

[Erik Marklund]

Dear Soumadwip,

This is not a problem with do_dssp, but with your deep installation. My guess 
is that you have not completed the installation of dssp.

Kind regards,
Erik
__
Erik Marklund, PhD
Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC
Uppsala Universtity
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 3 Feb 2017, at 07:51, soumadwip ghosh 
<soumadwipgh...@gmail.com<mailto:soumadwipgh...@gmail.com>> wrote:

Hello all,

I am trying to install dssp in centos 7 for determining the secondary
structure of a protein in combination with do_dssp. These are the steps I
followed:

1. installation directory : /opt/apps/dssp/dssp-2.2.1/

2. but there is no dssp executable in the dssp-2.2.1 directory

3. however there was a dssp.o file in the obj directory of dssp-2.2.1

4. we renamed the dssp.o file to dssp and moved it to dssp-2.2.1 directory

5. ln -s /opt/apps/dssp/dssp2.2.1/dssp /usr/local/bin/

6. export dssp=/usr/local/bin/dssp



but inspite of executing the above steps, when we run the do_dssp command we get
the following error : Fatal error: DSSP executable
(usr/local/bin/dssp/dssp) does
not exist (use setenv DSSP)

PS. we are using bash


I have read various threads on the errors related to do_dssp but could
not find a solution.

Any kind of help would be appreciated.


Best,

Soumadwip Ghosh

Research Associate

Indian Institute of Technology Bombay

India
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Re: [gmx-users] posre.itp for dimer protein

[Erik Marklund]

Hi,

Check your top-file. It will include all relevant posre.itp files if the POSRE 
preprocessor macro is defined, assuming you created your topology with pdb2gmx. 
Add -DPOSRE to the definitions in your mdp-file and everything will be taken 
care of.

Kind regards,
Erik

> On 1 Feb 2017, at 23:11, chemocev marker  wrote:
> 
> Hi
> I am running a simulation of a dimer protein and I did not included the
> posre.itp comments in my topology.top file and protein is moving out of the
> box. But I find that gromacs has produced the separate posre.itp for each
> chain. Should I include the posre.itp for both chain ? or there is some way
> to make only one posre.itp for the complete dimer protein.
> 
> 
> thanks
> 
> J Vitali
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Re: [gmx-users] (no subject)

[Erik Marklund]

Dear Mahbodeh,

No. You need to restart your simulations. If the beginning of the trajectories 
can be recovered, then you can make a continuation from the intact part, but 
that continuation will not be exact.

Kind regards,
Erik

> On 31 Jan 2017, at 06:51, Mahboobeh Eslami  wrote:
> 
> Hi dear GROMACS usersI hope you are well
> I performed a md simulation. When simulation was finished, I moved our files 
> to another place. Unfortunately, trajectory files (.trr and .xtc files) were 
> damaged. Can I produce new trajectory files form checkpoint file 
> (.cpt)?Please guide meThank you so muchBest
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Re: [gmx-users] Dynamics

[Erik Marklund]

Dear Rahul,

I really don’t think you understand the concept of pbc in molecular 
simulations. Please read up on the concept in appropriate literature.

Kind regards,
Erik
__
Erik Marklund, PhD
Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC
Uppsala Universtity
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 26 Jan 2017, at 09:25, RAHUL SURESH 
<drrahulsur...@gmail.com<mailto:drrahulsur...@gmail.com>> wrote:

Thank you

But if I am extending my simulation with protein outside the box, then
there will not be any effect of water molecules right.?


On Thu, 26 Jan 2017 at 1:25 PM, 
<jkrie...@mrc-lmb.cam.ac.uk<mailto:jkrie...@mrc-lmb.cam.ac.uk>> wrote:

Hi Rahul,



The protein being out of the box is not a problem except for visualisation

and some analysis (e.g. RMSD). For continuing the simulation, it is a

completely normal consequence of having periodic boundaries and you

shouldn't worry about it. You can then fIx the protein for visualisation

and analysis separately to running. See


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



To continue the simulation just use mdrun as normal but with the -cpi

flag. If you want more time than you originally set the mdp to ask for

then use tpbconv (gmx convert_tpr in gromacs 5 and later). See

http://www.gromacs.org/Documentation/How-tos/Extending_Simulations



Best wishes

James



Hi mark



I want to extend it for another 50ns. At 100ns protein is out of the box.

Now is t possible to apply boundary conditions and extend.?







On Wed, 25 Jan 2017 at 11:12 PM, Mark Abraham <mark.j.abra...@gmail.com>

wrote:



Hi,







On Wed, 25 Jan 2017 18:00 RAHUL SURESH <drrahulsur...@gmail.com> wrote:







from production output of a monomer for 100ns, there s a instability

in

the



structure from 83ns to 100ns.











Many things could be going on here...







Also .gro file shows, the protein is out of



the cube.











Mdrun doesn't care. There's infinitely many equivalent representations

of a



periodic system.






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











gmx make_ndx -f md.gro -o index.ndx



trjconv -f md.xtc -s md.tpr -n index.ndx -pbc mol -ur compact -center

-o



outputfile.xtc







I used the above commands to bring the protein to the center of the

box.







gmx trjconv -f outputfile.xtc -s md.tpr -o newmd.trr







And using the above command, extracted a trr file.







Now can I extend this job with this trr file as it is or should i give

any



periodic boundary conditions or should take the conformer structure at

80ns



and run for another 50ns?











None of this is needed. See



http://www.gromacs.org/Documentation/How-tos/Extending_Simulations







Whether it makes sense to try to repeat or extend or go back to the

start



and try to fix something depends on what the "instability" is, and what

is



causing it.







Mark







waiting for your valuable note.



--



*Regards,*



*Rahul Suresh*



*Research Scholar*



*Bharathiar University*



*Coimbatore*



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Re: [gmx-users] Farideh Khamseh shared "profileNH2.xlsx" with you

[Erik Marklund]

That ACF looks very strange. How did you calculate it?

Kind regards,
Erik

__
Erik Marklund, PhD
Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC
Uppsala Universtity
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 25 Jan 2017, at 19:51, Farideh Khamseh (via Dropbox) 
<no-re...@dropbox.com<mailto:no-re...@dropbox.com>> wrote:

Hi there,

Farideh Khamseh (farideh.kham...@gmail.com<mailto:farideh.kham...@gmail.com>) 
invited you to view the file " profileNH2.xlsx " on Dropbox.

View file[1]

Enjoy!
The Dropbox team

[1]: https://www.dropbox.com/l/scl/AADR0hVYXtrYU5y-yFnAEf-3KbNwewzJnMo
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Re: [gmx-users] simulation of ternary complex

[Erik Marklund]

Dera Maria,

Yes that is possible. Be sure to make a good choice of forcefield, so that you 
have decent parameters for all molecule types in your simulation.

Kind regards,
Erik
__
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Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC
Uppsala Universtity
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 24 Jan 2017, at 11:25, maria khan 
<mariabiochemi...@gmail.com<mailto:mariabiochemi...@gmail.com>> wrote:

Dear gromacs Users..

I want to simulate ternary complex of protein -DNA -ligand..Is it possible
to simulate it combinely?

secondly..Gromacs has no graphical interface to visualize results..how can
we resolve this issue..Using VMD i have some issues regarding trajectories..

Regards..

Maria khan.

ICS,,university of peshawar..
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Re: [gmx-users] How to concatenate tpr files?

[Erik Marklund]

Dear Leila,

The RMSD is, by default, calculated with respect to the coordinates in the tpr 
file, which is why you get different results with different tprs. Which one to 
choose depends on exactly what you want to measure.

Kind regards,
Erik

__
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Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC
Uppsala Universtity
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 23 Jan 2017, at 17:10, leila karami 
<karami.lei...@gmail.com<mailto:karami.lei...@gmail.com>> wrote:

Dear gromacs users,

About the concatenation trajectory files, I have a question.

I did 10 MD simulations (each section 10 ns). Now, I want to concatenate
all of the trajectories and determine RMSD on whole trajectory. To do this,
I used the following command:

gmx trjcat -f md1.trr md2.trr md3.trr md4.trr md5.trr md6.trr md7.trr
md8.trr md9.trr md10.trr -o all_md.xtc –settime

The whole trajectory file made correctly. To determined RMSD, I used the
following command.

gmx  rms  -f  all_md.xtc  -s  *.tpr  -n index.ndx  -o rmsd.xvg  -tu  ns

I want to know, which tpr file must be used? tpr1 or tpr2 or tpr3 or …?

I tried this command with md1.tpr and md10.tpr and in each time, RMSD had
the different values. So, should I concatenate the tpr files and use the
complete tpr file.

