Re: [gmx-users] is it necessary to mdrun posre_npt.mdp first and then posre_nvt.mdp

[Tsjerk Wassenaar]

No, what Mark means is that if you equilibrated temperature AND pressure
(NpT) there's no point in an NVT step, in which the pressure may go off
again, even though it's unlikely to matter much, because the volume is
already within proper range.

However, there's the 'posre' part still, which suggests that the
equilibrations were run with position restraints. Before production, there
should be some equilibration without these.

In the end, in this case it doesn't matter much. If the production
simulation runs, it runs. Do take care to cut off enough of the first part
to account for long term relaxation effects.

I think the biggest concern is that the worry suggests a lack of insight in
the process and theory of MD. Please do follow Marks advise and run through
a number of tutorials.

Cheers,

Tsjerk
On Mar 31, 2016 05:45, "sun"  wrote:

> What marks means clearly- you should use second equilibrium output file
> for final mdrun. i.e. posre_nvt
>
> Sent from my iPhone
>
> > On 31-Mar-2016, at 12:17 am, Mark Abraham 
> wrote:
> >
> > Hi,
> >
> > The reasoning behind doing equilibration is covered in various tutorials,
> > which might be good background for you for other things too. There's no
> > point doing a second equilibration phase if you are going to start
> > production MD from the end point of the first equilibration phase. That's
> > pure waste.
> >
> > Mark
> >
> > On Wed, Mar 30, 2016 at 8:28 PM Pradip Kaur 
> > wrote:
> >
> >> Sorry I didn't get you  ...can you please explain me in details
> >>> On 30-Mar-2016 11:44 pm, "Mark Abraham" 
> wrote:
> >>>
> >>> Hi,
> >>>
> >>> Why would you do some equilibration, then some further equilibration,
> and
> >>> then start from the point before the further equilibration?
> >>>
> >>> Mark
> >>>
> >>> On Wed, Mar 30, 2016 at 8:12 PM Pradip Kaur 
> >>> wrote:
> >>>
>  but i have one question  when i m running md.mdp which file should i
> >> use
> >>> as
>  input file ,posre_npt.pdb or posre_nvt.pdb ?
> 
>  On 30 March 2016 at 23:40, Pradip Kaur 
> >> wrote:
> 
> > thanks so much
> >
> >> On 30 March 2016 at 21:33, Mark Abraham 
> > wrote:
> >
> >> Hi,
> >>
> >> The purpose of these equilibration phases is to allow the system to
>  relax
> >> to the desired temperature and pressure. Since you observed that
> >> this
> >> happened before starting your production MD ;-) then there's no
> >> issue.
>  But
> >> in many cases you'll have an easier life if you do it the other way
> >> around.
> >>
> >> Mark
> >>
> >> On Wed, Mar 30, 2016 at 5:23 PM Pradip Kaur <
> >> kaur.pradip...@gmail.com
> 
> >> wrote:
> >>
> >>> i have run posre_npt.mdp first and then posre_nvt.mdp by mistake
> >> but
>  now
> >>> going through gromacs manual i found that posre_nvt.mdp is first
> >> run
>  and
> >>> then posre_npt.mdp, but i have already started  md.mdp run with
> >>> posre_nvt.pdb (which was last generated pdb file after mdrun of
> >>> posre_nvt.mdp ) there is no error till now, should i need to stop
> >> my
> >> run or
> >>> continue with it ?
> >>> --
> >>> Gromacs Users mailing list
> >>>
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> >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
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> >>> posting!
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> >>> * For 

Re: [gmx-users] QM calculation

[mohammad r]

Thank you very much Justin for your helpful answer. 

On Thursday, March 31, 2016 3:40 PM, Justin Lemkul  wrote:
 

 

On 3/31/16 12:19 AM, mohammad r wrote:
> Thank you Justin, I want to do QM calculationbefore running equilibration
> then run the MD simulation by GROMACS. Do you knowwhich software is
> appropriate and compatible with GROMACS that after QM calculation I can run
> the rest of simulation?

Again, for a pure QM calculation (geometry optimization, I presume) there is no 
interaction with GROMACS or any other software.  You do your optimization, 
output the coordinates, and then move on.  If I'm missing some critical detail, 
please describe exactly what you want to do.

-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] Number of simulated annealing points

[Mark Abraham]

Hi,

My guess is that you're fine. MAXPTR is probably just a hangover from
someone who didn't want to allocate memory dynamically.

Mark

On Fri, 1 Apr 2016 00:50 Tim Moore  wrote:

> I went back and tried to change MAXPTR to a larger value - I then get a
> different error saying input lines can only contain 4095 characters. After
> digging around the source code a bit more, I found this came from a defined
> constant STRLEN in src/gromacs/utility/cstringutil.h
> <
> https://github.com/gromacs/gromacs/blob/f3602aa73c3012363cea7013f28458754a9debdb/src/gromacs/utility/cstringutil.h
> >*.
> *I updated this to a larger value to accommodate my long lines in the mdp
> file. After re-installing, I can successfully grompp my input file, and it
> seems to be running fine.
>
> I'm assuming since make check passed without errors, I should not be
> concerned about any hidden, funky behavior. Is this a safe assumption? And
> is there any reason why setting STRLEN to a much larger number is a bad
> idea?
>
> On Wed, Mar 30, 2016 at 1:34 PM, Tim Moore  wrote:
>
> > Hi,
> >
> > I'm currently simulating bilayer systems, where our equilibration scheme
> > involves randomly adjusting the temperature to values within a given
> range.
> > The temperatures can be predetermined, so the we can use the simulated
> > annealing module within GROMACS. However, the maximum number of allowed
> > temperatures in simulated annealing is 254 points, meaning we can only
> use
> > 254 points before the cycle starts over (using periodic annealing). I
> need
> > many more set points than that, so this is a problem. I see in the source
> > code there is a parameter MAXPTR = 254 that defines the maximum number of
> > elements allowed. This brings me to my question: is there any reason to
> NOT
> > change this to a larger number to accommodate the larger number of
> > temperature points I need? I see two easy workarounds, the first being to
> > increase MAXPTR; the second being make a new parameter MAXPTR2 and use
> that
> > only for the str_nelem() calls associated with the annealing. Is either
> of
> > these preferred over the other, or is there a better solution? Also, what
> > is the motivation for setting MAXPTR = 254 - is it some sort of
> > optimization? Will setting MAXPTR to a higher value hurt performance?
> >
> > Thanks,
> >
> > --
> > Tim Moore
> >
>
>
>
> --
> Tim Moore
> --
> Gromacs Users mailing list
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Re: [gmx-users] Number of simulated annealing points

[Tim Moore]

I went back and tried to change MAXPTR to a larger value - I then get a
different error saying input lines can only contain 4095 characters. After
digging around the source code a bit more, I found this came from a defined
constant STRLEN in src/gromacs/utility/cstringutil.h
*.
*I updated this to a larger value to accommodate my long lines in the mdp
file. After re-installing, I can successfully grompp my input file, and it
seems to be running fine.

