Re: [gmx-users] install and mdrun problems

[Timofey Tyugashev]

Have you tried running stress test benchmarks for CPU and GPU? Or just 
looking up any similar issues reported by other users of your MB and CPU 
models?


Sudden shutdowns at high load are generally caused by power or cooling 
failure. Or both, like CPU or GPU VRMs overheating, since they're 
commonly both insufficient for the power they are supposed to pull 
through and insufficiently cooled at the same time.


03.03.2020 03:37, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет:

It looks like the reason of my PC shut down is lying in the Bios settings, but 
I don't know the version of BIOS, I can look it later, if you need.

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Re: [gmx-users] a99SB-disp forcefield

[Timofey Tyugashev]

Paul as Paul Robustelli, the paper author?

02.07.2019 17:00, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет:

Message: 3
Date: Tue, 2 Jul 2019 09:52:04 +0200
From: Jo?o Henriques
To:gmx-us...@gromacs.org, "Greener, Joe"
Subject: Re: [gmx-users] a99SB-disp forcefield
Message-ID:

Content-Type: text/plain; charset="UTF-8"

Ask Paul, they have a Gromacs version of it and he'll most likely be happy
to share it with you.

J

On Mon, Jul 1, 2019 at 8:19 PM Joe Greener  wrote:


Dear Gromacs users,

I am looking to use the a99SB-disp forcefield from Robustelli et al.
PNAS 2018 (https://www.pnas.org/content/115/21/E4758) in Gromacs 2019.3.

The details of the forcefield are in the paper supplementary material. I
have carried out the following steps:
- Downloaded the Amber99SB*-ILDN-Q forcefield from
http://www.gromacs.org/Downloads/User_contributions/Force_fields  as
ff99sb-star-ildn-q.tgz.
- Downloaded the TIP4P/2005 water model from the same site as ff03w.tgz
and extracted the water files.
- Modified the water parameters to match a99SB-disp and created a
pre-equilibrated water box.
- Modified the partial charges on certain residues as required.

Two steps remain that I could do with some advice on:

- The torsion parameters in the paper are given as phi_0, k_1, k_2, ...,
k_6. Sometimes k_2 onwards are missing, and values generally range -1.0
to 1.0. I have looked at the list of dihedral types in the Gromacs
manual and can't find which type these correspond to, or how to convert
the values to a valid dihedral format. I guess this format is the one
used by Desmond.
- The a99SB-disp forcefield has a non-bonded LJ override between all
backbone carbonyl oxygens and amide hydrogens. It seems I could have an
entry something like this in the forcefield files:

[ nonbond_params ]
O H1sigma_val   epsilon_val

Would this be sufficient to add this constraint?

Has anyone else tried to implement the a99SB-disp forcefield in Gromacs?
If not I'm happy to make it available if I get it working.

Best,
Joe

Joe Greener
Research Associate, UCL
http://jgreener64.github.io/

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Re: [gmx-users] More dihedrals generated than provided in the, force field & "No default Proper Dih. types" as a result

[Timofey Tyugashev]

28.12.2017 02:39, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет:

Message: 3
Date: Wed, 27 Dec 2017 13:46:37 -0500
From: Justin Lemkul<jalem...@vt.edu>
To:gmx-us...@gromacs.org
Subject: Re: [gmx-users] More dihedrals generated than provided in the
force field & "No default Proper Dih. types" as a result
Message-ID:<c76426b1-eb96-3043-dfe9-5ff6fb800...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



On 12/27/17 9:39 AM, Timofey Tyugashev wrote:

I'm building a protein with a cubic [Fe4S4] cluster using parameters
from a published paper.
This parameters provide only two dihedral angles types (S-FE-SG-CB and
FE-S-FE-SG, where S and FE belong to the cluster and SG and CB belong
to the Cys residue).
GROMACS automatically generates far more dihedrals with types like
S-FE-S-FE (looks like all of them are inta-cluster) which are omitted
in the source paper and are explicitly stated to be redundant for MD.
However? grommp generates errors and stops:

ERROR 49 [file topol.top, line 32916]:
? No default Proper Dih. types

How to solve this problem?

pdb2gmx automatically generates all possible dihedrals. If they are not
necessary in your force field description, either remove the offending
lines from your topology or assign them dihedral parameters with force
constants equal to zero so they impose no force.

-Justin
Yes, right after sending the message I realised that the redundant 
dihedrals could be simply removed from the .top file. Seems to be 
running fine now.

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[gmx-users] More dihedrals generated than provided in the force field & "No default Proper Dih. types" as a result

[Timofey Tyugashev]

I'm building a protein with a cubic [Fe4S4] cluster using parameters 
from a published paper.
This parameters provide only two dihedral angles types (S-FE-SG-CB and 
FE-S-FE-SG, where S and FE belong to the cluster and SG and CB belong to 
the Cys residue).
GROMACS automatically generates far more dihedrals with types like 
S-FE-S-FE (looks like all of them are inta-cluster) which are omitted in 
the source paper and are explicitly stated to be redundant for MD. 
However  grommp generates errors and stops:


ERROR 49 [file topol.top, line 32916]:
  No default Proper Dih. types

How to solve this problem?
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Re: [gmx-users] Workstation configuration advices?

[Timofey Tyugashev]

See this for GROMACS benchmarks and advice: 
http://onlinelibrary.wiley.com/doi/10.1002/jcc.24030/abstract


And AMBER benchmarks for GPUs, the situation should be about the same 
for GROMACS: http://ambermd.org/gpus/benchmarks.htm


Generally you don't need too many cores and Quadro or Tesla cards are 
pointless.


So for your GROMACS workstation you don't need workstation hardware. 
High-power consumer hardware will offer the same performance but several 
times cheaper.


Something like AMD Threadripper 1950X+GeForce GTX-1080Ti will likely 
outperform your suggested configuration while being several times cheaper.



SSDs (and storage in general) do not impact the calculation performance 
itself, but only general system handling (makes OS feel running more 
smooth and so on) and trajectory analysis. So, strictly speaking, you 
don't need anything more than what is necessary to install your OS, 
software and swap. But if money is not a concern, a larger one won't hurt.



10.11.2017 17:53, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет:

I am about to acquire a Workstation to mainly run GROMACS.


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Re: [gmx-users] problem about installing the latest version of, MOPAC

[Timofey Tyugashev]

10.10.2017 21:46, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет:

Message: 4
Date: Tue, 10 Oct 2017 21:26:11 +0900
From: minky son
To:"gromacs.org_gmx-users@maillist.sys.kth.se"

Subject: [gmx-users] problem about installing the latest version of
MOPAC
Message-ID:<59dcbc64.86cd620a.4c0c5.4...@mx.google.com>
Content-Type: text/plain; charset="utf-8"



Dear gmx users,
I?m trying to install MOPAC 2016 and GROMACS_2016.4 for QM/MM calculation.
I have installed MOPAC, but it gives the following error when I configure  
?-DGMX_QMMM_PROGRAM=mopac? and then execute make command.
So how to set-up the latest version of MOPAC? Is it possible to use gromacs 
compatible with MOPAC7?
I have searched gromacs website, but information for gromacs version3 with 
MOPAC7 was only provided.
I want to use the latest version of MOPAC. Please give me any idea to solve 
this situation.
Thank you in advance.