How can I concatenate the tpr files?

Best
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Re: [gmx-users] Problem with the autocorrelation of Rg

[Erik Marklund]

I can reproduce your result, and if I change the value of a single datapoint 
by, say 5% or so, I get a non-zero acf. It could be that cmx analyze is too 
insensitive for numeric reasons, or it could also be that your data is too 
sparsely sampled to contain any trace of “memory” in the system. Have you tried 
calculating the act by other means, xmgrace for instance? Does that yield a 
similar result?

Kind regards,
Erik  

> On 23 Jan 2017, at 12:08, faride badalkhani <farideh.kham...@gmail.com> wrote:
> 
> Kindly find the Rg plot in the following link:
> 
> https://www.dropbox.com/s/8yqkrr0hym6c899/Rg9-polymer%2BLigand.xlsx?dl=0
> 
> Let me know if you need any other files or information.
> 
> Regards,
> F.
> 
> On Mon, Jan 23, 2017 at 2:07 PM, Erik Marklund <erik.markl...@kemi.uu.se>
> wrote:
> 
>> Hi,
>> 
>> Thanks. And the file Rg.xvg looks sound?
>> 
>> Kind regards,
>> Erik
>> 
>>> On 23 Jan 2017, at 11:33, faride badalkhani <farideh.kham...@gmail.com>
>> wrote:
>>> 
>>> Hi,
>>> 
>>> Thanks for the answer. I used the autocorrelation function of the squared
>>> radius of gyration cross-correlation of time course of Rg with itself
>> with
>>> the following command
>>> gmx analyze -f Rg.xvg -ac
>>> 
>>> and the autocorrelation is exactly zero.
>>> 
>>> it is worth mentioning that I have performed the same PMF calculations
>> on a
>>> polymer-drug system and I did not have any problem in that case. The only
>>> difference of that system with this one was in the terminal groups of
>>> polymer. The first polymer has protonated surface groups (NH3+) but the
>>> second one is neutral (acetylene).
>>> 
>>> Best,
>>> F.
>>> 
>>> On Mon, Jan 23, 2017 at 1:42 PM, Erik Marklund <erik.markl...@kemi.uu.se
>>> 
>>> wrote:
>>> 
>>>> Dear Farideh,
>>>> 
>>>> Can you please inform us about how you calculated the ac? Hard to help
>>>> otherwise. Also, is it exactly zero or just very small numbers?
>>>> 
>>>> Kind regards,
>>>> Erik
>>>> 
>>>>> On 23 Jan 2017, at 10:50, faride badalkhani <farideh.kham...@gmail.com
>>> 
>>>> wrote:
>>>>> 
>>>>> Dear GROMACS users,
>>>>> 
>>>>> I am performing umbrella sampling on a polymer-ligand system and I
>>>> generate
>>>>> configurations successfully but the problem is that when I plot the
>>>>> autocorrelation function of Rg for each window it is zero for the whole
>>>>> time of simulation. I changed the run time for each window but nothing
>>>>> changed. Moreover, the initial polymer-ligand structure is equilibrated
>>>>> well.
>>>>> Any comment or suggestion will be greatly appreciated.
>>>>> 
>>>>> Best,
>>>>> Farideh
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Re: [gmx-users] Problem with the autocorrelation of Rg

[Erik Marklund]

Hi,

Thanks. And the file Rg.xvg looks sound?

Kind regards,
Erik

> On 23 Jan 2017, at 11:33, faride badalkhani <farideh.kham...@gmail.com> wrote:
> 
> Hi,
> 
> Thanks for the answer. I used the autocorrelation function of the squared
> radius of gyration cross-correlation of time course of Rg with itself with
> the following command
> gmx analyze -f Rg.xvg -ac
> 
> and the autocorrelation is exactly zero.
> 
> it is worth mentioning that I have performed the same PMF calculations on a
> polymer-drug system and I did not have any problem in that case. The only
> difference of that system with this one was in the terminal groups of
> polymer. The first polymer has protonated surface groups (NH3+) but the
> second one is neutral (acetylene).
> 
> Best,
> F.
> 
> On Mon, Jan 23, 2017 at 1:42 PM, Erik Marklund <erik.markl...@kemi.uu.se>
> wrote:
> 
>> Dear Farideh,
>> 
>> Can you please inform us about how you calculated the ac? Hard to help
>> otherwise. Also, is it exactly zero or just very small numbers?
>> 
>> Kind regards,
>> Erik
>> 
>>> On 23 Jan 2017, at 10:50, faride badalkhani <farideh.kham...@gmail.com>
>> wrote:
>>> 
>>> Dear GROMACS users,
>>> 
>>> I am performing umbrella sampling on a polymer-ligand system and I
>> generate
>>> configurations successfully but the problem is that when I plot the
>>> autocorrelation function of Rg for each window it is zero for the whole
>>> time of simulation. I changed the run time for each window but nothing
>>> changed. Moreover, the initial polymer-ligand structure is equilibrated
>>> well.
>>> Any comment or suggestion will be greatly appreciated.
>>> 
>>> Best,
>>> Farideh
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Re: [gmx-users] Problem with the autocorrelation of Rg

[Erik Marklund]

Dear Farideh,

Can you please inform us about how you calculated the ac? Hard to help 
otherwise. Also, is it exactly zero or just very small numbers?

Kind regards,
Erik

> On 23 Jan 2017, at 10:50, faride badalkhani  wrote:
> 
> Dear GROMACS users,
> 
> I am performing umbrella sampling on a polymer-ligand system and I generate
> configurations successfully but the problem is that when I plot the
> autocorrelation function of Rg for each window it is zero for the whole
> time of simulation. I changed the run time for each window but nothing
> changed. Moreover, the initial polymer-ligand structure is equilibrated
> well.
> Any comment or suggestion will be greatly appreciated.
> 
> Best,
> Farideh
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Re: [gmx-users] Simulation in vacuum

[Erik Marklund]

Dear Mijiddorj,

We have had good energy conservation with bond constraints and a 1 fs time step 
under double precision, using a setup similar to yours. We did not remove 
rotation however, because we wanted to honour the rotational temperature of the 
system. Whether that is an important choice or not is for you to decide, but do 
note that the spinning ice cube effect is an artefact arising from the 
thermostat, which is turned off in your setup.

Whether bonds should be constrained or not is related to what your scientific 
questions are, and the time step depends on what bonds are constrained, if any. 
I can’t remember what LINCS parameters we used, but be prepared to increase the 
order and/or iter. Consult the manual for details.

Kind regards,
Erik

__
Erik Marklund, PhD
Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC
Uppsala Universtity
erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>

On 20 Jan 2017, at 11:01, Мижээ Батсайхан 
<b.mijidd...@gmail.com<mailto:b.mijidd...@gmail.com>> wrote:

Dear gmx users,

I would like to get experience of simulation in vacuum. Please suggest me
tutorials, and advice me.

I read about following comments which written on Shourjiya Sanyal tutorial.
Can you discuss about it?

In vacuum simulation, integration should be reduced compared to solvent
phase simulation. Periodic boundary conditions, non-bonded interaction
cutoffs, temperature coupling and pressure coupling were all turned off.
Center of mass translation and rotation around the center of mass are to be
removed to avoid the fast spin of the protein. One should also constrain
the hydrogen bond using algorithms like SHAKE/LINCS.

http://www.shourjya.thinkbiosolution.com/md-simulation-in-gas-phasevacuum-with-gromacs/


Best regards,
Mijiddorj
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Re: [gmx-users] Creating a temperature gradient in water

[Erik Marklund]

Dear Ibrahim,

Do you use pbc? If so, how does that work with your gradient?

Kind regards,
Erik

> On 10 Jan 2017, at 15:00, ibrahim khalil  
> wrote:
> 
> Dear gromacs users,
> 
> I have a simulation box containing nothing but water (TIP3P). I want to
> create a temperature gradient within water (ie. 300K in the left side and
> 500K in the right side of the simulation box).
> 
> I have successfully applied different temperatures to different groups in
> my other simulations (for example, different temperatures for water and
> proteins).
> 
> How can apply different temperatures within the same group of liquids (in
> my case, water)?
> 
> Thanks in advance.
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Re: [gmx-users] generation of ions additional to solvent molecules

[Erik Marklund]

Dear Raag,

Where would those extra ions go? If you need a higher number density of ions 
than the solvent (assuming the box is full of water, plus the protein) you will 
most likely raise the pressure of the system to bizarre levels. What ion 
concentration are you aiming for? Is that a reasonable concentration?