I'm assuming since make check passed without errors, I should not be
concerned about any hidden, funky behavior. Is this a safe assumption? And
is there any reason why setting STRLEN to a much larger number is a bad
idea?

On Wed, Mar 30, 2016 at 1:34 PM, Tim Moore  wrote:

> Hi,
>
> I'm currently simulating bilayer systems, where our equilibration scheme
> involves randomly adjusting the temperature to values within a given range.
> The temperatures can be predetermined, so the we can use the simulated
> annealing module within GROMACS. However, the maximum number of allowed
> temperatures in simulated annealing is 254 points, meaning we can only use
> 254 points before the cycle starts over (using periodic annealing). I need
> many more set points than that, so this is a problem. I see in the source
> code there is a parameter MAXPTR = 254 that defines the maximum number of
> elements allowed. This brings me to my question: is there any reason to NOT
> change this to a larger number to accommodate the larger number of
> temperature points I need? I see two easy workarounds, the first being to
> increase MAXPTR; the second being make a new parameter MAXPTR2 and use that
> only for the str_nelem() calls associated with the annealing. Is either of
> these preferred over the other, or is there a better solution? Also, what
> is the motivation for setting MAXPTR = 254 - is it some sort of
> optimization? Will setting MAXPTR to a higher value hurt performance?
>
> Thanks,
>
> --
> Tim Moore
>



-- 
Tim Moore
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Re: [gmx-users] Error: Lost Particles while sorting

[Szilárd Páll]

On Thu, Mar 31, 2016 at 9:25 PM, Smith, Micholas D. 
wrote:

> Hi,
>
> Good to know. I'll ask the supercomputing folks to update gromacs from
> 5.0.4 to 5.0.7 at the next scheduled downtime.
>

I don't think the machine needs to be offline just to install a version of
GROMACS. ;)


> -Micholas
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> Abraham 
> Sent: Thursday, March 31, 2016 3:22 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Error: Lost Particles while sorting
>
> Hi,
>
> I was thinking of http://redmine.gromacs.org/issues/1153 but on general
> principles that should not have showed up in 5.0. Nonetheless the early 5.0
> versions had enough GPU-related issues that you still want to follow my
> suggestion and see how you go.
>
> Mark
>
> On Thu, 31 Mar 2016 20:11 Smith, Micholas D.  wrote:
>
> > Thanks, Mark. I didn't see this bug noted in the bug list so I thought I
> > was just going crazy
> >
> > ===
> > Micholas Dean Smith, PhD.
> > Post-doctoral Research Associate
> > University of Tennessee/Oak Ridge National Laboratory
> > Center for Molecular Biophysics
> >
> > 
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> > Abraham 
> > Sent: Thursday, March 31, 2016 2:57 PM
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] Error: Lost Particles while sorting
> >
> > Hi,
> >
> > Starting a new series of calculations on the earliest of a series of
> patch
> > releases means you have chosen to accept all the bugs that have been
> fixed
> > since. ;-) This indeed looks like one of them. Get e.g. 5.0.7 installed.
> >
> > Mark
> >
> > On Thu, 31 Mar 2016 19:40 Smith, Micholas D.  wrote:
> >
> > > Dear other users (and developers)
> > >
> > >
> > > I moved some simulations that were working pretty well on one
> > > supercomputer to another (the previous one did not have gpu nodes) to
> > take
> > > advantage of some gpus, but I am now getting a sporadic error:
> > >
> > >
> > > 
> > >
> > > Program gmx_mpi, VERSION 5.0
> > > Source code file:
> > > /autofs/na4_sw/xk6/gromacs/5.0/cle5.2_gnu4.8.2/source/src/grom
> > > acs/mdlib/nbnxn_search.c, line: 728
> > >
> > > Software inconsistency error:
> > > Lost particles while sorting
> > > For more information and tips for troubleshooting, please check the
> > GROMACS
> > > website at http://www.gromacs.org/Documentation/Errors
> > >
> > > -
> > >
> > >
> > > in one of my simulations (but not the others), when I start to use more
> > 16
> > > MPI processes per simulation. I should note that I am using mdrun
> > -multidir
> > > in order to launch these simulations at the same time, and it doesn't
> > seem
> > > to be a specific simulation that it causing the issue. Additionally, it
> > is
> > > rather sporadic, sometimes the simulations will run with no problems,
> > other
> > > times it run for 2 minutes and then fails (and I get stuck back in the
> > > queue). Any ideas?
> > >
> > >
> > >
> > > ===
> > > Micholas Dean Smith, PhD.
> > > Post-doctoral Research Associate
> > > University of Tennessee/Oak Ridge National Laboratory
> > > Center for Molecular Biophysics
> > > --
> > > 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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[gmx-users] Rotation of single moleculae in vacuum

[VITALY V. CHABAN]

I simulate a single flexible molecule with no PBC starting from its
optimized configuration (L_BFGS) and immediately turning T-coupling on.
>From the very beginning, the molecule starts to rotate around COM. Although
this motion may not matter for an isolated molecule, I'd be happy to
understand a physical origin of this behavior.
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Re: [gmx-users] Suggestion to update online .mdp options for pull code

[Szilárd Páll]

On Thu, Mar 31, 2016 at 8:37 PM, Mark Abraham 
wrote:

> Hi,
>
> On Thu, 31 Mar 2016 19:23 Christopher Neale 
> wrote:
>
> > Dear developers:
> >
> > The online manual lists pull-code options here:
> > http://manual.gromacs.org/current/online/mdp_opt.html#pull
>
>
> No, because those pages are version stamped e.g. 5.0.7 because that version
> has to have its online documentation somewhere, and 5.1.x has different
> needs. When we released every few years these things didn't change or
> matter much, but now the pace of GROMACS change is much faster than
> people's changes in usage, so version-specific documentation is what we
> must have.
>
> that seem to have not been updated since:
> >
> http://manual.gromacs.org/documentation/5.1/ReleaseNotes/new-features.html#changed-the-way-pull-directions-are-selected
> >
> > It took me a while to figure out what was going on since the .mdp options
> > are not listed in the pdf manual either.
> >
>
> Indeed, but you can find all the 5.1 documentation (various new content
> also) via the link I suggested to you recently. Google can now do a good
> job of finding at least this documentation, whereas it can't ever find
> anything in a big pdf lump...