QM/MM calculation interfacing is not maintained in current GROMACS versions.
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Re: [gmx-users] Higher that usual salt bridge occupancies in Amber99sb*-ildn forcefield despite adding nonbonded corrections

[Timofey Tyugashev]

Care to share a link? I'm interested in reading it, but can't locate the 
paper with a casual search.


21.04.2017 01:30, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет:

The forcefield modifications have been extensively validated by the Aksementiev 
group (JCTC, 2016) against experimental data on both Gromacs and NAMD,


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Re: [gmx-users] Implicit and Explicit solvation

[Timofey Tyugashev]

Implicit solvation treats solvent as a continuous medium (a kind of 
modifier for , while explicit one treats it as a set of explicit 
(surprise!) particles. I guess you can start reading from relevant 
Wikipedia articles.
Implicit is way faster to compute, the system itself also settles far 
quicker, but it's considered more inaccurate and harder to optimize for 
GPU. It's also possible to have a hybrid approach, when the whole system 
is solvated implicitly, but select solvent molecules are explicitly 
included in the model.


In GROMACS implicit solvent is depreciated, so you should either use 
explicit solvent, or pick a different MD engine if you want implicit.

23.12.2016 18:00, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет:

Message: 1
Date: Fri, 23 Dec 2016 16:25:33 +0530
From: Syed Azeem
To: "gromacs.org_gmx-users"

Subject: [gmx-users] Implicit and Explicit solvation
Message-ID:

Content-Type: text/plain; charset=UTF-8

Hi all,

What's the difference between Implicit and Explicit solvation?
Is there any difference in setting up the system for simulation?
Which is computationally effiecient?

Thanks in advance

Azeem


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Re: [gmx-users] qmmm

[Timofey Tyugashev]

IIRC, there are some serious bugs with all QMMM interfaces except 
Gaussian. For Gaussian it's just out of date.

01.11.2016 18:00, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет:

Message: 3
Date: Tue, 1 Nov 2016 10:57:07 +
From: "Adamu, Aliyu"
To:"gmx-us...@gromacs.org"  
Subject: [gmx-users] qmmm
Message-ID:



Content-Type: text/plain; charset="us-ascii"

Hello Justin

could you please help me out on how to get over this problem? I want to run 
QM/MM calculation in GROMACS 4.6.7 and ORCA version 3.03. before i run the 
mdrun command i set the environment variables: BASENAME and ORCA_PATH by typing 
the following command in the shell:

BASENAME=topol
ORCA_PATH=/home/birg/orca

But when i type the command for the mdrun as:

mdrun -v -c qmmm1out.gro

it gives me error massage that reads as:


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[gmx-users] Building metalloprotein topology?

[Timofey Tyugashev]

I want to model a metalloprotein with a Fe-containing cofactor 
coordinated by several cysteine residues. I have obtained FF parameters 
for the cluster.
What is the proper procedure for building the correct input for GROMACS 
simulation?

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Re: [gmx-users] GROMACS 2016.1 released

[Timofey Tyugashev]

There is only one way to update GROMACS: rm your current installation 
and install the new version in the same folder.



29.10.2016 17:00, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет:

Message: 1
Date: Sat, 29 Oct 2016 11:07:59 +0530
From: Nikhil Maroli
To:gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] GROMACS 2016.1 released
Message-ID:

Re: [gmx-users] mpirun error

[Timofey Tyugashev]

19.10.2016 12:01, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет:

Go and have a look at some tutorials which use GROMACS 5 or higher, and
read the manual and documentation. A "No such file or directory" error
means exactly that - there is no such binary in the gromacs 5.1 directory
structure.

Andrew
In Linux "No such file or directory" doesn't always mean that there is 
no such file. It could also be cause by other issues.


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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 150, Issue 68

[Timofey Tyugashev]

As I understand it, QMMM actually works only with Gaussian and only with 
group cut-off scheme (deprecated in GROMACS5, no GPU support, limited 
multithreading).



Date: Fri, 14 Oct 2016 17:14:36 -0400
From: Xianchi Dong
To:gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] QMMM install on GMX5.1
Message-ID:
Content-Type: text/plain; charset=us-ascii

Hi all,
Does anyone know how to install qmmm code like mopac to gmx5.1?

Best,
Xianchi


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Re: [gmx-users] About the QM/MM MD of Gromacs (???)

[Timofey Tyugashev]

So the only QM software that GROMACS can run for QMMM is Gaussian (09?), 
in single-thread CPU-only mode and with cut-off setting that's listed as 
depreciated, right?

08.09.2016 21:11, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет:

Message: 3
Date: Thu, 8 Sep 2016 13:05:38 +
From: "Groenhof, Gerrit"
To:"gromacs.org_gmx-users@maillist.sys.kth.se"

Subject: Re: [gmx-users] About the QM/MM MD of Gromacs (???)
Message-ID:
<858a7947bc0fe04da05e1786a6d51d4533080...@um-excdag-a05.um.gwdg.de>
Content-Type: text/plain; charset="us-ascii"

Hi,

Orca with gromacs >= 5 has not been tested and there are some indications that 
it is broken (redmine issue 1934).

QM/MM with Gaussian is working, as long as you use a group based cut-offs and 
run mdrun on a single thread (-nt 1).

I therefore recommend to use gaussian (with the gau script 
athttp://wwwuser.gwdg.de/~ggroenh/qmmm.html#gaussian  no source code of 
Gaussian is required), or stick to an older version of gromacs that supports 
ORCA.

Best,

Gerrit




Dear all:
 I want to do the QM/MM MD calculation by gromacs. ORCA is my QM program 
for QM/MM calculation. But how can I configure this option by cmake?
 For older version of gromacs, we just need to run the command:
 ./configure --with-qmmm-orca --without-qmmm-gaussian
 But for newer version of gromacs, we can only use the cmake to configure 
this option. Then how can I do? What is the command?
 Thank you!
 Best wishes,
 Junbo


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[gmx-users] A questin to Justin on methods in the PPARγ-RXRα-DNA complex paper

[Timofey Tyugashev]

I was looking for examples of calculation setups. So I have a couple of 
questions about one used in this paper 
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0123984#sec008

Parameters are amber99sb-ildn and gaff:
"Simulations were carried out with GROMACS [40,41], version 4.6. All 
bonds were con-
strained using the P-LINCS algorithm [42], allowing an integration time 
step of 2 fs. The Verlet
cutoff scheme [43] was used with a minimum cutoff of 1.0 nm for 
short-range Lennard-Jones
interactions and the real-space contribution to the smooth Particle Mesh 
Ewald algorithm

[44,45]"
Why all-bonds constraints are applied? Isn't AMBER FF are supposed to be 
used with h-bond constraints? Is there any notable difference between 1 
and 2fs timestep in this setup?