Kind regards,
Erik

> On 6 Jan 2017, at 07:05, Raag Saluja  wrote:
> 
> Hi!
> 
> I wanted to study the impact of certain ions on a particular protein.
> Earlier, I used to simply replace the solvent molecules with the ions.
> However, in the current case I need to add a very large number of ions,
> which exceeds the number of solvent molecules.So its giving me an error.
> 
> The command I used was:
> 
> genion -s ions.tpr -o PDB_solv_ions.gro -p topol.top -pname K -nname CL -np
> 84300
> 
> Is there a way to add ions additional to the solvent molecules, instead of
> replacing them?
> 
> Thank you and regards,
> 
> Raag Saluja
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Re: [gmx-users] correction of pmf profile due to entropic decrease

[Erik Marklund]

Dear Alex,

No. First of all, this is taken care of by gmx wham if I remember correctly. 
And it does so by looking at the dimensionality of your umbrella sampling 
setup. Secondly, there are cases where you don’t want that correction at all. 
The manual mentions one such example. In such cases the entropic contribution 
must be removed.

Kind regards,
Erik

> On 7 Dec 2016, at 19:33, Alex  wrote:
> 
> Any suggestion please?
> Thank you.
> 
> 
> On Tue, Dec 6, 2016 at 1:16 PM, Alex  wrote:
> 
>> 
>> Hello gmx user,
>> 
>> Do we need always correct the PMF profile from US by the
>> "$k_{B}T*log[4π(\epsilon)^2]$" factor in which epsilon is reaction
>> coordinate in order to removes the entropic decrease? as been mentioned
>> here:
>> 
>> 10.1021/ct100494z
>> 
>> Hub, J. S.; de Groot, B. L.; van der Spoel, D.J. Chem. Theory
>> Comput.2010,6, 3713-3720
>> 
>> Best regards,
>> Alex
>> 
>> 
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Re: [gmx-users] trjconv

[Erik Marklund]

Dear Apramita,

Unfortunately, the short answer is that you need to think it through. What is 
being calculated, and how is the trajectory information affected by trjconv? If 
you for instance apply trjconv -fit rot+trans prior to RDF calculations, you 
might influence the results.

Kind regards,
Erik

> On 29 Nov 2016, at 07:36, Apramita Chand  wrote:
> 
> Dear Justin,Gregory and Erik,
> I'd asked earlier whether trjconv might change calculation of
> properties.For diffusion probably, I could avoid applying trjconv before
> analysis. For RDF, I checked before and after trjconv, there is a slight
> difference in the RDFs. For instance , I'm studying a peptide-water-urea
> system . On increasing concentration of urea, before I apply trjconv , the
> interaction decreases . After applying trjconv , it increases slightly.
> But how do I know for sure whether I should apply it or not?
> Say I calculate properties like RDF,RMSD, etc after applying trjconv and
> properties like diffusion,lifetimes without trjconv ; would that be right?
> My peptide isn't broken or anything . It just seems to be partially out of
> the box.
> 
> Please advise.
> 
> 
> Regards,
> Apramita
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Re: [gmx-users] Regarding trjconv

[Erik Marklund]

Dear Aparamita,

trjconv can enable or preclude subsequent analysis of trajectories, depending 
on what you want to do. For example, by fitting chosen groups to a reference 
structure. By centering your protein, you effectively remove all lateral 
diffusion, so it’s not surprising that a very low diffusion coefficient is 
reported for the processed trajectory.

Kind regards,
Erik

> On 17 Nov 2016, at 08:53, Apramita Chand  wrote:
> 
> Dear All,
> I had one doubt regarding g_trjconv which I used to center my protein after
> simulation. I got different diffusion values when I used the .xtc file
> before and after applying trjconv. Which one should be used?  Is trjconv
> just for visualisation or is necessary for analysis too? Does it change the
> values or interactions in any way?
> For example, the diffusion values that I got were
>  Before trjconv   After Trjconv
> Urea -  1.6628  2.089
> Protein  -0.09270.000108
> Water   2.513  2.59
> 
> Please advise. Which values should be taken?
> 
> Regards
> Apramita
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Re: [gmx-users] Molecular dynamic simulations of Protein-DNA complex

[Erik Marklund]

Dear Khadija,

Whether this is a real problem or not is not clear from what you have told us. 
It could be that what you see in the simulation is real, or it could be that 
the physical model is inadequate. Or you might even be reporting a 
visualisation artefact.

Can you please elaborate what you mean by “deformations”?

Kind regards,
Erik

> On 24 Oct 2016, at 10:06, Khadija Amine  wrote:
> 
> Dear Gromacs users,
> 
> I have run 20ns of MD simulations of my protein-DNA complex.
> 
> All my trajectory files have been combined in a same final file.
> 
> I have visualized that trajectory file using pymol software. Unfortunately,
> the DNA structure and some parts of the complexed protein structure show
> deformations.
> 
> How can I prevent this issue and obtain correct structure, movement of my
> complex?
> 
> This is the first time I perform MD for the protein - DNA complex.
> 
> Thank you
> 
> *Khadija AMINE*
> 
> 
> *Computational Biology*
> *Postdoctoral Research Associate*
> *Carnegie Mellon University*
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Re: [gmx-users] gromacs 2016 vs 5.1.4

[Erik Marklund]

Dear Nikhil,

Use gmx2016. The 5.1.X versions only get bug fixes and a few backports now as 
far as I know.

Kind regards,
Erik

> On 11 Oct 2016, at 07:19, Nikhil Maroli  wrote:
> 
> Dear all
> 
> We have Workstation with GTX 1070 Cards, Which Gromacs I should install
> Gromacs 2016 or  5.1.4 .. ? , I have seen 2016 is much better but later
> there was an updated version of v5  ,Would like to get it confirmed.
> 
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Re: [gmx-users] Center-of-Mass motion removal setting for Membrane system with multiple peptides.

[Erik Marklund]

Hi,

I don’t simulate membranes much, so perhaps someone else’s input might be more 
valuable. But unless the relative motion of the membrane with respect to the 
rest is artificial and not just diffusion, I would still recommend COM-motion 
removal of the whole system.

Kind regards,
Erik

> On 28 Sep 2016, at 16:39, Abhi Acharya  wrote:
> 
> Thank you Eric for your clarification. However, I have seen that in
> membrane simulations, its is suggested to couple membrane, and solvent and
> solute to two different COM groups. The argument is that in case of
> membrane systems, there is an inherent tendency of lateral drift of
> membranes; with a single COM for the whole system, even though the COM
> would remain essentially unchanged, there may be appreciable drift of the
> membrane relative to the rest of the system. Could you possibly shed some
> light on this?
> 
> Following the above argument, probably for my system I should assign
> membrane to one COM group and the rest of the system (including solute
> solvent and the peprides ) to other. What do you think?
> 
> Thank you.
> 
> Regards,
> Abhishek Acharya
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Re: [gmx-users] Center-of-Mass motion removal setting for Membrane system with multiple peptides.

[Erik Marklund]

Periodic systems should be translation invariant, and diffusion across periodic 
boundaries normally is not a concern. There are occasional exceptions to this, 
mostly (only?) because of technical implementation details. Unless your system 
warrants special treatment (and from what you’ve told us so far I don’t think 
that’s the case) I’d say that separate coupling of COM removal would only add 
artefacts. Take the extreme example of separate COM-motion removal of a single 
Na+ and a single CL-. They would be locked in place throughout the simulation. 
The same effect would come into play also for a group of Na+ and a group of Cl- 
with separate COM-motion removal, albeit in a more subtle way. What you suggest 
is similar.