That's incorrect, see:
https://support.google.com/webmasters/answer/35287?hl=en

PDFs are fully indexed by Google (and other engines), contribute to
pagerank, and to the best of my knowledge there should be only minor
drawback to search-friendliness wrt HTML pages.

As far as I know, PDFs can be made ill-suited for naviagtion/search by lack
of index, missing or dummy tags and properties, and to some extent by the
lack of PDF/A standard compliance. Not sure how well does the manual's PDF
version do in this respect, but I'll check.


> I plan to move more content to the new format
> as time passes, but it's a big job!
>
> Mark
>
>
> > Thank you,
> > Chris.
> > --
> > Gromacs Users mailing list
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Re: [gmx-users] Error: Lost Particles while sorting

[Smith, Micholas D.]

Hi,

Good to know. I'll ask the supercomputing folks to update gromacs from 5.0.4 to 
5.0.7 at the next scheduled downtime. 

-Micholas


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Mark Abraham 

Sent: Thursday, March 31, 2016 3:22 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Error: Lost Particles while sorting

Hi,

I was thinking of http://redmine.gromacs.org/issues/1153 but on general
principles that should not have showed up in 5.0. Nonetheless the early 5.0
versions had enough GPU-related issues that you still want to follow my
suggestion and see how you go.

Mark

On Thu, 31 Mar 2016 20:11 Smith, Micholas D.  wrote:

> Thanks, Mark. I didn't see this bug noted in the bug list so I thought I
> was just going crazy
>
> ===
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> Abraham 
> Sent: Thursday, March 31, 2016 2:57 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Error: Lost Particles while sorting
>
> Hi,
>
> Starting a new series of calculations on the earliest of a series of patch
> releases means you have chosen to accept all the bugs that have been fixed
> since. ;-) This indeed looks like one of them. Get e.g. 5.0.7 installed.
>
> Mark
>
> On Thu, 31 Mar 2016 19:40 Smith, Micholas D.  wrote:
>
> > Dear other users (and developers)
> >
> >
> > I moved some simulations that were working pretty well on one
> > supercomputer to another (the previous one did not have gpu nodes) to
> take
> > advantage of some gpus, but I am now getting a sporadic error:
> >
> >
> > 
> >
> > Program gmx_mpi, VERSION 5.0
> > Source code file:
> > /autofs/na4_sw/xk6/gromacs/5.0/cle5.2_gnu4.8.2/source/src/grom
> > acs/mdlib/nbnxn_search.c, line: 728
> >
> > Software inconsistency error:
> > Lost particles while sorting
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> >
> > -
> >
> >
> > in one of my simulations (but not the others), when I start to use more
> 16
> > MPI processes per simulation. I should note that I am using mdrun
> -multidir
> > in order to launch these simulations at the same time, and it doesn't
> seem
> > to be a specific simulation that it causing the issue. Additionally, it
> is
> > rather sporadic, sometimes the simulations will run with no problems,
> other
> > times it run for 2 minutes and then fails (and I get stuck back in the
> > queue). Any ideas?
> >
> >
> >
> > ===
> > Micholas Dean Smith, PhD.
> > Post-doctoral Research Associate
> > University of Tennessee/Oak Ridge National Laboratory
> > Center for Molecular Biophysics
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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Re: [gmx-users] Error: Lost Particles while sorting

[Mark Abraham]

Hi,

I was thinking of http://redmine.gromacs.org/issues/1153 but on general
principles that should not have showed up in 5.0. Nonetheless the early 5.0
versions had enough GPU-related issues that you still want to follow my
suggestion and see how you go.

Mark

On Thu, 31 Mar 2016 20:11 Smith, Micholas D.  wrote:

> Thanks, Mark. I didn't see this bug noted in the bug list so I thought I
> was just going crazy
>
> ===
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> Abraham 
> Sent: Thursday, March 31, 2016 2:57 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Error: Lost Particles while sorting
>
> Hi,
>
> Starting a new series of calculations on the earliest of a series of patch
> releases means you have chosen to accept all the bugs that have been fixed
> since. ;-) This indeed looks like one of them. Get e.g. 5.0.7 installed.
>
> Mark
>
> On Thu, 31 Mar 2016 19:40 Smith, Micholas D.  wrote:
>
> > Dear other users (and developers)
> >
> >
> > I moved some simulations that were working pretty well on one
> > supercomputer to another (the previous one did not have gpu nodes) to
> take
> > advantage of some gpus, but I am now getting a sporadic error:
> >
> >
> > 
> >
> > Program gmx_mpi, VERSION 5.0
> > Source code file:
> > /autofs/na4_sw/xk6/gromacs/5.0/cle5.2_gnu4.8.2/source/src/grom
> > acs/mdlib/nbnxn_search.c, line: 728
> >
> > Software inconsistency error:
> > Lost particles while sorting
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> >
> > -
> >
> >
> > in one of my simulations (but not the others), when I start to use more
> 16
> > MPI processes per simulation. I should note that I am using mdrun
> -multidir
> > in order to launch these simulations at the same time, and it doesn't
> seem
> > to be a specific simulation that it causing the issue. Additionally, it
> is
> > rather sporadic, sometimes the simulations will run with no problems,
> other
> > times it run for 2 minutes and then fails (and I get stuck back in the
> > queue). Any ideas?
> >
> >
> >
> > ===
> > Micholas Dean Smith, PhD.
> > Post-doctoral Research Associate
> > University of Tennessee/Oak Ridge National Laboratory
> > Center for Molecular Biophysics
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] Error: Lost Particles while sorting

[Smith, Micholas D.]

Thanks, Mark. I didn't see this bug noted in the bug list so I thought I was 
just going crazy

===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Mark Abraham 

Sent: Thursday, March 31, 2016 2:57 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Error: Lost Particles while sorting

Hi,

Starting a new series of calculations on the earliest of a series of patch
releases means you have chosen to accept all the bugs that have been fixed
since. ;-) This indeed looks like one of them. Get e.g. 5.0.7 installed.

Mark

On Thu, 31 Mar 2016 19:40 Smith, Micholas D.  wrote:

> Dear other users (and developers)
>
>
> I moved some simulations that were working pretty well on one
> supercomputer to another (the previous one did not have gpu nodes) to take
> advantage of some gpus, but I am now getting a sporadic error:
>
>
> 
>
> Program gmx_mpi, VERSION 5.0
> Source code file:
> /autofs/na4_sw/xk6/gromacs/5.0/cle5.2_gnu4.8.2/source/src/grom
> acs/mdlib/nbnxn_search.c, line: 728
>
> Software inconsistency error:
> Lost particles while sorting
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> -
>
>
> in one of my simulations (but not the others), when I start to use more 16
> MPI processes per simulation. I should note that I am using mdrun -multidir
> in order to launch these simulations at the same time, and it doesn't seem
> to be a specific simulation that it causing the issue. Additionally, it is
> rather sporadic, sometimes the simulations will run with no problems, other
> times it run for 2 minutes and then fails (and I get stuck back in the
> queue). Any ideas?
>
>
>
> ===
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] Suggestion to update online .mdp options for pull code

[Christopher Neale]

Indeed, sorry that I missed that stamp in the upper right. I was confused by 
the word "current" in the html address, I guess. 