Is box-solute distance of 1.0nm sufficient for 1.0nm LJ cuttof?
And why run three independent 500ns simulations instead of one or two of 
longer duration? Only to check for reproducibility or are there any 
additional reasons?

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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 142, Issue 115

[Timofey Tyugashev]

In this paper the following is used: "...All bonds were constrained 
using the P-LINCS algorithm [42], allowing an integration time step of 2 
fs..." for amber99sb-ildn.
On the other hand, isn't h-bond only constraints is the usual way for 
AMBER? The papers for FFs say so. And I've seen recommendations on the 
mailing list to constrain h-bonds only for AMBER or CHARMM.
I've seen the option for virtual sites, but entries for some DNA bases 
are missing and so they are of no use to me now. Maybe I'll try it 
sometime in the future with protein only model. Or if manage to build 
the missing ones.

19.02.2016 19:51, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет:

Message: 2
Date: Fri, 19 Feb 2016 14:51:29 +0100
From: Szil?rd P?ll
To: Discussion list for GROMACS users
Cc: Discussion list for GROMACS users

Subject: Re: [gmx-users] correct rlist and Verlet scheme
Message-ID:

[gmx-users] Strange behaviour of sorient.

[Timofey Tyugashev]

Shifting to other topics. ;-)
I tried using gmx sorient as quick estimate for water presence around 
the specific atom.
I use -rmax 0.5 option to limit the radius to 5A, but the resulting 
scount.xvg file (number of molecules as function of r) contains data for 
up to 5 nm with step of 0.02 nm.

Is it working as intended? Is there any way to increase the resolution?
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Re: [gmx-users] correct rlist and Verlet scheme

[Timofey Tyugashev]

And here my hope for quick and  easy solution hath end.
All of the points you make ring true. Especially ones about software 
engineering and funding in science (or maybe I'm more familiar with them).


Actually, ne relatively recent paper, "Phosphorylation of PPARγ Affects 
the Collective Motions of the PPARγ-RXRα-DNA Complex" 
(http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0123984#sec008), 
uses AMBER99SB-ILDN with GROMACS 4.6 and Justin Lemkul is listed as the 
first author. And the simulated structure is a protein-DNA complex. So 
it should be very close to my case.
The one thing that looks strange to me: both rvdw (LJ interacions) and 
box-solute distance set at 1.0 nm. Shouldn't the latter be larger to 
avoid probable periodic image interactions problems?
Otherwise, looks like my settings are generally the same, except 
forgetting that LINCS allows 2fs step.



17.02.2016 19:45, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет:

Message: 4
Date: Wed, 17 Feb 2016 13:45:46 +
From: Mark Abraham<mark.j.abra...@gmail.com>
To:gmx-us...@gromacs.org,gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] correct rlist and Verlet scheme
Message-ID:
<camnumarkusmbzbrvneie35aahdwkpo-mgbejewxzgpueew6...@mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

Hi,

Yes, what you say is true, but very much "in short" and AFAIK true of all
MD packages.:-)

If e.g. AMBER (or anyone else) has a test suite for any force field, then
we'll seriously consider implementing it, to e.g. verify before each
release.:-)  IMO, defining such a suite is a research topic itself -
particularly as the original parameterizations did so in the context of
limitations in the methods of the day. If a force field was parameterized
with a fixed buffer because nobody then knew how large a buffer was
necessary for a given quality of relevant observable, it does not follow
that the only possible acceptable practice now is to use that fixed buffer.

Similar considerations apply to things like e.g. the use of long-ranged
corrections for dispersion interactions. e.g. AMBER99 was parameterized
without such corrections, so probably has built into its parameters some
compensating errors, and any kind of validation-by-replication should in
principle not use such corrections. But these days, I think that nobody
would actually recommend parameterizing a force field without something
like that, and experience suggests that using one is an improvement, even
if though the change is not officially sanctioned anywhere that I know of.
IMO showing that some range of force fields shows satisfactory agreement
with experiment under certain .mdp setting combinations is useful evidence
of an implementation that is valid, and that is what one can see in the
literature.

The state of the art in software engineering is that nobody much has time
to test all the things that they'd like to test. (One large exception is
software for control of devices that potentially affect human health.)
Scientific software development has additional challenges because the
people doing it are often lacking in formal training in best practice, and
have to appear to publish science, in order to keep attracting funding, and
this directly conflicts with spending time on good software engineering
practice that granting and tenure committees will ignore later in their
careers...

Mark

On Wed, Feb 17, 2016 at 1:01 PM Timofey Tyugashev<tyugas...@niboch.nsc.ru>
wrote:


>In short, FFs were tested to some degree when they were added in GROMACS
>to reproduce AMBER results, but there is no certainty if they actually
>do this now and 'correct' mdp settings to run them are unknown. For any
>of the versions that are listed in GROMACS.
>Is that correct, or I'm missing something in translation?
>
>16.02.2016 18:03,gromacs.org_gmx-users-requ...@maillist.sys.kth.se  ?:

> >Message: 2
> >Date: Tue, 16 Feb 2016 11:23:06 +
> >From: Mark Abraham<mark.j.abra...@gmail.com>
> >To:gmx-us...@gromacs.org,gromacs.org_gmx-users@maillist.sys.kth.se
> >Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 142, Issue
> >   76
> >Message-ID:
> >   <

>camnumasutdhr8sot1qt4xdczogsdjsfgo8umiuhrpffxxfa...@mail.gmail.com>

> >Content-Type: text/plain; charset=UTF-8
> >
> >Hi,
> >
> >The ports of all the AMBER force fields were all tested to reproduce

>AMBER

> >when when they were added to GROMACS. Many of our regressiontests use

>those

> >force fields, so there is reason to expect that they all continue to

>work.

> >The Verlet scheme is tested to implement what the documentation says it
> >does. There have been bugs introduced (and fixed) in how GROMACS
> >preprocessing tools implement the requirements of AMBER force fields,
> >including ILDN.
> &g

Re: [gmx-users] correct rlist and Verlet scheme

[Timofey Tyugashev]

Yes, the implementation is clearly different from AMBER and I don't 
really want to try hard to get Identical results.
I picked AMBER ff99sb-ildn because it looked to be both quite popular 
for protein and nucleic acids simulations (going by the number of cites 
for its paper)  and reasonably recent.
Our home-grown software uses a derivative of ff99 for implicit solvent 
calculations, so I wanted to spare myself the trouble of parametrising 
non-standard residues and ligands by using a ff from the same family and 
using already existing ones.


So i'm interested  in simply running it in gromacs with adequate setup. 
And I'm just not sure what .mdp parameters to set.


For P.S.: Different version of it. Authors use different cutoffs.