Kind regards,
Erik

> On 27 Sep 2016, at 11:33, Abhi Acharya <abhi117acha...@gmail.com> wrote:
> 
> Actually, I am really not sure whether diffusion out of the box will affect
> the results or not. As long as the system is able to correctly simulate the
> intended biological phenomenon i.e. interaction of peptides with membrane,
> it is fine. Intuitively, one may say that for a semi-isotropic membrane
> system diffusion along XY direction should be fine; but any diffusion along
> Z would not be acceptable. Not sure, how this can be correctly handled.
> 
> There have been studies like this with other peptides, but none of them
> have commented on the above aspect.
> 
> On Tue, Sep 27, 2016 at 2:36 PM, Erik Marklund <erik.markl...@kemi.uu.se>
> wrote:
> 
>> Hi Abhi,
>> 
>> No, restricting the COM motion of the entire system is perfectly fine in
>> most cases. From the conservation of momentum, the COM should not change
>> its velocity at all. One reason the COM motion needs to be kept at bay
>> explicitly is because the accumulation of numerical error during the
>> simulation. If you separately remove the COM motion of separate groups you
>> will however affect the diffusion of one group relative to the other, for
>> example. Is diffusion out of the simulation box really a concern in your
>> case?
>> 
>> Erik
>> 
>>> On 27 Sep 2016, at 10:40, Abhi Acharya <abhi117acha...@gmail.com> wrote:
>>> 
>>> Another thing which I don't understand is in case of the peptide group,
>>> which I expect to diffuse freely, would COM motion removal be non
>> physical?
>>> The starting system has 16 peptides added to one side of the membrane.
>> Now
>>> to allow the peptides to diffuse freely and interact with the membrane, I
>>> would assume that translational, rotational and conformational freedom
>>> would be required. Wouldn't restricting the COM restrict its dof?
>>> 
>>> Thanks.
>>> 
>>> On Tue, Sep 27, 2016 at 1:59 PM, Abhi Acharya <abhi117acha...@gmail.com>
>>> wrote:
>>> 
>>>> What I meant to ask was a way to ensure that the peptides and membrane
>> COM
>>>> don't drift out of the simulation box, but the peptides should be free
>> to
>>>> move ( relative to the membrane) within the box. Basically, the best
>> way to
>>>> simulate the diffusion and subsequent interaction of the peptides with
>> the
>>>> lipid membrane.
>>>> 
>>>> What I can surmise from previous similar studies is that creating
>> separate
>>>> comm groups for Membrane, solute and ion and the peptide should be the
>>>> correct way. Also, I wanted to know how different nstcomm values would
>>>> effect the result especially in the context of complex systems such as
>>>> this.
>>>> 
>>>> Just wanted to be sure, before I start the production runs.
>>>> 
>>>> 
>>>> 
>>>> On Tue, Sep 27, 2016 at 1:01 PM, Erik Marklund <
>> erik.markl...@kemi.uu.se>
>>>> wrote:
>>>> 
>>>>> 
>>>>>> On 27 Sep 2016, at 06:26, Abhi Acharya <abhi117acha...@gmail.com>
>>>>> wrote:
>>>>>> 
>>>>>> Dear Gromacs users,
>>>>>> 
>>>>>> I am trying to perform a simulations of different concentration of
>>>>> peptides
>>>>>> in a box with lipid bilayer. In this context, I had a query regarding
>>>>> the
>>>>>> correct Center-of-Mass removal settings; what would be the correct way
>>>>> to
>>>>>> ensure that the Membrane is stationary during long simulations while
>> the
>>>>>> peptides, solutes etc freely diffuse in the box. Based on my
>>>>> understanding,
>

Re: [gmx-users] Center-of-Mass motion removal setting for Membrane system with multiple peptides.

[Erik Marklund]

Hi Abhi,

No, restricting the COM motion of the entire system is perfectly fine in most 
cases. From the conservation of momentum, the COM should not change its 
velocity at all. One reason the COM motion needs to be kept at bay explicitly 
is because the accumulation of numerical error during the simulation. If you 
separately remove the COM motion of separate groups you will however affect the 
diffusion of one group relative to the other, for example. Is diffusion out of 
the simulation box really a concern in your case?

Erik

> On 27 Sep 2016, at 10:40, Abhi Acharya <abhi117acha...@gmail.com> wrote:
> 
> Another thing which I don't understand is in case of the peptide group,
> which I expect to diffuse freely, would COM motion removal be non physical?
> The starting system has 16 peptides added to one side of the membrane. Now
> to allow the peptides to diffuse freely and interact with the membrane, I
> would assume that translational, rotational and conformational freedom
> would be required. Wouldn't restricting the COM restrict its dof?
> 
> Thanks.
> 
> On Tue, Sep 27, 2016 at 1:59 PM, Abhi Acharya <abhi117acha...@gmail.com>
> wrote:
> 
>> What I meant to ask was a way to ensure that the peptides and membrane COM
>> don't drift out of the simulation box, but the peptides should be free to
>> move ( relative to the membrane) within the box. Basically, the best way to
>> simulate the diffusion and subsequent interaction of the peptides with the
>> lipid membrane.
>> 
>> What I can surmise from previous similar studies is that creating separate
>> comm groups for Membrane, solute and ion and the peptide should be the
>> correct way. Also, I wanted to know how different nstcomm values would
>> effect the result especially in the context of complex systems such as
>> this.
>> 
>> Just wanted to be sure, before I start the production runs.
>> 
>> 
>> 
>> On Tue, Sep 27, 2016 at 1:01 PM, Erik Marklund <erik.markl...@kemi.uu.se>
>> wrote:
>> 
>>> 
>>>> On 27 Sep 2016, at 06:26, Abhi Acharya <abhi117acha...@gmail.com>
>>> wrote:
>>>> 
>>>> Dear Gromacs users,
>>>> 
>>>> I am trying to perform a simulations of different concentration of
>>> peptides
>>>> in a box with lipid bilayer. In this context, I had a query regarding
>>> the
>>>> correct Center-of-Mass removal settings; what would be the correct way
>>> to
>>>> ensure that the Membrane is stationary during long simulations while the
>>>> peptides, solutes etc freely diffuse in the box. Based on my
>>> understanding,
>>>> I am using the following settings in the parameter file:
>>>> 
>>>> nstcomm = 100
>>>> comm_mode   = linear
>>>> comm_grps   = MEMB SOL_ION Peptide
>>>> 
>>>> Here the Peptide group includes a total of say 16 peptides. Would this
>>> be
>>>> the correct way to perform the simulation?
>>>> 
>>>> Is is possible to set individual nstcomm values for each group so as to
>>>> ensure that the peptides diffuse freely while the membrane stays
>>> stationary?
>>> 
>>> Why do you want that in the first place? Membranes aren’t stationary.
>>> 
>>> Kind regards,
>>> Erik
>>> 
>>>> 
>>>> The full mdp settings I intend to use is provided in the following link:
>>>> 
>>>> https://drive.google.com/file/d/0B9VrCGta6IxES3NHU3lRbGJ4d00
>>> /view?usp=sharing
>>>> 
>>>> Please advise of what would be the best settings to perform the
>>> simulation.
>>>> 
>>>> Best Regards,
>>>> Abhishek Acharya
>>>> C-CAMP
>>>> Bangalore.
>>>> --
>>>> 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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>>> 
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Re: [gmx-users] Center-of-Mass motion removal setting for Membrane system with multiple peptides.

[Erik Marklund]

> On 27 Sep 2016, at 06:26, Abhi Acharya  wrote:
> 
> Dear Gromacs users,
> 
> I am trying to perform a simulations of different concentration of peptides
> in a box with lipid bilayer. In this context, I had a query regarding the
> correct Center-of-Mass removal settings; what would be the correct way to
> ensure that the Membrane is stationary during long simulations while the
> peptides, solutes etc freely diffuse in the box. Based on my understanding,
> I am using the following settings in the parameter file:
> 
> nstcomm = 100
> comm_mode   = linear
> comm_grps   = MEMB SOL_ION Peptide
> 
> Here the Peptide group includes a total of say 16 peptides. Would this be
> the correct way to perform the simulation?
> 
> Is is possible to set individual nstcomm values for each group so as to
> ensure that the peptides diffuse freely while the membrane stays stationary?

Why do you want that in the first place? Membranes aren’t stationary.

Kind regards,
Erik

> 
> The full mdp settings I intend to use is provided in the following link:
> 
> https://drive.google.com/file/d/0B9VrCGta6IxES3NHU3lRbGJ4d00/view?usp=sharing
> 
> Please advise of what would be the best settings to perform the simulation.
> 
> Best Regards,
> Abhishek Acharya
> C-CAMP
> Bangalore.
> -- 
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Re: [gmx-users] Interest of c alpha atoms for least square fitting?

[Erik Marklund]

Yes

> On 22 Sep 2016, at 06:45, Seera Suryanarayana  wrote:
> 
> Dear gromacs users,
> 
> Can I give my interest of c alpha atoms for least square fitting in gmx rms
> for RMSD calculation?
> 
> Thanks in advance
> Surya
> Graduate student
> India.
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Re: [gmx-users] Large (600k particle) semi-isotropic lipid bilayer system transformed into vacuum-separated coordinates by grompp and mdrun

[Erik Marklund]

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
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Re: [gmx-users] forced conformational change by MD

[Erik Marklund]

Dear Pappu,

You could use position restraints for the two conformations and switch between 
them by gradually shifting the lambda parameter from zero to one.