Searching "pull" on http://manual.gromacs.org/documentation/5.1.2/index.html 
did pull up what I wanted:
http://manual.gromacs.org/documentation/5.1.2/user-guide/mdp-options.html?highlight=pull#mdp-pull

The new documentation system is quite nice.

Thanks again Mark!
Chris.

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Mark Abraham 

Sent: 31 March 2016 14:37
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Suggestion to update online .mdp options for pull  
code

Hi,

On Thu, 31 Mar 2016 19:23 Christopher Neale 
wrote:

> Dear developers:
>
> The online manual lists pull-code options here:
> http://manual.gromacs.org/current/online/mdp_opt.html#pull


No, because those pages are version stamped e.g. 5.0.7 because that version
has to have its online documentation somewhere, and 5.1.x has different
needs. When we released every few years these things didn't change or
matter much, but now the pace of GROMACS change is much faster than
people's changes in usage, so version-specific documentation is what we
must have.

that seem to have not been updated since:
> http://manual.gromacs.org/documentation/5.1/ReleaseNotes/new-features.html#changed-the-way-pull-directions-are-selected
>
> It took me a while to figure out what was going on since the .mdp options
> are not listed in the pdf manual either.
>

Indeed, but you can find all the 5.1 documentation (various new content
also) via the link I suggested to you recently. Google can now do a good
job of finding at least this documentation, whereas it can't ever find
anything in a big pdf lump... I plan to move more content to the new format
as time passes, but it's a big job!

Mark


> Thank you,
> Chris.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
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Re: [gmx-users] Error: Lost Particles while sorting

[Mark Abraham]

Hi,

Starting a new series of calculations on the earliest of a series of patch
releases means you have chosen to accept all the bugs that have been fixed
since. ;-) This indeed looks like one of them. Get e.g. 5.0.7 installed.

Mark

On Thu, 31 Mar 2016 19:40 Smith, Micholas D.  wrote:

> Dear other users (and developers)
>
>
> I moved some simulations that were working pretty well on one
> supercomputer to another (the previous one did not have gpu nodes) to take
> advantage of some gpus, but I am now getting a sporadic error:
>
>
> 
>
> Program gmx_mpi, VERSION 5.0
> Source code file:
> /autofs/na4_sw/xk6/gromacs/5.0/cle5.2_gnu4.8.2/source/src/grom
> acs/mdlib/nbnxn_search.c, line: 728
>
> Software inconsistency error:
> Lost particles while sorting
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> -
>
>
> in one of my simulations (but not the others), when I start to use more 16
> MPI processes per simulation. I should note that I am using mdrun -multidir
> in order to launch these simulations at the same time, and it doesn't seem
> to be a specific simulation that it causing the issue. Additionally, it is
> rather sporadic, sometimes the simulations will run with no problems, other
> times it run for 2 minutes and then fails (and I get stuck back in the
> queue). Any ideas?
>
>
>
> ===
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
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> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] Error: Lost Particles while sorting

[Smith, Micholas D.]

Dear other users (and developers)


I moved some simulations that were working pretty well on one supercomputer to 
another (the previous one did not have gpu nodes) to take advantage of some 
gpus, but I am now getting a sporadic error:




Program gmx_mpi, VERSION 5.0
Source code file: /autofs/na4_sw/xk6/gromacs/5.0/cle5.2_gnu4.8.2/source/src/grom
acs/mdlib/nbnxn_search.c, line: 728

Software inconsistency error:
Lost particles while sorting
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

-


in one of my simulations (but not the others), when I start to use more 16 MPI 
processes per simulation. I should note that I am using mdrun -multidir in 
order to launch these simulations at the same time, and it doesn't seem to be a 
specific simulation that it causing the issue. Additionally, it is rather 
sporadic, sometimes the simulations will run with no problems, other times it 
run for 2 minutes and then fails (and I get stuck back in the queue). Any ideas?



===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
-- 
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Re: [gmx-users] Suggestion to update online .mdp options for pull code

[Mark Abraham]

Hi,

On Thu, 31 Mar 2016 19:23 Christopher Neale 
wrote:

> Dear developers:
>
> The online manual lists pull-code options here:
> http://manual.gromacs.org/current/online/mdp_opt.html#pull


No, because those pages are version stamped e.g. 5.0.7 because that version
has to have its online documentation somewhere, and 5.1.x has different
needs. When we released every few years these things didn't change or
matter much, but now the pace of GROMACS change is much faster than
people's changes in usage, so version-specific documentation is what we
must have.

that seem to have not been updated since:
> http://manual.gromacs.org/documentation/5.1/ReleaseNotes/new-features.html#changed-the-way-pull-directions-are-selected
>
> It took me a while to figure out what was going on since the .mdp options
> are not listed in the pdf manual either.
>

Indeed, but you can find all the 5.1 documentation (various new content
also) via the link I suggested to you recently. Google can now do a good
job of finding at least this documentation, whereas it can't ever find
anything in a big pdf lump... I plan to move more content to the new format
as time passes, but it's a big job!

Mark


> Thank you,
> Chris.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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[gmx-users] Suggestion to update online .mdp options for pull code

[Christopher Neale]

Dear developers:

The online manual lists pull-code options here: 
http://manual.gromacs.org/current/online/mdp_opt.html#pull
that seem to have not been updated since: 
http://manual.gromacs.org/documentation/5.1/ReleaseNotes/new-features.html#changed-the-way-pull-directions-are-selected

It took me a while to figure out what was going on since the .mdp options are 
not listed in the pdf manual either.

Thank you,
Chris.
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Re: [gmx-users] Looking for the source of the H-REMD slowdown when decoupling a lot of atoms

[Michael Shirts]

> One more question: why does the free energy code have to use its own kernel? 
> I realize that I'm going to sound like an idiot here, but why can't one just 
> tweak parameters outside of the kernel and then have the optimized kernel do 
> the dynamics? I presume that one has to step outside of the kernel to do the 
> replica exchanges, so why can't the code just use the optimized kernel to do 
> the dynamics between exchanges?

The optimized energy code only codes very specific interactions;
vanilla Coulomb, and Lennard-Jones.  If it coded the more general
interactions (such as soft-core) it would be significantly slower.