17.02.2016 23:16, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет:

Message: 1
Date: Wed, 17 Feb 2016 18:07:28 +0100
From: Szil?rd P?ll
To: Discussion list for GROMACS users
Cc: Discussion list for GROMACS users

Subject: Re: [gmx-users] correct rlist and Verlet scheme
Message-ID:

Re: [gmx-users] correct rlist and Verlet scheme

[Timofey Tyugashev]

In short, FFs were tested to some degree when they were added in GROMACS 
to reproduce AMBER results, but there is no certainty if they actually 
do this now and 'correct' mdp settings to run them are unknown. For any 
of the versions that are listed in GROMACS.

Is that correct, or I'm missing something in translation?

16.02.2016 18:03, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет:

Message: 2
Date: Tue, 16 Feb 2016 11:23:06 +
From: Mark Abraham<mark.j.abra...@gmail.com>
To:gmx-us...@gromacs.org,gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 142, Issue
76
Message-ID:
<camnumasutdhr8sot1qt4xdczogsdjsfgo8umiuhrpffxxfa...@mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

Hi,

The ports of all the AMBER force fields were all tested to reproduce AMBER
when when they were added to GROMACS. Many of our regressiontests use those
force fields, so there is reason to expect that they all continue to work.
The Verlet scheme is tested to implement what the documentation says it
does. There have been bugs introduced (and fixed) in how GROMACS
preprocessing tools implement the requirements of AMBER force fields,
including ILDN.

To be able to say "this force field is tested to work correctly with this
cutoff scheme in this version of GROMACS" requires the community to agree
on what that means, e.g. a large collection of single-point energies+forces
agree to within a certain precision, and simulations done in a particular
model physics produce these ensembles with these observables, etc. That
hasn't happened yet. As far as I know, the ability of the different AMBER
code versions to correctly continue to implement all the AMBER force fields
has a similar kind of question mark over it. Just having the same name is
not enough;-)

Mark

On Tue, Feb 16, 2016 at 11:17 AM Timofey Tyugashev<tyugas...@niboch.nsc.ru>
wrote:


>So, are there any other Amber force fields more suitable and more tested
>for GROMACS?
>
>15.02.2016 21:00,gromacs.org_gmx-users-requ...@maillist.sys.kth.se  ?:

> >Message: 1
> >Date: Mon, 15 Feb 2016 13:15:02 +
> >From: Mark Abraham<mark.j.abra...@gmail.com>
> >To:gmx-us...@gromacs.org,gromacs.org_gmx-users@maillist.sys.kth.se
> >Subject: Re: [gmx-users] correct rlist and Verlet scheme
> >Message-ID:
> >   <

>camnumatmbmgvbfj49ez+4k_bftdmkyfyiw5iz-eecwicujb...@mail.gmail.com>

> >Content-Type: text/plain; charset=UTF-8
> >
> >Hi,
> >
> >On Mon, Feb 15, 2016 at 12:17 PM Timofey Tyugashev<

>tyugas...@niboch.nsc.ru>

> >wrote:
> >

> >> >I've studied the relevant sections of the manual, but I don't consider
> >> >myself to be familiar enough with this field to successfully guess the
> >> >right settings.
> >> >
> >> >ff99sb-ildn is included in the gromacs distribution, so shouldn?t be
> >> >there some recommended settings for it?

> >Ideally, yes. But nobody has made a particular effort for that

>combination.

> >
> >Or else how was it tested to run

> >> >properly?
> >> >

> >In principle, one would have to e.g. show that
> >https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970904/   can be

>replicated.

> >That's not a straightforward proposition...

>--
>Gromacs Users mailing list
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>* Please search the archive at
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 142, Issue 76

[Timofey Tyugashev]

So, are there any other Amber force fields more suitable and more tested 
for GROMACS?


15.02.2016 21:00, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет:

Message: 1
Date: Mon, 15 Feb 2016 13:15:02 +
From: Mark Abraham<mark.j.abra...@gmail.com>
To:gmx-us...@gromacs.org,gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] correct rlist and Verlet scheme
Message-ID:
<camnumatmbmgvbfj49ez+4k_bftdmkyfyiw5iz-eecwicujb...@mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

Hi,

On Mon, Feb 15, 2016 at 12:17 PM Timofey Tyugashev<tyugas...@niboch.nsc.ru>
wrote:


>I've studied the relevant sections of the manual, but I don't consider
>myself to be familiar enough with this field to successfully guess the
>right settings.
>
>ff99sb-ildn is included in the gromacs distribution, so shouldn?t be
>there some recommended settings for it?

Ideally, yes. But nobody has made a particular effort for that combination.

Or else how was it tested to run

>properly?
>

In principle, one would have to e.g. show that
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970904/  can be replicated.
That's not a straightforward proposition...

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Re: [gmx-users] correct rlist and Verlet scheme

[Timofey Tyugashev]

 used." If PME was used at all.;-)  So you can be guided
also by the parameters reported by successful users of these forcefields,
particularly those of the various force field and software authors.

rlist is a free parameter so long as you choose it large enough to avoid
missing a significant number of interactions over the lifetime of the list
- but it affects performance strongly. rcoulomb can be varied for
equivalent accuracy if matching changes occur to PME parameters. VDW
parameters should generally follow the force field derivation precisely
(but add long-range corrections for dispersion) - GROMACS will not change
these. You should check out the background information in the reference
manual, sections 3.4.2 and 3.17.5

Mark

On Fri, Feb 12, 2016 at 1:56 PM Hardy, Adam<ah...@hw.ac.uk>  wrote:


>There are people more qualified than me to explain the fine details of
>this, but in brief:
>
>Verlet on it's own doesn't adjust rvdw or rcoloumb (rcoulomb may be
>adjusted if you rae using PME for the coulomb interactions), but by default
>it will adjust the neighbour list cut-off (rlist) to remain with a
>specified energy tolerance given by verlet-buffer-tolerance. You can
>overide this behaviour and manually set rlist by setting
>verlet-buffer-tolerance=-1. Whether you want to or not will depend on why
>the forcefield has specified that cut-off, it may well be to achieve the
>same purpose, which is to propely catch interactions between atoms which
>move in or out of the cut-off radii between rlist update steps.
>
>Adam
>
>________
>From:gromacs.org_gmx-users-boun...@maillist.sys.kth.se  <
>gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Timofey
>Tyugashev<tyugas...@niboch.nsc.ru>
>Sent: 12 February 2016 12:47
>To:gromacs.org_gmx-users@maillist.sys.kth.se
>Subject: [gmx-users] correct rlist and Verlet scheme
>
>I have trouble in correctly setting cut-offs with Verlet scheme to match
>force-field specific settings.
>It automatically adjusts cut-off and it looks like they change their
>values from ones recommended for the force field.
>Is there a way to correct it and set up them properly?
>
>The paper on FF lists 1.0 nm for short-range electrostatic and LJ
>interactions.
>The cut-off of pairlists is 1.05 nm.
>
>The forcefield is 99SB-ILDN and is present in GROMACS itself.
>--
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[gmx-users] correct rlist and Verlet scheme

[Timofey Tyugashev]

I have trouble in correctly setting cut-offs with Verlet scheme to match 
force-field specific settings.
It automatically adjusts cut-off and it looks like they change their 
values from ones recommended for the force field.