Kind regards,
Erik


> On 1 Sep 2016, at 12:47, Pappu Kumar  wrote:
> 
> I want to run MD to simulate conformational change from one protein structure 
> to another. But I am not sure how do that in gromacs. It would be like doing 
> morphing through MD and see what kind of changed take place around the 
> protein. Thank you.
> 
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Re: [gmx-users] How to run MD simulation remotely

[Erik Marklund]

Dear Charles,

Is mdrun_mpi available on the node side? Nothing in the script suggests it is, 
but sometimes part of the environment is inherited from the session where sub 
was run. Do you get any output files at all? I would expect the stdout and 
stderr to provide some error message.

Kind regards,
Erik

> On 9 Jul 2016, at 10:55, charles k.davis  wrote:
> 
> Dear all,
> 
> My name is Charles, PhD student at National Institute of Technology,
> Calicut, India.
> 
> I'm facing problem in giving Gromacs MD simulation job remotely (via ssh
> command) in a Hybrid Cluster system. The system administrator told me to
> copy paste the following script
> 
> *#! /bin/bash *
> *#PBS - q small *
> *#PBS -e errorfile.err *
> *#PBS -o logfile.log *
> *#PBS -l select=2:ncpus=16  *
> *tpdir=`echo $PBS_JOBID | cut -f 1 -d .` *
> *tempdir=/scratch/job$tpdir *
> *mkdir -p $tempdir *
> *cd $tempdir *
> *cp -R $PBS_O_WORKDIR/* . *
> *mpirun -np 32 -hostfile $PBS_NODEFILE mdrun_mpi -v -s input.tpr -c
> output.gro*
> *mv ../job$tpdir $PBS_O_WORKDIR/.*
> 
> 
> in a text document and save it as* script.sh* and to submit the job run the
> following command in terminal,
> 
> 
> 
> *qsub script.sh*
> This method is not working for us. It will show that the job has been taken
> up but soon it will vanish.
> 
> In our lab workstation (which we control directly, not remotely) we use the
> following commands lines,
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> *pdb2gmx -f Protein.pdb -o Protein.gro -p Protein.top -water spc
> -ignhgenrestr -f UNK.gro -o posre_UNK.itp -fc 1000 1000 1000grompp -v -f
> minim.mdp -c Protein.gro -p Protein.top -o Protein-EM-vacuum.tprmdrun -v
> -deffnm Protein-EM-vacuum -c Protein_minimized.gro -nt 1editconf -f
> Protein_minimized.gro -o Protein_minimized_box.gro -d 1.1 -bt cubicgenbox
> -cp Protein_minimized_box.gro -cs spc216.gro -p Protein.top -o
> Protein-water.grogrompp -v -f minim_water.mdp -c Protein-water.gro -p
> Protein.top -o Protein-water.tprgenion -s Protein-water.tpr -o
> Protein-water-ions.gro -p Protein.top -conc 0.15 -neutral -pname NA -nname
> CLgrompp -v -f minim_water.mdp -c Protein-water-ions.gro -p Protein.top -o
> Protein-EM-solvated.tprmdrun -v -deffnm Protein-EM-solvated -o
> Protein_minim_traj_water.trr -c Protein_minimized_water.gro -e
> minim_ener_water.edrmake_ndx -f Protein_minimized_water.gro -o
> index.ndxgrompp -v -f nvt.mdp -c Protein_minimized_water.gro -p Protein.top
> -o nvt.tprmdrun -v -deffnm nvtgrompp -f npt.mdp -c nvt.gro -t nvt.cpt -p
> Protein.top -o npt.tpr -n index.ndx mdrun -v -deffnm nptgrompp -f md.mdp -c
> npt.gro -t npt.cpt -p Protein.top -o Protein_md_1.tpr -n index.ndx mdrun -v
> -deffnm Protein_md_1*
> 
> to do the simulation and keeping the files md.mdp, minim.mdp,
> minim_water.mdp, npt.mdp and nvt.mdp in the work directory. We also keep
> protein file as Protein.pdb and ligand file as UNK.pdb, UNK.gro and UNK.itp.
> 
> Can someone help me sort out this problem.
> 
> Many thanks,
> 
> Regards,
> 
> Charles K Davis
> PhD Student
> School of Biotechnology,
> National Institute of Technology,
> Calicut, Kerala, India-673 601
> Cell Phone: +91 9495595458
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Re: [gmx-users] Hbond occupancy

[Erik Marklund]

gmx hbond

> On 8 Jul 2016, at 12:24, Amali Guruge  wrote:
> 
> Dear All,
> 
> Can anyone know how to calculate H bond occupancy with Gromacs?
> 
> Thank you
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Re: [gmx-users] charge of aminoacids in an special pH

[Erik Marklund]

Hi,

In addition, if you only wish to alter the protonation states of, say, 
aspartates, you can use the -asp flag so that you don’t have to go through all 
possible titratable residues. See vmx pdb2gmx for more residue-specific options.

Erik

> On 28 Jun 2016, at 09:34, Marlon Sidore  wrote:
> 
> You can change the protonation state of amino acids with pdb2gmx -inter
> option.
> It will ask you the protonation state of every AA. You could also start
> with a tool like propka in order to know which ones are protonated.
> 
> Best regards,
> 
> Marlon Sidore
> 
> 
> PhD Student
> Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
> CNRS - UMR7255
> 31, Chemin Joseph Aiguier
> 13402 cedex 20 Marseille
> France
> 
> 
> 2016-06-28 9:18 GMT+02:00 Atila Petrosian :
> 
>> Dear Gromacs users,
>> 
>> I want to study MD simulation of my protein in an special pH (2).
>> 
>> I want to investigate partially unfolding in this protein.
>> 
>> How to set charge of aminoacids in pdb file, prior to start MD?
>> 
>> Any help will highly appreciated.
>> 
>> Best
>> --
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Re: [gmx-users] Number of H bonds formed between ligand and amino acid residues

[Erik Marklund]

Hi Amali,


gmx hbond identifies typical acceptor and donor groups by default. In fact, 
analysing non-standard donors/acceptors is a bit underdeveloped. What the 
program basically does, if memory serves me right, is to identify N and O with 
H bound to them, or optionally without H in case of acceptors. If you wish to 
analyse the hbonds separated by residue number you may wan to either run vmx 
bond multiple times with one group being a single residue and the other the 
ligand, or you can run it once with the -hbm and -hbn options and extract the 
information from the resulting matrix.

Kind regards,
Erik


> On 28 Jun 2016, at 08:59, Amali Guruge  wrote:
> 
> Thank you very much for the answer. How we identify residues involving in H
> bonds? In index file do we have to specify them?
> 
> On Tue, Jun 28, 2016 at 11:45 AM, Subhomoi Borkotoky 
> wrote:
> 
>> Hello,
>> 
>> Please use the "hbond"  utility in gromacs.
>> 
>> gmx hbond [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]] [-n
>> [<.ndx>]][-num [<.xvg>]
>> 
>> 
>> On Tue, Jun 28, 2016 at 11:24 AM, Amali Guruge 
>> wrote:
>> 
>>> Dear Gromacs users,
>>> 
>>> I carried out 20 ns long MD simulation for my receptor-ligand complex
>> using
>>> Gromacs software. Now I want to calculate number of hydrogen bonds formed
>>> in the ligand and receptor corresponding to the residue number. Can
>> anyone
>>> help me?
>>> 
>>> 
>>> Thank you.
>>> --
>>> Gromacs Users mailing list
>>> 
>>> * Please search the archive at
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>>> posting!
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>>> send a mail to gmx-users-requ...@gromacs.org.
>>> 
>> 
>> 
>> 
>> --
>> Yours Sincerely,
>> --
>> SUBHOMOI BORKOTOKY,
>> Centre for Bioinformatics
>> Pondicherry University
>> Pondicherry,INDIA.
>> 
>> Alternate Email: subho...@mails.bicpu.edu.in
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Re: [gmx-users] selection of start or end terminus

[Erik Marklund]

Dear Alex,

A single amino acid is not a peptide sine it has no peptide bonds.