We've come up with some ways to handle free energy calculations with
optimized inner loops (I think we're talking about the same thing Mark
-- though we should coordinate to be sure), but that will take a
little time.

One alternate possibility would be to create N replicas of the system,
with slightly different parameters, but where all systems use the
standard functional form, and then combine the results internall.  For
something like REST2, then this could work, since one is only linearly
scaling the interactions between two parts A and B of the system; so
it would be possible to represent each system as a separate physical
system. This could work fairly well for small numbers of replicas,
though might have some problems with large numbers of replicas. If
each replica was an entire new system, it could make replica exchange
quite slow, since calculating the energies of a given configuration
with a different replica's energy function would be very costly.

Right now, for alchemical interactions, there are only two
representations of the system, and then lambda interpolates between
the two representations of the systems to create the alchemical
intermediates. Changing the way the code is structured would again
require some significant changes and time.

On Thu, Mar 31, 2016 at 10:49 AM, Christopher Neale
 wrote:
> Dear Szilárd, Mark, and Michael:
>
> Thank you for your suggestions.
>
> 1. I did use the icc compiler
> 2. I tested usage of nstlist=10 by setting verlet-buffer-tolerance=-1 (I had 
> already set nstlist=10 but mdrun changes that to 25 in my previous setup) -- 
> this did not improve the performance
> 3. I tested increasing .mdp option nstdhdl from 200 to 20,000 both with and 
> without also increasing the mdrun -replex option from 200 to 20,000 -- this 
> did not improve the performance
> 4. I tried to test more than one openMP thread per rank. I am fuzzy on this 
> part of the usage, but I tried "ibrun -np 4 gmx_mpi mdrun -ntomp 6" and it 
> was a lot slower (I think it only used 4 cores?); I also tried as above but 
> with also -ntmpi 4 and it errored with a message about not being able to set 
> thread-MPI since I didn't compile with it. In any event, I doubted that an 
> optimization here would get back most of the 12x performance loss so I didn't 
> pursue this further.
>
> The good news is that there is a beta version of the H-REMD fork of Plumed 
> that works with gromacs 5.1, so I have a viable route for now.
>
> One more question: why does the free energy code have to use its own kernel? 
> I realize that I'm going to sound like an idiot here, but why can't one just 
> tweak parameters outside of the kernel and then have the optimized kernel do 
> the dynamics? I presume that one has to step outside of the kernel to do the 
> replica exchanges, so why can't the code just use the optimized kernel to do 
> the dynamics between exchanges?
>
> Thank you again for all of your help,
> Chris.
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  on behalf of Szilárd Páll 
> 
> Sent: 30 March 2016 12:59
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Looking for the source of the H-REMD slowdown when 
> decoupling a lot of atoms
>
> Chris,
>
> I can suggest two possible tweaks, these won't do miracles, but may give
> you a bit better performance.
>
> * icc is better than gcc at optimizing the naiive free energy kernel code.
> I observed in the past up to 1.5x faster free energy kernel performance
> with icc 15 vs gcc 4.9 or so.
>
> * The default nstlist heuristic/suggestion assumes fast non-bondeds. In
> your case, depending on how long is the list buffer with the nstlist you
> use (25?), you may be able to gain a bit of performance by shifting load
> back to the search with a smaller nstlist, e.g. 10.
>
> These two combined could give in best case 2x, I guess.
>
> What I find slightly unusual in the logs you posted on redmine is the 3-4x
> slowdown in PME and constraints (I'd expect ~2x in PME and less in
> constraints), but it could be that this too is simply because most
> interaction in the system are perturbed which trigger non-optimized
> code-paths.
>
> Cheers,
> --
> Szilárd
>
> On Wed, 

Re: [gmx-users] -pbc nojump failure

[Irem Altan]

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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Re: [gmx-users] Looking for the source of the H-REMD slowdown when decoupling a lot of atoms

[Christopher Neale]

Dear Szilárd, Mark, and Michael:

Thank you for your suggestions. 

1. I did use the icc compiler
2. I tested usage of nstlist=10 by setting verlet-buffer-tolerance=-1 (I had 
already set nstlist=10 but mdrun changes that to 25 in my previous setup) -- 
this did not improve the performance
3. I tested increasing .mdp option nstdhdl from 200 to 20,000 both with and 
without also increasing the mdrun -replex option from 200 to 20,000 -- this did 
not improve the performance
4. I tried to test more than one openMP thread per rank. I am fuzzy on this 
part of the usage, but I tried "ibrun -np 4 gmx_mpi mdrun -ntomp 6" and it was 
a lot slower (I think it only used 4 cores?); I also tried as above but with 
also -ntmpi 4 and it errored with a message about not being able to set 
thread-MPI since I didn't compile with it. In any event, I doubted that an 
optimization here would get back most of the 12x performance loss so I didn't 
pursue this further.

The good news is that there is a beta version of the H-REMD fork of Plumed that 
works with gromacs 5.1, so I have a viable route for now.

One more question: why does the free energy code have to use its own kernel? I 
realize that I'm going to sound like an idiot here, but why can't one just 
tweak parameters outside of the kernel and then have the optimized kernel do 
the dynamics? I presume that one has to step outside of the kernel to do the 
replica exchanges, so why can't the code just use the optimized kernel to do 
the dynamics between exchanges? 

Thank you again for all of your help,
Chris.


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Szilárd Páll 

Sent: 30 March 2016 12:59
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Looking for the source of the H-REMD slowdown when 
decoupling a lot of atoms

Chris,

I can suggest two possible tweaks, these won't do miracles, but may give
you a bit better performance.

* icc is better than gcc at optimizing the naiive free energy kernel code.
I observed in the past up to 1.5x faster free energy kernel performance
with icc 15 vs gcc 4.9 or so.

* The default nstlist heuristic/suggestion assumes fast non-bondeds. In
your case, depending on how long is the list buffer with the nstlist you
use (25?), you may be able to gain a bit of performance by shifting load
back to the search with a smaller nstlist, e.g. 10.

These two combined could give in best case 2x, I guess.

What I find slightly unusual in the logs you posted on redmine is the 3-4x
slowdown in PME and constraints (I'd expect ~2x in PME and less in
constraints), but it could be that this too is simply because most
interaction in the system are perturbed which trigger non-optimized
code-paths.