Is there a way to correct it and set up them properly?

The paper on FF lists 1.0 nm for short-range electrostatic and LJ 
interactions.

The cut-off of pairlists is 1.05 nm.

The forcefield is 99SB-ILDN and is present in GROMACS itself.
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 142, Issue 24

[Timofey Tyugashev]

Message: 4
Date: Thu, 4 Feb 2016 07:51:27 -0500
From: Justin Lemkul<jalem...@vt.edu>
To:gmx-us...@gromacs.org
Subject: Re: [gmx-users] trjconv options?
Message-ID:<56b3494f.4070...@vt.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed



On 2/4/16 4:27 AM, Timofey Tyugashev wrote:

>
>

>>Message: 2
>>Date: Wed, 3 Feb 2016 07:37:42 -0500
>>From: Justin Lemkul<jalem...@vt.edu>
>>To:gmx-us...@gromacs.org
>>Subject: Re: [gmx-users] trjconv options?
>>Message-ID:<56b1f496.5090...@vt.edu>
>>Content-Type: text/plain; charset=windows-1252; format=flowed
>>
>>
>>
>>On 2/3/16 6:34 AM, Timofey Tyugashev wrote:

>>> >Thank you for replies on my previous questions.
>>> >And now I have another one dealing with trjconv.
>>> >
>>> >I have a simulation of  a three-chain protein/nucleic acid complex. 
Naturally,
>>> >it gets broken in three separate strands by PBC.
>>> >After trying several, I settled on using options '-pbc mol' with '-ur 
compact'
>>> >which makes the complex look decent again and it looks like that does the 
job.
>>> >But I'm worried about a possibility of something getting unrepaired by this
>>> >option and getting unnoticed by me. What is the way to check for it?

>>Any molecules that appear to fly away suddenly will be a pretty dead giveaway.
>>
>>In general, for multimeric complexes, you need to do a lot more work, e.g.
>>centering on a single chain after making molecules whole and removing jumps.  
If
>>a simple -pbc mol -ur compact does the trick, probably nothing has actually
>>crossed a periodic boundary yet.
>>

>>> >Also it keeps tumbling around the cell during the trajectory. It's 
annoying. Is
>>> >there a way to pin down the cluster and stop it from rotating?

>>This is what trjconv -fit is for.
>>
>>-Justin

>Well, both vmd and pymol render .gro file (and trajectory files) with DNA
>strands and protein positioned in different corners of the box.
>Also, editconf -pbc has no effect on .gro file with the broken complex. How 
it's
>supposed to behave?
>
>So in this case I should at first run trjconv with '-pbc whole', make second 
run
>with '-pbc nojump', then make third run with '-pbc mol' to properly repair the
>trajectory?
>I guess for -fit I should pick 'progressive' option?

Complex systems require complex operations.  Start with
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow  
because that order of operations generally works well.  Then see posts in the

archive, because this comes up frequently.  Typically, after making molecules
whole and removing jumps, you can center on a custom index group that defines
some useful center.  Then you can do whatever fitting you like.
I've already looked at this page and it's not very helpful due to it's 
vague wording, so I guess trial and error is the only suitable way to 
get results. Due to the unstructured nature of mailing lists it's very 
hard to find relevant previous discussions. Probably that's why the 
topic comes up so frequently.

Anyway, thank you for your suggestions.
In your answer you suggest to go whole-jump-center route an the linked 
page says whole-cluster-jump-center. What is the difference between them?
How is centering done? Define a new group, like one aminoacid in the 
middle of a protein, use '-center' on it and it'll be put in the 
designated position in box (specified by '-boxcenter')?

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[gmx-users] ff99SB-ILDN and .mdp parameters

[Timofey Tyugashev]

Also I have some doubts about proper mdp parameters to use for AMBER 
ff99SB-ILDN. GROMACS site recently updated ones for CHARMM 
(http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM), 
but not for AMBER.

Currently I use the following options for MD run:

continuation= yes   ; first dynamics run
constraint_algorithm = lincs
constraints = all-bonds
lincs_iter  = 1 ; default
lincs_order = 4 ; default
; Neighborsearching
cutoff-scheme   = Verlet
ns_type = grid
nstlist = 40
rcoulomb= 1.0   ; Short-range electrostatic cut-off
rvdw= 1.0   ; Short-range Van der Waals cut-off
rlist   = 1.0   ; Short-range neighbor list
rlistlong   = 1.05  ; Long-range neighbor list
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling
tcoupl  = V-rescale ; Berendsen-modified
tc-grps = Protein_DNA Water_and_ions; two groups
tau_t   = 0.1   0.1 ; time constant, in ps
ref_t   = 300   300 ; reference temperature, one for 
each group, in K
; Pressure coupling
pcoupl  = Parrinello-Rahman ; pressure coupling is on for NPT
pcoupltype  = isotropic ; uniform scaling of box vectors
tau_p   = 2.0   ; time constant, in ps
ref_p   = 1.0   ; reference pressure, in bar
compressibility = 4.5e-5; isothermal compressibility of 
water, bar^-1
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no; assign velocities from Maxwell distribution




Paper for this FF provides the following parameters for computation 
set-up and I tried to implement them in .mdp, but I'm not sure how 
correct my interpretation is.


   Each system was equilibrated at 300 K and 1 atm with 2.4 ns of MD
   simulation in the NPT ensemble. Then, MD simulations were carried
   out in the NVT ensemble for 720 ns using the Nosé-Hoover thermostat
   with a relaxation time of 1 ps. All simulations were performed using
   the Desmond MD program^16
    version
   2.1.1.0 and either the Amber ff99SB^7
    or the
   modified Amber ff99SB force field described herein, which we have
   termed ff99SB-ILDN. All bonds involving hydrogen atoms were
   constrained with the SHAKE algorithm.^17
    A cutoff
   of 10 Å was used for the Lennard-Jones interaction and the
   short-range electrostatic interactions. The smooth particle mesh
   Ewald method^18
    with a
   32 × 32 × 32 grid and a fourth-order interpolation scheme was used
   to compute the long-range electrostatic interactions. The pairlists
   were updated every 10 fs with a cutoff of 10.5 Å. We used a
   multistep RESPA scheme^19
    for the
   integration of the equations of motion with timesteps of 2.0, 2.0,
   and 6.0 fs for the bonded, short-range nonbonded, and long-range
   nonbonded interactions, respectively. To check for potential biases
   introduced by long-range interactions between peptides in periodic
   images, we repeated these simulations for four of the amino acids
   (Xaa: Ile, Leu, Asp, and Asn) using a larger box with side length 37
   Å. We found that the results of these control simulations were
   within error of those using the smaller box sizes.