Kind regards,
Erik

> On 22 Jun 2016, at 20:19, Alexander Alexander  
> wrote:
> 
> Thanks for your response.
> 
> And then why does "1" go wrong for a single amino acid in  zwitterions
> form, as well? Isn't a single amino acid is a kind of peptide with only one
> residue?
> 
> Thanks.
> Regards,
> Alex
> 
> On Wed, Jun 22, 2016 at 8:05 PM, Justin Lemkul  wrote:
> 
>> 
>> 
>> On 6/22/16 12:53 PM, Alexander Alexander wrote:
>> 
>>> Dear Gromacs user,
>>> 
>>> In the selection of start or end terminus type for peptide in OPLS_AA
>>> force
>>> field, what is the diffeece between option 0 and 1 in below list? I am
>>> interested in the Zwitterion form, but the option 0 is Zwitterion form if
>>> I
>>> am not wrong!
>>> 
>>> 
>>> Select start terminus type for 
>>> 0: NH3+
>>> 1: ZWITTERION_NH3+ (only use with zwitterions containing exactly one
>>> residue)
>>> 2: NH2
>>> 3: None
>>> 
>>> And why choosing 1 introduces a tiny amount of charge (0.010 e) in the
>>> system and then the whole system in not neutral anymore but 0 is fine. It
>>> is clear below the differences and origination of the extra charge in
>>> \alpha-C, but how can I fix this if I want to choose 1? Can I simply edit
>>> the topol file by replacing the opls_299 to opls_283 ... .?
>>> 
>>> 
>>> Choosing 0.  :-)
>>> 
>>> ; residue   1 LEU rtp LEU  q +1.0
>>>  5  opls_293B  1LEU CA  10.25 12.011
>>> 
>>> ;residue   7 GLU rtp GLU  q -2.0
>>> 112   opls_283  7GLU CA 37   0.04 12.011
>>> 
>>> 
>>> Choosing 1.   :-(
>>> 
>>> ;residue   1 LEU rtp LEU  q +0.9
>>>   5   opls_299  1LEU CA  1 0.15 12.011
>>> 
>>> ;residue   7 GLU rtp GLU  q -1.9
>>> 112   opls_299  7GLU CA 37   0.15 12.011
>>> 
>>> 
>> pdb2gmx tells you what to do:
>> 
>> "only use with zwitterions containing exactly one residue"
>> 
>> Do you have more than one residue?  If yes, this is a wrong choice.
>> 
>> -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
>> 
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Re: [gmx-users] Calculating Eccentricity

[Erik Marklund]

Dear Sanket,

Removing periodicity is difficult if SDS molecules transiently leave the 
micelle and return after having moved one or more unit cells. You might want to 
try using gmx clustsize to generate snapshots along the trajectory and use 
trjconv on them to put all molecules in the same unit cell. Have never used 
those tools for that purpose so I can’t guarantee that it will work.

Kind regards,
Erik

> On 15 Jun 2016, at 07:28, 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] Open-closed transition in a dimeric enzyme, WTM simulations

[Erik Marklund]

Dear Tarak,

My guess is that your reaction coordinate is ill-chosen and that it fails to 
capture some significant transitions in orthogonal directions. This can be 
difficult to know beforehand unfortunately.

Kind regards,
Erik

> On 10 Jun 2016, at 19:09, tarak karmakar  wrote:
> 
> Dear All,
> I am studying an enzyme where the closing of a loop should happen upon
> ligand binding to the active site. In unbiased simulations, even after 300
> ns of simulation time the loop does not close the reaction center. Thus, we
> realized that the open-closed conformational change may have a high free
> energy barrier, inaccessible by the unbiased trajectory. Thus, we performed
> well-tempered metadynamics (WTM) simulations to study that event.
> 
> In WTM simulations, we see the opening and closing of the loop almost five
> to six times within 300 ns time span. The free energy associated with this
> event has barriers of only few kJ/mol (almost flat surface). Now, given
> these low values of the free energy barriers, I would expect to observe the
> open-closed transitions in the unbiased simulations. However, we do not see
> that transition in the unbiased trajectories.
> 
> So, my questions are,
> 1) Are the collective variables used here inappropriate? (Although I see
> the open-closed
> transition a many times in the metadynamics trajectory.)
> 
> 2) Is the free energy not converged? (plotting hills heights a function of
> time, decays close to zero after 200-250 ns)
> 
> 3) How would I make sure that the free energy is converged? (block averages
> using -stride in plumed) How would I decide the blocks from the COLVAR plot?
> 
> Any suggestions would be highly appreciated.
> 
> -- 
> Regards,
> Tarak
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Re: [gmx-users] gmx hbond - specify precise atom names involved

[Erik Marklund]

Hi,

Not as of yet I’m afraid.

Erik

> On 3 May 2016, at 08:16, Nash, Anthony  wrote:
> 
> 
> Hi all,
> 
> Can gmx hbond accept user specified atoms for the donors (default OH and
> NH) and acceptor (default O and N)? I don¹t seem to find any mention of
> this in the -help text.
> 
> I have a post-trans modified protein from a rather bulk cross-linked
> peptide chain. I defined unique atom times but I have used a unique set of
> atom names. 
> 
> Thanks
> Anthony 
> 
> 
> 
> 
>> 
> 
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Re: [gmx-users] a suitable forcefield for ions

[Erik Marklund]

Hi,

Which ions? The monovalent ions commonly used with Amber have a tendency to 
cluster in unrealistic ways at moderate concentrations if memory serves me 
right.

Kind regards,
Erik

> On 25 May 2016, at 10:41, mah maz  wrote:
> 
> Hi all,
> 
> i need forcefield parameters for ions. can anyone tell me which forcefield
> contains ions? can i do ion simulations with amber ff?
> 
> Thank you
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Re: [gmx-users] query

[Erik Marklund]

To clarify: Your gromacs appears to be compiled for different hardware, most 
likely on a different machine. I strongly recommend to build on the same 
machine you will be running on.

Kind regards,
Erik

> On 18 May 2016, at 11:28, Nikhil Maroli  wrote:
> 
> This is the problem with installation. try installing it again
> 1.gromacs from source
> 2.correct g_mmpbsa from source/binary you have to check with binary first 
> -sometimes it will work from binary 
> 
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Re: [gmx-users] water model

[Erik Marklund]

Dear Mahdiyeh,

For water molecules the constraints can be solved analytically with SETTLE, so 
no need to invoke SHAKE. SETTLE is used by default so just simulate as normal 
and you will have rigid water.

Kind regards,
Erik

> On 9 May 2016, at 09:04, mahdiyeh poorsargol  wrote:
> 
> Dear all
> I am a beginner in gromacs. I want to use water in my system. I choose the
> SPC/E water model in the topol.top file by:
> 
> ; Include water topology
> #include "spce.itp"
> 
> My question is, is rigid water molecule in the SPC/E model or should use
> the SHAKE algorithm for water in order to fix the length of bonds and
> angles?
> I would be more than pleased if someone could guide me.
> Thank You in advance
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Re: [gmx-users] gromacs fftw installation

[Erik Marklund]

Dear Neha,

with -DGMX_BUILD_OWN_FFTW=ON you tell gromacs to download and build its own 
fftw. Turn this option off.

Kind regards,
Erik

> On 6 May 2016, at 09:05, Neha Gandhi  wrote:
> 
> Dear List,
> 
> I am trying to install gromacs on a machine which is not allowed to connect
> to the internet.
> I have installed fftw in a directory /home/gandhin/fftw using --enable-float
> 
> I am trying to install gromacs but it always tries to download fftw and
> therefore the installation ends up in error.
> 
> I am using following command
> CMAKE_PREFIX_PATH=/home/gandhin/fftw-3.3.3/ cmake ..
> -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=on -DGMX_GPU=on -DGMX_SIMD=NONE
> -DCMAKE_C_COMPILER=${MPICCDIR}mpicc -DCMAKE_CXX_COMPILER=${MPICCDIR}mpicxx
> -DCMAKE_INSTALL_PREFIX=/home/gandhin/gromacs-5.0.7
> 
> Any suggestion would be helpful.
> 
> 
> -- 
> Regards,
> Dr. Neha S. Gandhi,
> Vice Chancellor's Research Fellow,
> Queensland University of Technology,
> 2 George Street, Brisbane, QLD 4000
> Australia
> LinkedIn
> Research Gate
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Re: [gmx-users] distance restraint between 2 molecules

[Erik Marklund]

Hi,

Or use the pull code.

Kind regards,
Erik
 
> On 27 Apr 2016, at 08:09, Catarina A. Carvalheda dos Santos 
>  wrote:
> 
> Hi Hong,
> 
> You have (at least) two options:
> 
> 1) Edit the specbond.dat file so that the pdb2gmx creates a covalent bond
> between the ligand and the protein (the bonded terms for this interaction
> have to be present in the force field files);
> 
> 2) Use position restrains on these two atoms instead.
> 
> Chose whatever makes more sense for your system.
> 
> Hope this helps.
> 
> Regards,
> 
> -- 
> 
> Catarina A. Carvalheda
> PhD Student
> Computational Biology Division
> SLS & SSE
> University of Dundee
> DD1 5EH, Dundee, Scotland, UK
> Hi Gromacs users,
> I want to assign a distance restraint between 2 atom, one belongs to
> protein and one belongs to ligand. I have a .top file for protein and
> include .itp of ligand. However, it seem Gromacs only perform distance
> restraint between 2 atom within same molecule.
> except the merging two molecules into a single moleculetype, is there any
> option that i can keep protein and ligand itp files seperately?
> 
> Thank you so much.
> Hongtham
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Re: [gmx-users] Protein is Jumping from water Box

[Erik Marklund]

Dear Abid,

I wouldn’t call it an issue nor an error. Your protein is still interacting 
with some periodic copy of the solvent molecules. See 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions.