Cheers,
--
Szilárd

On Wed, Mar 30, 2016 at 3:05 PM, Mark Abraham 
wrote:

> Hi,
>
> Yeah, unfortunately Michael's pretty much right - the free-energy kernel is
> currently that cousin nobody talks about (or to). It's essentially
> unchanged since GROMACS 4.0 days, except that the Verlet scheme has some
> kludge so that it can call the same kernel that the group scheme used to
> call. But it has none of the optimizations and also some simplifying
> pessimizations. The result is highly unsuitable for Chris's use case, but
> not horrible for the more normal case of perturbing a small part of a
> system. For now, I can only suggest trying a run with more than one OpenMP
> thread per rank, but there's nothing in the log file snippets that fills me
> with any hope that it would be noticeably faster.
>
> We have a pile of infrastructure built and in the works that will lead to
> being able to offer similarly optimized free-energy kernels, but they won't
> see the light of day until next year, I'm afraid. A set of sample .tprs at
> Redmine 742 would be most welcome, however - it's very good for us to know
> when/that we're optimizing a workflow someone actually wants to run, but
> currently has reason to avoid.
>
> Mark
>
> On Wed, Mar 30, 2016 at 8:05 AM Michael Shirts  wrote:
>
> > Hi, Chris: I'm pretty sure that it's because the nonbonded free
> > energies are much slower than the standard free energies.  You state:
> >
> > > I took a look at gmxlib/nonbonded/nb_free_energy.c in v.5.1.2, but I
> was
> > unable to find a function called "gmx_waste_time_here()" and beyond that
> I
> > was out of my depth.
> >
> > But it's much more the fact that the non-free energy nonbondeds are
> > SUPER optimized.
> >
> > I don't see a particularly viable way around this for now. The only
> > thing I can think of splitting the neighborlists into two force calls,
> > and scaling the forces and energies coming out of those.  That would
> > be a huge pain.
> >
> > On Tue, Mar 29, 2016 at 9:50 PM, Christopher Neale
> >  wrote:
> > > Dear Users:
> > >
> > > I 

Re: [gmx-users] a question related to minim.mdp

[Christopher Neale]

It depends on what you want to do. If you simply want to minimize the system so 
that the dynamics will be stable in MD, then I have never needed more than 500 
steps of minimization (though in some cases I find it necessary to use flexible 
waters and solutes via the mdp options define=-DFLEXIBLE and constraints=none). 
On the other hand, if you're trying to find a minimized structure for normal 
mode analysis, I gather from previous posts that one has to get really right to 
the potential energy minimum, which would mean setting nsteps arbitrarily large 
and letting the program define when no more minimization can be accomplished 
(perhaps among other things like the right combination of minimization schemes).

Chris.


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Brett 

Sent: 31 March 2016 12:22
To: gmx-us...@gromacs.org
Subject: [gmx-users] a question related to minim.mdp

Dear all,


Following is a minim.mdp from the website, in which "nsteps  = 5".


Here what I want to ask is, does it mean the larger the protein, the larger the 
value of nsteps? Or for any size of protein regardless of mw, as for it has 
specified "emtol   = 500.0",  " nsteps  = 5" will always work?


Brett


minim.mdp was as following,

"; ions.mdp - used as input into grompp to generate ions.tpr
; Parameters describing what to do, when to stop and what to save
integrator  = steep ; Algorithm (steep = steepest descent minimization)
emtol   = 500.0; Stop minimization when the maximum force < 1000.0 
kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range 
forces
cutoff-scheme = Verlet
ns_type = grid  ; Method to determine neighbor list (simple, grid)
coulombtype = PME   ; Treatment of long range electrostatic interactions
rcoulomb= 1.4   ; Short-range electrostatic cut-off
rvdw= 1.4   ; Short-range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions"
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[gmx-users] a question related to minim.mdp

[Brett]

Dear all,


Following is a minim.mdp from the website, in which "nsteps  = 5".


Here what I want to ask is, does it mean the larger the protein, the larger the 
value of nsteps? Or for any size of protein regardless of mw, as for it has 
specified "emtol   = 500.0",  " nsteps  = 5" will always work?


Brett


minim.mdp was as following,

"; ions.mdp - used as input into grompp to generate ions.tpr 
; Parameters describing what to do, when to stop and what to save 
integrator  = steep ; Algorithm (steep = steepest descent minimization) 
emtol   = 500.0; Stop minimization when the maximum force < 1000.0 
kJ/mol/nm 
emstep  = 0.01  ; Energy step size 
nsteps  = 5 ; Maximum number of (minimization) steps to perform 
 
; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions 
nstlist = 1 ; Frequency to update the neighbor list and long range 
forces 
cutoff-scheme = Verlet 
ns_type = grid  ; Method to determine neighbor list (simple, grid) 
coulombtype = PME   ; Treatment of long range electrostatic interactions 
rcoulomb= 1.4   ; Short-range electrostatic cut-off 
rvdw= 1.4   ; Short-range Van der Waals cut-off 
pbc = xyz   ; Periodic Boundary Conditions"
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Re: [gmx-users] is it necessary to mdrun posre_npt.mdp first and then posre_nvt.mdp

[Pradip Kaur]

 can i use only one equilibrium(only posre_npt.mdp)  i.e if after em.mdp if
i run posre_npt file and use the output of posre_npt file for final mdrun?


On 31 March 2016 at 20:32, Pradip Kaur  wrote:

> Hi ,
> I started mdrun with posre_npt .mdp  and I have ignored posre_nvt.mdp
> becoz  posre_nvt equilibrium is unnecessary if it is run after
> posre_nvt.mdp
> So ,as I already have run em.mdp  first  then posre_npt and finally
> posre_nvt .So in order to avoid further problems I took posre_npt .pdb as
> input (which was generated after running mdrun of em.mdp )for mdrun of
> MD.mdp  .
>
> Please correct me if I m wrong.
> On 31-Mar-2016 9:15 am, "sun"  wrote:
>
>> What marks means clearly- you should use second equilibrium output file
>> for final mdrun. i.e. posre_nvt
>>
>> Sent from my iPhone
>>
>> > On 31-Mar-2016, at 12:17 am, Mark Abraham 
>> wrote:
>> >
>> > Hi,
>> >
>> > The reasoning behind doing equilibration is covered in various
>> tutorials,
>> > which might be good background for you for other things too. There's no
>> > point doing a second equilibration phase if you are going to start
>> > production MD from the end point of the first equilibration phase.
>> That's
>> > pure waste.
>> >
>> > Mark
>> >
>> > On Wed, Mar 30, 2016 at 8:28 PM Pradip Kaur 
>> > wrote:
>> >
>> >> Sorry I didn't get you  ...can you please explain me in details
>> >>> On 30-Mar-2016 11:44 pm, "Mark Abraham" 
>> wrote:
>> >>>
>> >>> Hi,
>> >>>
>> >>> Why would you do some equilibration, then some further equilibration,
>> and
>> >>> then start from the point before the further equilibration?
>> >>>
>> >>> Mark
>> >>>
>> >>> On Wed, Mar 30, 2016 at 8:12 PM Pradip Kaur > >
>> >>> wrote:
>> >>>
>>  but i have one question  when i m running md.mdp which file should i
>> >> use
>> >>> as
>>  input file ,posre_npt.pdb or posre_nvt.pdb ?
>> 
>>  On 30 March 2016 at 23:40, Pradip Kaur 
>> >> wrote:
>> 
>> > thanks so much
>> >
>> >> On 30 March 2016 at 21:33, Mark Abraham 
>> > wrote:
>> >
>> >> Hi,
>> >>
>> >> The purpose of these equilibration phases is to allow the system to
>>  relax
>> >> to the desired temperature and pressure. Since you observed that
>> >> this
>> >> happened before starting your production MD ;-) then there's no
>> >> issue.
>>  But
>> >> in many cases you'll have an easier life if you do it the other way
>> >> around.
>> >>
>> >> Mark
>> >>
>> >> On Wed, Mar 30, 2016 at 5:23 PM Pradip Kaur <
>> >> kaur.pradip...@gmail.com
>> 
>> >> wrote:
>> >>
>> >>> i have run posre_npt.mdp first and then posre_nvt.mdp by mistake
>> >> but
>>  now
>> >>> going through gromacs manual i found that posre_nvt.mdp is first
>> >> run
>>  and
>> >>> then posre_npt.mdp, but i have already started  md.mdp run with
>> >>> posre_nvt.pdb (which was last generated pdb file after mdrun of
>> >>> posre_nvt.mdp ) there is no error till now, should i need to stop
>> >> my
>> >> run or
>> >>> continue with it ?
>> >>> --
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Re: [gmx-users] -pbc nojump failure

[Tsjerk Wassenaar]

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
> > > --
> > > Gromacs Users mailing list
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> > > posting!
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Re: [gmx-users] -pbc nojump failure

[Irem Altan]

Hi,

Thanks. If I do that, the reference structure would be what’s in the .tpr file, 
right?

Best,
Irem

> On Mar 31, 2016, at 8:22 AM, 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
>>> --
>>> Gromacs Users mailing list
>>> 
>>> * Please search the archive at
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>>> 
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Re: [gmx-users] -pbc nojump failure

[Irem Altan]

Hi,

Thanks for your suggestion. Unsurprisingly, the structure in 
nvt_water_frozen.tpr is also fragmented. Is there a way to use the input .pdb 
file as reference, somehow?

Best,
Irem

> On Mar 31, 2016, at 12:45 AM, 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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Re: [gmx-users] pdb2gmx & terminal residues

[Justin Lemkul]

On 3/31/16 10:41 AM, Brett wrote:

Dear Justin and All,

The full screen output was as following and I am looking forward to getting a 
reply from you.




  gmx pdb2gmx -f practice.pdb -o target_processed.gro  -ignh
   :-) GROMACS - gmx pdb2gmx, VERSION 5.1.2 (-:

 GROMACS is written by:
  Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar Bjelkmar
  Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian Fritsch
   Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent Hindriksen
  Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten Kutzner
 Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff
Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk
Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf
and the project leaders:
 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:  gmx pdb2gmx, VERSION 5.1.2
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Command line:
   gmx pdb2gmx -f practice.pdb -o target_processed.gro -ignh


Select the Force Field:
 From '/usr/local/gromacs/share/gromacs/top':
  1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 
1999-2012, 2003)
  2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
  3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 
461-469, 1996)
  4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 
1049-1074, 2000)
  5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 
2006)
  6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 
78, 1950-58, 2010)
  7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
  8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
  9: GROMOS96 43a1 force field
10: GROMOS96 43a2 force field (improved alkane dihedrals)
11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
10.1007/s00249-011-0700-9)
15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
14

Using the Gromos54a7 force field in directory gromos54a7.ff

Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos54a7.ff/watermodels.dat

Select the Water Model:
  1: SPCsimple point charge, recommended
  2: SPC/E  extended simple point charge
  3: None
1
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.r2b
Reading practice.pdb...
Read 331 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 42 residues with 331 atoms

   chain  #res #atoms
   1 'N'42331

All occupancies are one
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos54a7.ff/atomtypes.atp
Atomtype 58
Reading residue database... (gromos54a7)
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.rtp
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing proper dihedrals found on the same bond as a proper 
dihedral
Residue 108
Sorting it all out...
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.hdb
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb
Processing chain 1 'N' (331 atoms, 42 residues)
Identified residue ASP288 as a starting terminus.
Identified residue ILE329 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Start terminus ASP-288: NH3+
End terminus ILE-329: COO-
Checking for duplicate atoms
Now there are 330 atoms. Deleted 1 duplicates.
Generating any missing hydrogen atoms and/or adding termini.
Now there are 42 residues with 417 atoms
Making bonds...
Number of bonds was 424, now 419
Generating angles, dihedrals and pairs...

WARNING: WARNING: Residue 1 named ASP of a molecule in the input file was mapped
to an entry in the 

Re: [gmx-users] pdb2gmx & terminal residues

[Brett]

Dear Justin and All,

The full screen output was as following and I am looking forward to getting a 
reply from you.




 gmx pdb2gmx -f practice.pdb -o target_processed.gro  -ignh
  :-) GROMACS - gmx pdb2gmx, VERSION 5.1.2 (-:

GROMACS is written by:
 Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar Bjelkmar  
 Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian Fritsch
  Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent Hindriksen
 Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten Kutzner 
Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff
   Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk  
   Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers 
   Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf  
   and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:  gmx pdb2gmx, VERSION 5.1.2
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Command line:
  gmx pdb2gmx -f practice.pdb -o target_processed.gro -ignh


Select the Force Field:
>From '/usr/local/gromacs/share/gromacs/top':
 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 
1999-2012, 2003)
 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 
461-469, 1996)
 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 
1049-1074, 2000)
 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 
2006)
 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 
78, 1950-58, 2010)
 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
 8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
 9: GROMOS96 43a1 force field
10: GROMOS96 43a2 force field (improved alkane dihedrals)
11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
10.1007/s00249-011-0700-9)
15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
14

Using the Gromos54a7 force field in directory gromos54a7.ff

Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos54a7.ff/watermodels.dat

Select the Water Model:
 1: SPCsimple point charge, recommended
 2: SPC/E  extended simple point charge
 3: None
1
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.r2b
Reading practice.pdb...
Read 331 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 42 residues with 331 atoms

  chain  #res #atoms
  1 'N'42331 

All occupancies are one
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos54a7.ff/atomtypes.atp
Atomtype 58
Reading residue database... (gromos54a7)
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.rtp
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing proper dihedrals found on the same bond as a proper 
dihedral
Residue 108
Sorting it all out...
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.hdb
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb
Opening force field file 
/usr/local/gromacs/share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb
Processing chain 1 'N' (331 atoms, 42 residues)
Identified residue ASP288 as a starting terminus.
Identified residue ILE329 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Start terminus ASP-288: NH3+
End terminus ILE-329: COO-
Checking for duplicate atoms
Now there are 330 atoms. Deleted 1 duplicates.
Generating any missing hydrogen atoms and/or adding termini.
Now there are 42 residues with 417 atoms
Making bonds...
Number of bonds was 424, now 419
Generating angles, dihedrals and pairs...