If understand the manual correctly, the Verlet option for cut-off scheme 
overrides rlist settings anyway and autotunes it.

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Re: [gmx-users] trjconv options?

[Timofey Tyugashev]

Message: 2
Date: Wed, 3 Feb 2016 07:37:42 -0500
From: Justin Lemkul<jalem...@vt.edu>
To:gmx-us...@gromacs.org
Subject: Re: [gmx-users] trjconv options?
Message-ID:<56b1f496.5090...@vt.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed



On 2/3/16 6:34 AM, Timofey Tyugashev wrote:

>Thank you for replies on my previous questions.
>And now I have another one dealing with trjconv.
>
>I have a simulation of  a three-chain protein/nucleic acid complex. Naturally,
>it gets broken in three separate strands by PBC.
>After trying several, I settled on using options '-pbc mol' with '-ur compact'
>which makes the complex look decent again and it looks like that does the job.
>But I'm worried about a possibility of something getting unrepaired by this
>option and getting unnoticed by me. What is the way to check for it?

Any molecules that appear to fly away suddenly will be a pretty dead giveaway.

In general, for multimeric complexes, you need to do a lot more work, e.g.
centering on a single chain after making molecules whole and removing jumps.  If
a simple -pbc mol -ur compact does the trick, probably nothing has actually
crossed a periodic boundary yet.


>Also it keeps tumbling around the cell during the trajectory. It's annoying. Is
>there a way to pin down the cluster and stop it from rotating?

This is what trjconv -fit is for.

-Justin
Well, both vmd and pymol render .gro file (and trajectory files) with 
DNA strands and protein positioned in different corners of the box.
Also, editconf -pbc has no effect on .gro file with the broken complex. 
How it's supposed to behave?


So in this case I should at first run trjconv with '-pbc whole', make 
second run with '-pbc nojump', then make third run with '-pbc mol' to 
properly repair the trajectory?

I guess for -fit I should pick 'progressive' option?
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[gmx-users] trjconv options?

[Timofey Tyugashev]

Thank you for replies on my previous questions.
And now I have another one dealing with trjconv.

I have a simulation of  a three-chain protein/nucleic acid complex. 
Naturally, it gets broken in three separate strands by PBC.
After trying several, I settled on using options '-pbc mol' with '-ur 
compact' which makes the complex look decent again and it looks like 
that does the job.
But I'm worried about a possibility of something getting unrepaired by 
this option and getting unnoticed by me. What is the way to check for it?
Also it keeps tumbling around the cell during the trajectory. It's 
annoying. Is there a way to pin down the cluster and stop it from rotating?

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[gmx-users] Rarefied trajectory

[Timofey Tyugashev]

If need to generate for analysis a trajectory with fewer frames than in 
the original one (get 1000 frames from 10ns trajectory with 1 
frames), what approach would be better:

Use gmx trjconv with option '-skip 10',
Or use gmx filter with options '-ol lowpass.xtc' and '-nf 10'?
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Re: [gmx-users] trajectory file

[Timofey Tyugashev]

16.12.2015 00:55, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет:
04.12.2015 14:43,gromacs.org_gmx-users-requ...@maillist.sys.kth.se  
>?:

>>I ran the production MD and got the trajectory file (xtcformat) but as
>>I?m new to MD I don?t know how to visualize it. I opened it withvmd
>>and it could read the atoms and frames but didn?t show anything when
>>playingthe frames. I don?t know whether another program can do it or
>>my xtc is notcorrect.

>You can also read GROMACS trajectories with PyMOL. It offers quite
>nice visualisation options.
>Use 'load' command to load the coordinate file first, then load the
>trajectory itself using 'load_traj' command.

Only problem with pymol is that it eats very large amount of memory. I
cannot evel load trajectory of large nucleoprotein complex (~200k atoms
for complex itself without solvent) if it has ~1000 frames on
workstation with 64G ram.
Personally  I haven't noticed any qualitative difference in memory 
consumption compared with vmd when viewing same .xtc files. It either 
works or it does not. But my simulations are different (~5-10k atoms 
without solvent and tens of ns on 32G RAM system).
IIRC, there were some options in pymol for processing trajectories. 
Maybe they do influence the performance.

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Re: [gmx-users] trajectory file

[Timofey Tyugashev]

04.12.2015 14:43, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет:

I ran the production MD and got the trajectory file (xtcformat) but as I?m new 
to MD I don?t know how to visualize it. I opened it withvmd and it could read 
the atoms and frames but didn?t show anything when playingthe frames. I don?t 
know whether another program can do it or my xtc is notcorrect.
You can also read GROMACS trajectories with PyMOL. It offers quite nice 
visualisation options.
Use 'load' command to load the coordinate file first, then load the 
trajectory itself using 'load_traj' command.

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[gmx-users] Checking solvent water positions

[Timofey Tyugashev]

Is there any way to check if solvent waters can be positioned close 
enough (around 3,5A) to a specific atom in the protein during the MD run 
and how stable their positions are (i.e for how long a water molecule 
stays within a certain radius from this atom)?


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Re: [gmx-users] 2. QM/MM (Timofey Tyugashev)

[Timofey Tyugashev]

Thank you for reply.
Is the information in the link still valid? The page is dated 09.01.07, 
almost nine years ago, and refers to GROMACS 3.3. Much water has gone 
under the bridge since then.
On choice of division and methods: I'm trying to think hard about it and 
consult people experienced with QM. I have looked though several papers 
dealing with similar systems but with different software.
I'm reasonably sure about what methods and bases I should use, but still 
very uncertain on how to configure and make it run properly.

Message: 1
Date: Tue, 10 Nov 2015 11:31:03 +
From: "Groenhof, Gerrit"<ggro...@gwdg.de>
To:"gromacs.org_gmx-users@maillist.sys.kth.se"
<gromacs.org_gmx-users@maillist.sys.kth.se>
Subject: Re: [gmx-users] 2. QM/MM (Timofey Tyugashev)
Message-ID:
<858a7947bc0fe04da05e1786a6d51d4526337...@um-excdag-a05.um.gwdg.de>
Content-Type: text/plain; charset="us-ascii"



I'm looking to try a QM/MM simulation for a protein-DNA system using
Gussian09 & GROMACS 4.6 (these are available at the local cluster).
Does anyone has any experience working and getting results in this
environment? Are there any notable problems? Should I pay special
attention to any particular topics?


Hi,

The easiest is to use the gau script 
athttp://wwwuser.gwdg.de/~ggroenh/qmmm.html#gaussian

Concerning notable problems, the main issue is to decide your QM/MM division 
and QM method and verify the validity of your choices.
best,
Gerrit


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[gmx-users] QM/MM

[Timofey Tyugashev]

I'm looking to try a QM/MM simulation for a protein-DNA system using 
Gussian09 & GROMACS 4.6 (these are available at the local cluster).
Does anyone has any experience working and getting results in this 
environment? Are there any notable problems? Should I pay special 
attention to any particular topics?