Kind regards,
Erik

On 27 Apr 2016, at 05:23, Abid Channa 
> wrote:

Dear Gromacs users,
I have run 40 ns simulation , after 20 ns simulation my protein is continuously 
jumping from water Box. Is there any periodic boundary conditions issue with my 
system or an other error is that . Kindly give your valuable remarks.
Thanks,
Regards,
Abid Ali Channa,
Junior Research Fellow,
Lab No.  P-133, Computational Chemistry Unit,
Dr .Panjwani Center for Molecular Medicine and Drug Research (PCMD),
International Center for Chemical and Biological Sciences  (ICCBS),
University of Karachi-75270.Karachi-Pakistan.UAN # (92-21) 111-222-292 Ext. 
(309)
 Cell # +923013553051.
http://www.iccs.edu/
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Re: [gmx-users] g_hbond: range checking error

[Erik Marklund]

Hi,

Strange. Do you get the same error with 5.1.2? If so, can you please file a 
redmine issue (http://redmine.gromacs.org/) and upload the input files that 
generate this error? Assign the issue to me.

Kind regards
Erik Marklund

On 26 Apr 2016, at 12:01, Shubhangi Gupta 
<ignahbuhs.gup...@gmail.com<mailto:ignahbuhs.gup...@gmail.com>> wrote:

Hi all,


I want to calculate the number of hydrogen bonds between protein
and solvent. I am using g_hbond (gromacs 5.0.2) with the two groups -
protein and SOL. When i run the command, I get a *Range Checking error*

*Variable gx has value -3. It should have been within [0 ..19]*

However when i do the same and choose the two groups as protein and
protein, the command goes through.

Any help is greatly appreciated.

Thanks


Regards,
Shubhangi Gupta
PhD Research Scholar (YUS lab)
Dept of Chemistry
Indian Institute of Technology Bombay
Powai, Mumbai-400076.


e-mail ID: ignahbuhs.gup...@gmail.com<mailto:ignahbuhs.gup...@gmail.com>
  144033...@iitb.ac.in<mailto:144033...@iitb.ac.in>
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Re: [gmx-users] Flat-bottom potential SEGFAULT

[Erik Marklund]

Hi,

>From what I have observed so far this appears to be a cluster configuration 
>issue rather than a gromacs error. Thanks for your input.

Kind regards,
Erik

On 29 Mar 2016, at 15:14, Erik Marklund 
<erik.markl...@chem.ox.ac.uk<mailto:erik.markl...@chem.ox.ac.uk>> wrote:


On 28 Mar 2016, at 01:52, Justin Lemkul 
<jalem...@vt.edu<mailto:jalem...@vt.edu>> wrote:



On 3/26/16 12:47 PM, Erik Marklund wrote:
Dear dynamicists,

I am using flat bottom potentials to prevent water molecules from evaporating 
from a droplet in vacuum. The manual suggests this is pretty straightforward, 
but we run into a segfault with our approach. Having never used flat-bottom 
potentials before, chances are we are doing something wrong without realising 
it. Let me describe what we do and perhaps you can tell me where things go 
wrong.

We make our own copy of tip3p.itp, in which we put a [ position_restraints ] 
directive for the OW1, HW2, and HW3 atoms:
[ position_restraints ]
; id func_typeg   r  k
121   10 1000
221   10 1000
321   10 1000

We then create a new gro-file, where we move all water atoms in the middle of 
the box. This is to be used for reference coordinates in the next step.

We run grompp, where we provide the new gro file using the -r flag.

We launch mdrun, which segfaults. If we prepare the system without the -r flag 
in the previous step everything runs fins, but the reference point for the 
flat-bottom potential is presumably wrong.

Where might the error be?


I just did this with a toy system of a single water molecule and it worked 
quite well.  What version of GROMACS are you using?  Does a simple test like I 
did work?

-Justin

Hi,

Forgot to mention the version. It is 5.1.1. Will run some simple tests like 
yours and get back with more info.

Kind regards,
Erik


--
==

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<mailto:jalem...@outerbanks.umaryland.edu> | 
(410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Problem in implementing do_dssp

[Erik Marklund]

Dear Rishikesh,

No, you misunderstand. We don’t suggest to issue “do_dssp”, but to run dssp, 
which you say is located in /usr/local/bin, to make sure it works the way it 
should.

Kind regards,
Erik

> On 6 Apr 2016, at 18:08, Rishikesh Parulekar <rishi05parule...@gmail.com> 
> wrote:
> 
> while running directly it shows do_dssp command not found.
> 
> 
> On Wed, Apr 6, 2016 at 10:29 PM, Justin Lemkul <jalem...@vt.edu> wrote:
> 
>> 
>> 
>> On 4/6/16 12:57 PM, Rishikesh Parulekar wrote:
>> 
>>> Hi ErikMarklund,
>>>Ya I have tested dssp as it shows all flags options with gmx_mpi
>>> do_dssp -h that means executable is locatable but it is not giving output
>>> after selecting group protein ends with fatal error : failed to execute
>>> command. Try specifying your dssp version with the -ver option
>>> 
>>> 
>> Executing gmx do_dssp is not a valid test of whether or not your dssp
>> works. That just means your gmx binary is capable of displaying help
>> information. Please do as Erik and I both suggested and try to run the dssp
>> binary directly, not via gmx do_dssp.
>> 
>> -Justin
>> 
>> 
>> On Wed, Apr 6, 2016 at 10:14 PM, Rishikesh Parulekar <
>>> rishi05parule...@gmail.com> wrote:
>>> 
>>> Hi Justin Lemkul,
>>>> It works with gmx binary complied with mpi as u can see this is my
>>>> command
>>>> : gmx_mpi do_dssp -f md.trr -s md.tpr -o ss.xpm -sc protein.xvg -ver 2 .
>>>> After executing command I am able to select group for dssp calculation
>>>> but
>>>> it ends with fatal error : failed to execute command. Try specifying your
>>>> dssp version with the -ver option
>>>> 
>>>> On Wed, Apr 6, 2016 at 9:52 PM, Erik Marklund <
>>>> erik.markl...@chem.ox.ac.uk
>>>> 
>>>>> wrote:
>>>>> 
>>>> 
>>>> Dear Rishikesh,
>>>>> 
>>>>> And you have tested that your dssp runs properly on your computer? Do
>>>>> you
>>>>> run do_dssp from a script? If so, can you please show the script and
>>>>> maybe
>>>>> someone spots something?
>>>>> 
>>>>> Kind regards,
>>>>> Erik
>>>>> 
>>>>> On 6 Apr 2016, at 17:03, Rishikesh Parulekar <
>>>>>> 
>>>>> rishi05parule...@gmail.com> wrote:
>>>>> 
>>>>>> 
>>>>>> Hi all,
>>>>>> Is there any possible solution for my mentioned problem of do_dssp
>>>>>> implementation fatal error.
>>>>>> 
>>>>>> regards
>>>>>> 
>>>>>> On Wed, Apr 6, 2016 at 6:36 PM, Rishikesh Parulekar <
>>>>>> rishi05parule...@gmail.com> wrote:
>>>>>> 
>>>>>> my error is not regarding the mismatch of name for the software. It has
>>>>>>> recognised the software at usr/local/bin but it is showing fatal error
>>>>>>> 
>>>>>> : failed
>>>>> 
>>>>>> to execute command. Try specifying your dssp version with the -ver
>>>>>>> 
>>>>>> option.
>>>>> 
>>>>>> If the problem is with path of software the error of setenv have
>>>>>>> 
>>>>>> occured.
>>>>> 
>>>>>> Hence I have mentioned the ver in the command : gmx_mpi do_dssp -f
>>>>>>> 
>>>>>> md.trr
>>>>> 
>>>>>> -s md.tpr -o ss.xpm -sc protein.xvg -ver 2 but still the same error.
>>>>>>> 
>>>>>>> On Wed, Apr 6, 2016 at 6:32 PM, Rishikesh Parulekar <
>>>>>>> rishi05parule...@gmail.com> wrote:
>>>>>>> 
>>>>>>> dssp executable is directly downloaded from the
>>>>>>>> ftp://ftp.cmbi.ru.nl/pub/software/dssp site and it has ready to use
>>>>>>>> executable file for version 2.0.4. So this is the case and it has
>>>>>>>> 
>>>>>>> been kept
>>>>> 
>>>>>> under path /usr/local/bin with dssp name.
>>>>>>>> 
>>>>>>>> On Wed, Apr 6, 2016 at 6:17 PM, Sarath Chandra <
>>>>>>>> sarathchandrada...@gmail.com> wrote:
>>>>>>>> 
>>>>>>

Re: [gmx-users] Problem in implementing do_dssp

[Erik Marklund]

Dear Rishikesh,

And you have tested that your dssp runs properly on your computer? Do you run 
do_dssp from a script? If so, can you please show the script and maybe someone 
spots something?