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Re: [gmx-users] Virtual sites error

[Timofey Tyugashev]

This looks very strange that from the whole assortment of the molecules 
in the force field only a humble methyl group in thymine lacks proper 
definition causes such an error.
Even nucleotides which I added myself to the force field files don't 
produce any errors
Is there any way to remedy this without significant hassle? What things 
are exactly lacking?

--

Message: 4
Date: Thu, 8 Oct 2015 11:15:17 +
From: Erik Marklund <erik.markl...@chem.ox.ac.uk>
To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org>
Subject: Re: [gmx-users] Virtual sites error
Message-ID: <89ae0bec-6d9f-49a0-83e2-5ad8d7734...@chem.ox.ac.uk>
Content-Type: text/plain; charset="us-ascii"

Unfortunately, the parameters required for certain virtual sites in nucleic 
acids are not define in the force field files that are shipped with Gromacs.

Erik Marklund, PhD
Postdoctoral Research Fellow
Fulford JRF, Somerville College

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ


On 7 Oct 2015, at 11:33, Timofey Tyugashev <tyugas...@niboch.nsc.ru> wrote:

Trying to add hydrogen virtual sites to the model (using -vsites h option in 
pdb2gmx) results in a salvo of error messages when running grommp to create 
.tpr file after the solvation:

ERROR 1 [file topol_DNA_chain_A2.itp, line 1033]:
  No default Constr. No Conn. types


ERROR 2 [file topol_DNA_chain_A2.itp, line 1034]:
  No default Constr. No Conn. types

This lines in constraints section in the .itp file refer to pairs of two MCH3 
and one MC atoms, which should serve (the way I understand the situation) as 
replacement methyl group in thymine. There are several more pairs of same 
errors corresponding to different thymine methyl groups in the DNA strands.

Here is the relevant sections of the itp file for the first two errors:

[ constraints ]
;  aiaj functc0c1
2 3 2
  110   111 2
  110   112 2
  111   112 2

[ atoms ]

   110 CM321 DT C5110 0.0025 12.01   ; qtot -2.867
   111   MCH3321 DT   MC71111  0 7.517   ; qtot -2.867
   112   MCH3321 DT   MC72111  0 7.517   ; qtot -2.867
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[gmx-users] Virtual sites error

[Timofey Tyugashev]

Trying to add hydrogen virtual sites to the model (using -vsites h 
option in pdb2gmx) results in a salvo of error messages when running 
grommp to create .tpr file after the solvation:


ERROR 1 [file topol_DNA_chain_A2.itp, line 1033]:
  No default Constr. No Conn. types


ERROR 2 [file topol_DNA_chain_A2.itp, line 1034]:
  No default Constr. No Conn. types

This lines in constraints section in the .itp file refer to pairs of two 
MCH3 and one MC atoms, which should serve (the way I understand the 
situation) as replacement methyl group in thymine. There are several 
more pairs of same errors corresponding to different thymine methyl 
groups in the DNA strands.


Here is the relevant sections of the itp file for the first two errors:

[ constraints ]
;  aiaj functc0c1
2 3 2
  110   111 2
  110   112 2
  111   112 2

[ atoms ]

   110 CM321 DT C5110 0.0025 12.01   ; qtot 
-2.867
   111   MCH3321 DT   MC71111  0 7.517   ; qtot 
-2.867
   112   MCH3321 DT   MC72111  0 7.517   ; qtot 
-2.867

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[gmx-users] Hydrogen virtual sites and AMBER FF

[Timofey Tyugashev]

IIRC, Mark Abraham wrote that there are some issues with implementation 
of vsites with amber ffs in GROMACS.
Any more details? Is it possible to use amber99sb-ildn with -vsite 
option to speed up calculation?

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[gmx-users] Translating .frcmod and .prep to .itp

[Timofey Tyugashev]

I have parameters for 8-oxoguanine in FRCMOD and PREP files. Adding 
information from .prep file to dna.rtp an creating a modified entry in 
dna.hdb is simple enough.
However I'm stuck now translating bond and angle data from .frcmod to 
.itp file, as its notation system is very different and its GROMACS 
manual section (5.3.3) lacks any substantial description of its formatting.
Is there any scripts or howtos for this, or at least a more detailed 
description  for ffbonded.itp?

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Re: [gmx-users] Protein-DNA simulation LINKS error

[Timofey Tyugashev]

Thanks for the advice, Justin and Mark.

After rerunning the simulation with guanine in the DNA I've found no 
noticeable problems.

Now I'm looking for another possible sources for mistakes.
1.The input PDB file is formatted using amber conventions, i.e. DG5 and 
DG3 for terminal guanosine  residues, CYX for S--S linked cystine and so 
on. Could it result in any erroneous interpretations by pdb2gmx?
2. I think I correctly created 8-oxoguanine entry in amber force field 
files by copying and modifying existing one for normal guanine, but I 
want to re-check myself just to be sure. Is there anything more in-depth 
available than rather laconic instruction from the GROMACS site? I've 
tried searching through the maillist, but looks like nothing similar 
came up (It's a pity that no forum exist, looking for past answers would 
be far simpler).
3. Could an accidental simultaneous execution of two or three jobs on 
one workstation (scheduling script was set incorrectly once) cause LINKS 
errors?

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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 135, Issue 5

[Timofey Tyugashev]

No, I may have misleadingly phrased my question but I do use 8-oxoguanosine 
parameters calculated and published in a paper for AMBER years ago. I am simply 
worried about correctly formatting them into force field definition files in 
GROMACS.
A far simpler task than calculating and verifying the numbers themselves all by 
myself.


01.07.2015 18:51, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет:
-- Message: 6 Date: Wed, 01 Jul 2015 
08:41:09 -0400 From: Justin Lemkul jalem...@vt.edu To: 
gmx-us...@gromacs.org Subject: Re: [gmx-users] Protein-DNA simulation 
LINKS error Message-ID: 5593dfe5.20...@vt.edu Content-Type: 
text/plain; charset=windows-1252; format=flowed On 7/1/15 8:08 AM, 
Timofey Tyugashev wrote:

Thanks for the advice, Justin and Mark.

After rerunning the simulation with guanine in the DNA I've found no noticeable
problems.
Now I'm looking for another possible sources for mistakes.
1.The input PDB file is formatted using amber conventions, i.e. DG5 and DG3 for
terminal guanosine  residues, CYX for S--S linked cystine and so on. Could it
result in any erroneous interpretations by pdb2gmx?

pdb2gmx throws obvious errors if there is a problem.  AMBER uses unique
nomenclature for termini, which is consistent with what you describe here.


2. I think I correctly created 8-oxoguanine entry in amber force field files by
copying and modifying existing one for normal guanine, but I want to re-check
myself just to be sure. Is there anything more in-depth available than rather
laconic instruction from the GROMACS site? I've tried searching through the
maillist, but looks like nothing similar came up (It's a pity that no forum
exist, looking for past answers would be far simpler).