Kind regards,
Erik

> On 6 Apr 2016, at 17:03, Rishikesh Parulekar  
> wrote:
> 
> Hi all,
> Is there any possible solution for my mentioned problem of do_dssp
> implementation fatal error.
> 
> regards
> 
> On Wed, Apr 6, 2016 at 6:36 PM, Rishikesh Parulekar <
> rishi05parule...@gmail.com> wrote:
> 
>> my error is not regarding the mismatch of name for the software. It has
>> recognised the software at usr/local/bin but it is showing fatal error : 
>> failed
>> to execute command. Try specifying your dssp version with the -ver option.
>> If the problem is with path of software the error of setenv have occured.
>> Hence I have mentioned the ver in the command : gmx_mpi do_dssp -f md.trr
>> -s md.tpr -o ss.xpm -sc protein.xvg -ver 2 but still the same error.
>> 
>> On Wed, Apr 6, 2016 at 6:32 PM, Rishikesh Parulekar <
>> rishi05parule...@gmail.com> wrote:
>> 
>>> dssp executable is directly downloaded from the
>>> ftp://ftp.cmbi.ru.nl/pub/software/dssp site and it has ready to use
>>> executable file for version 2.0.4. So this is the case and it has been kept
>>> under path /usr/local/bin with dssp name.
>>> 
>>> On Wed, Apr 6, 2016 at 6:17 PM, Sarath Chandra <
>>> sarathchandrada...@gmail.com> wrote:
>>> 
 dssp executable generally gets installed as mkdssp.
 
 Check if this is the case.
 
 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 6 April 2016 at 18:00, Rishikesh Parulekar <
 rishi05parule...@gmail.com>
 wrote:
 
> I have named dssp executable with proper name in usr/local/bin but
 still
> the error persists. I have also shown the path for the dssp with
 export.
> 
> On Wed, Apr 6, 2016 at 2:27 PM, Sarath Chandra <
> sarathchandrada...@gmail.com
>> wrote:
> 
>> do_dssp is looking for /usr/local/bin/dssp and if your dssp
 executable
> has
>> some other name do_dssp will fail.
>> 
>> Before you run do_dssp you need to set the DSSP variable.
>> 
>> for bash environment do this:
>> 
>> export DSSP=`which dssp-2.0.4-linux-amd64`
>> 
>> 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 6 April 2016 at 13:16, Rishikesh Parulekar <
> rishi05parule...@gmail.com>
>> wrote:
>> 
>>> Hi dear all,
>>> 
>>> I am trying to analyse the secondary structure of my protein
 by
>> using
>>> do_dssp on gromacs-5.1.2. However it consistently showing the fatal
>> error:
>>> failed to execute command. Try specifying your dssp version with
 the
> -ver
>>> option.
>>> I am using dssp executable file i.e dssp-2.0.4-linux-amd64 and it
 has
>> been
>>> properly placed in /usr/local/bin and also command with -ver
 option has
>>> also been executed
>>> gmx_mpi do_dssp -f md.trr -s md.tpr -o ss.xpm -sc protein.xvg -ver
 2
> but
>>> the fatal error still persists. I am actually not getting the valid
>>> solution after many executions.
>>> 
>>> Thanks in advance,
>>> 
>>> Rishikesh S. Parulekar
>>> Research scholar,
>>> Department of Microbiology,
>>> Shivaji University,Kolhapur
>>> India
>>> --
>>> Gromacs Users mailing list
>>> 
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Re: [gmx-users] on -dt of trjcat and trjconv

[Erik Marklund]

Dear Brett,

MOD refers to the modulus operator. For example, trjconv -f infile.xvg -s 
infile.tpr -dt 1000 -o outfile.xvg will downsample a trajectory and save only 
the frames at multiples of 1000 ps (0 ps, 1000 ps, 2000 ps, …), assuming that 
infile.xvg starts at 0 ps.

Kind regards,
Erik

> On 4 Apr 2016, at 05:21, Brett  wrote:
> 
> Dear All,
> 
> For both trjcat and trjconv, there was an option "-dt", which the on-line 
> GROMACS material explained as following, "Only write frame when t MOD dt = 
> first time (ps) ".
> 
> Will you please explain to me what is the meaning of "Only write frame when t 
> MOD dt = first time (ps)", by a detailed example with command?
> 
> Brett
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Re: [gmx-users] -pbc nojump failure

[Erik Marklund]

Dear Irem,

You may want to run the trajectory through trjconv and translate it, or use 
e.g. -pbc whole, so that the protein is intact at frame 1. Then you can run 
trjconv -pbc nojump on the resulting trajectory. This usually requires a bit of 
trial and error.

Kind regards,
Erik

> On 31 Mar 2016, at 18:36, Irem Altan  wrote:
> 
> I think the problem is that I can’t seem to start from an unfragmented 
> structure. I start from the .pdb file, where the protein is a whole, and end 
> up with a .tpr file that is fragmented. The interesting thing is, this did 
> not happen with version 4.6.5 (I now use 5.1.2). Do I have to do something 
> extra while preparing the simulation system? 
> 
> Here is what I’m currently doing:
> 
> gmx pdb2gmx -f .pdb -o box.gro -p topol.top (then I choose 
> amber99sb and tip4pew)
> gmx solvate -cp box.gro -cs tip4p -p topol.top -o box_h2o.gro
> gmx grompp -f ions.mdp -c box_h2o.gro -o ions.tpr -p topol.top
> gmx genion -s ions.tpr -p topol.top -o ions.gro -neutral -conc 0.05  (I 
> choose to replace the solvation waters, SOL)
> gmx -f minim.mdp -p topol.top -c ions.gro -o em.tpr
> gmx mdrun -v -deffnm em
> gmx grompp -f nvt.mdp -p topol.top -c em.gro -o nvt_water_frozen.tpr
> 
> Then I run the simulation with mdrun. The .mdp files are almost identical to 
> Justin’s files from the Lysozyme tutorial. In the above steps, is there 
> something that seems like it could cause the fragmentation issue? 
> 
> Best,
> Irem
> 
>> On Mar 31, 2016, at 11:54 AM, Tsjerk Wassenaar  wrote:
>> 
>> No! You can't do that, because fitting will cause the PBC and the
>> coordinates to mismatch. So 'nojump' after that will for sure screw up the
>> coordinates. Check the trjconv workflow on the Gromacs site.
>> 
>> Cheers,
>> 
>> Tsjerk
>> On Mar 31, 2016 14:23, "Francesco Carbone"  wrote:
>> 
>>> You could try to fit first (-fit rot+trans) and fix pbc (-pbc nojump)
>>> later.
>>> 
>>> Cheers,
>>> 
>>> Fra
>>> 
>>> On 31 March 2016 at 05:45, Tsjerk Wassenaar  wrote:
>>> 
 Hi Irem,
 
 Check the structure in nvt_water_frozen.tpr:
 
 gmx editconf -f nvt_water_frozen.tpr -o ref.pdb
 
 Cheers,
 
 Tsjerk
 On Mar 31, 2016 00:04, "Irem Altan"  wrote:
 
> Hi,
> 
> I am simulating a protein in its unit cell. I use the original .pdb
>>> file
> as an input, so the initial molecule is not fragmented. At the end of
>>> the
> simulation, I generate a .pdb file containing the trajectory of the
 protein
> as follows:
> 
> gmx trjconv -f nvt_water_frozen.trr -s nvt_water_frozen.tpr -dt 20 -pbc
> nojump -o prot.pdb
> 
> Despite the fact that I use -pbc nojump, I still get all the
>>> coordinates
> wrapped into the unit cell, and therefore the protein fragmented. What
> could be wrong? (I use GROMACS 5.1.2)
> 
> Best,
> Irem
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