Generating force field parameters is well beyond the scope of what is or should
be included in GROMACS documentation.  We provide a few resources in terms of
the implementation, but given the vast scope of this topic, and the expert
knowledge required, it is impossible to teach people to derive parameters
suitably.  For that, you need to read and understand the literature regarding
the parametrization theory and methods of your chosen force field.  At least
you've arrived at your answer - you have sub-optimal parameters for 8-oxoG that
cause a crash.  Now the task is to derive parameters of suitable quality.



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Re: [gmx-users] Protein-DNA simulation LINKS error

[Timofey Tyugashev]

Looking through the paper for the FF I see that the values specified are 
1.0 nm and 1.05 nm for cutoffs. If I used longer cutoffs than specified, 
then why it should affect the systme in a deleterious way?
Anyway, now I'll try simulations with values from the paper, both for 
oxoguanine and plain guanine complexes.
Is the dodecahedron box size of 1.3 sufficient for this cutoffs, or 
should I pick even bigger one just to be on the safe side?

Message: 5
Date: Wed, 24 Jun 2015 07:44:41 -0400
From: Justin Lemkuljalem...@vt.edu
To:gmx-us...@gromacs.org
Subject: Re: [gmx-users] Protein-DNA simulation LINKS error
Message-ID:558a9829.4030...@vt.edu
Content-Type: text/plain; charset=utf-8; format=flowed



On 6/24/15 7:41 AM, Timofey Tyugashev wrote:

24.06.2015 15:58,gromacs.org_gmx-users-requ...@maillist.sys.kth.se  ?:


--

Message: 5
Date: Wed, 24 Jun 2015 05:58:47 -0400
From: Justin Lemkuljalem...@vt.edu
To:gmx-us...@gromacs.org
Subject: Re: [gmx-users] Protein-DNA simulation LINKS error
Message-ID:558a7f57.7000...@vt.edu
Content-Type: text/plain; charset=windows-1252; format=flowed



On 6/24/15 5:20 AM, Erik Marklund wrote:

Hi Timofey,

If I recall correctly, there is no constrainttype defined for the pair MCH3
CT in ffbonded.itp, which is needed for making a 4out virtual site for the
methyl group in thymine. You need to work out the geometry that yields the
correct moment of inertia for the methyl group and define a constraint type
accordingly.


There are virtual sites in this system?  I saw no mention of this; have I 
missed
something?


Kind regards,
Erik



On 24 Jun 2015, at 06:38, Timofey Tyugashevtyugas...@niboch.nsc.ru  wrote:


I have ordinary DNA and an oxoguanine site? What actions should I take to
correct these vsite parameters?

If you're using virtual sites, back up and don't do that.  Solve simple issues
before doing harder things.  If you have a non-standard residue like 8-oxoG,
then perhaps its parameters are insufficient.  Try running with a normal DNA
(e.g. G instead of 8-oxoG) and see if that works first, before doing something
atypical.

-Justin

I haven?t planned to use virtual sites for this simulations yet. A short
calculation with normal guanine worked fine, one with longer time is still in
queue for calculation, so I'll definitely check it later.
Looking through the literature I've encountered different cutoff values, mainly
from 1.0 to 1.4 for forcefields, so I simply picked the middle one of 1.2. How
bad it is?

Read the AMBER99sb-ILDN paper.  Use those values.  You can't pick some arbitrary
value in the ballpark of what different models use.  That doesn't make sense.
Cutoffs are part of the force field; treat them as such.

Your problem almost certainly comes from an inaccurate 8-oxoG topology if normal
guanine works fine.

-Justin


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Re: [gmx-users] Protein-DNA simulation LINKS error

[Timofey Tyugashev]

Just to make sure I want to recheck myself:
Lennard-Jones interactions cutoffs (set at 10A in the paper) are defined 
by rvdw
short-range electrostatic interactions (set at 10A in the paper two) are 
defined by rlist and rcoulomb, but when I use Verlet scheme, rlist is 
ignored anyway.
long-range electrostatic interactions (they are specified separately in 
AMBER99SB-ildn paper at 10,5A) are defined by rlistlong. Are there any 
other parameters I need to set to use this twin-range cutoff scheme?

24.06.2015 18:25, gromacs.org_gmx-users-requ...@maillist.sys.kth.se пишет:

Read the AMBER99sb-ILDN paper.  Use those values.  You can't pick some arbitrary
value in the ballpark of what different models use.  That doesn't make sense.
Cutoffs are part of the force field; treat them as such.

Your problem almost certainly comes from an inaccurate 8-oxoG topology if normal
guanine works fine.

-Justin


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Re: [gmx-users] Protein-DNA simulation LINKS error

[Timofey Tyugashev]

I have ordinary DNA and an oxoguanine site? What actions should I take 
to correct these vsite parameters?

Message: 1
Date: Tue, 23 Jun 2015 22:24:20 +
From: Erik Marklund erik.markl...@chem.ox.ac.uk
To: gmx-us...@gromacs.org gmx-us...@gromacs.org
Subject: Re: [gmx-users] Protein-DNA simulation LINKS error
Message-ID: 61edbf38-6d1f-4089-8ebe-03caaaff6...@chem.ox.ac.uk
Content-Type: text/plain; charset=us-ascii

The vsite parameters are not complete for DNA/RNA. Perhaps you have faster 
oscillations in your system than you intended to have.

Erik


On 23 Jun 2015, at 21:15, Justin Lemkul jalem...@vt.edu wrote:



On 6/23/15 7:13 AM, Timofey Tyugashev wrote:

I'm trying a few simulations of a enzyme-DNA complex and while in short
timeframes (up to 5ns) the behaviour looks quite normal, a 10ns simulation
crashes with numerous LINCS warnings.
Maybe there are some errors in mdp configuration file? To mine inexperienced eye
they look good enough.
I'm using AMBER99SB-ILDN with TIP3 water model and 1.0 dodecahedron water box,
system requires around 30 Na atoms to compensate the charge. I also create a
combined group Protein_DNA using make ndx.
Here are the MDPs:

Ions: http://pastebin.com/xCUqiDM0
EM: http://pastebin.com/WcXdXBWf
NVT: http://pastebin.com/sdVqfGDM
NPT: http://pastebin.com/AsMVC7yH
MD: http://pastebin.com/sne7Fpzt

Any help?

AMBER99sb-ILDN uses different cutoffs so correct those, but that alone is not 
necessarily to blame for the crash.  In general, here's the usual 
troubleshooting protocol:

http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

-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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[gmx-users] Looking for FF parameters for bivalent metals and oxoguanine

[Timofey Tyugashev]

I'm investigating several protein-DNA systems with AMBER 99SB force 
field . Some of them involve 8-oxoG lesions and metal-dependent enzymes.
Is there any reliable calculated parameters for them or any reliable and 
reasonably quick way to derive them?

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