WARNING: WARNING: Residue 1 named ASP of a molecule in the input file was mapped
to an entry in the topology database, but the atom H used in
an interaction of 

Re: [gmx-users] pdb2gmx & terminal residues

[Justin Lemkul]

On 3/31/16 8:18 AM, Brett wrote:

Dear Justin and All,

For terminal residue, regardless I select 0, 1, 2, the error messages always 
exist.

I have opened the pdb by swiss deep view and resaved it, the same error message 
still exist.


However if I choose force field 6: AMBER99SB-ILDN protein, the error message 
disappear.

Will you please give suggestions on getting rid of the warning messages for the 
terminal residues by pdb2gmx?



Please provide the full, unfiltered screen output from a functional and 
nonfunctional run through pdb2gmx.  There is no reason this shouldn't work out 
of the box.


-Justin


Brett









At 2016-03-31 19:12:38, "Justin Lemkul"  wrote:



On 3/30/16 10:41 PM, Brett wrote:

Dear All,

When I do "mx pdb2gmx -f practice.pdb -o target_processed.gro  -ignh" with force
field, it gave me the warning as following,

"WARNING: WARNING: Residue 1 named ASP of a molecule in the input file was 
mapped
to an entry in the topology database, but the atom H used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.



WARNING: WARNING: Residue 42 named ILE of a molecule in the input file was 
mapped
to an entry in the topology database, but the atom O used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.
"
I find Residue 1 (Asp) was exactly my N-terminal residue and Residue 42 was
exactly my C-terminal residue.

Here I copied the coordinates part for the N- and C-terminal residues here:

ATOM  17737  N   ASP N 288 177.107 183.312 121.044  1.00500.00   N
ATOM  17738  CA  ASP N 288 177.038 182.924 122.484  1.00500.00   C
ATOM  17739  CB  ASP N 288 176.431 184.048 123.329  1.00500.00   C
ATOM  17740  CG  ASP N 288 177.329 185.261 123.401  1.00500.00   C
ATOM  17741  OD1 ASP N 288 178.383 185.181 124.068  1.00500.00   O
ATOM  17742  OD2 ASP N 288 176.982 186.286 122.782  1.00500.00   O
ATOM  17743  C   ASP N 288 176.265 181.626 122.691  1.00500.00   C
ATOM  17744  O   ASP N 288 176.684 180.791 123.483  1.00500.00   O
ATOM  17745  N   ARG N 289 175.144 181.458 121.984  1.00500.00   N
(Residue 1 named ASP by GROMACS)
.

ATOM  18058  O   SER N 328 177.424 180.662 130.523  1.00500.00   O
ATOM  18059  N   ILE N 329 176.478 178.748 129.872  1.00500.00   N
ATOM  18060  CA  ILE N 329 175.525 179.385 128.948  1.00500.00   C
ATOM  18061  CB  ILE N 329 174.867 178.368 127.980  1.00499.43   C
ATOM  18062  CG1 ILE N 329 175.920 177.731 127.065  1.00498.96   C
ATOM  18063  CD1 ILE N 329 175.462 176.450 126.400  1.00498.79   C
ATOM  18064  CG2 ILE N 329 173.789 179.040 127.126  1.00498.79   C
ATOM  18065  C   ILE N 329 174.437 180.100 129.753  1.00498.62   C
ATOM  18066  O   ILE N 329 173.671 179.471 130.483  1.00498.27   O
ATOM  18067  O   ILE N 329 174.302 181.322 129.689  1.00496.91   O
(Residue 42 named ILE  by GROMACS)
TER
END

I myself cannot find anything wrong for my 2 terminal residues.

Will you please take a look to see how to modify the 2 terminal residues so that
the pdb2gmx will not give the warning messages?

I am looking forward to getting a reply from you.



The only way the above errors would show up is if you chose "None" for your
termini; choosing an appropriate NH3+/COO- will correct this. Note you have two
"O" in your C-terminal ILE, which is wrong as there should only be one, the
other should be OXT or whatever the force field wants (but again, the .tdb
patching mechanism takes care of this).

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==
--
Gromacs Users mailing list

* Please search the archive at 
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--
==

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

Re: [gmx-users] Own coarse-grained forcefield

[Justin Lemkul]

On 3/31/16 9:35 AM, Michał Kadlof wrote:

I would like to build my own coarse-grained forcefield for virtual 
beads-on-chain polymer. All I want for now is LJ Potential, and a spring 
between neighbours. Below are files that I have already have in my ff. The last 
file is my experimental structure in PDB format. When I run:

gmx pdb2gmx -f polimer10.pdb -o polimer10.gro

I got topol.top but there are no bonds.  What do I miss?





==> atomtypes.atp <==
B   1.0 ;   Simplest bead

==> beads.rtp <==
[ bondedtypes ]
; bonds angles  dihedrals   impropers
1 1 1 1

[ BEA ]

[ atoms ]
; name  type charge chargegroup
B   B   0.000   0



You're not assigning any bonds, so pdb2gmx doesn't write any bonds.

-Justin


==> ffbonded.itp <==
[ bondtypes ]
; i j   funcb0  kb
B B 1   1   1
[ angletypes ]
; i j k   functh0 cth ub0 cub
B B B 1 180 1

==> ffnonbonded.itp <==
[ atomtypes ]
;name   at.num  masscharge  ptype   sigma   epsilon
B   1   1.0 0.000   A   0.1 0.1

==> forcefield.doc <==
MYFORCEFIELDVery experimental forcefield

==> forcefield.itp <==

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2   yes 1.0 1.0

#include "ffnonbonded.itp"
#include "ffbonded.itp"

==> polimer10.pdb <==
ATOM  1  B   BEA A   1   0.000   0.000   0.000  0.00  0.00   C
ATOM  2  B   BEA A   2   1.000   0.000   0.000  0.00  0.00   C
ATOM  3  B   BEA A   3   2.000   0.000   0.000  0.00  0.00   C
ATOM  4  B   BEA A   4   3.000   0.000   0.000  0.00  0.00   C
ATOM  5  B   BEA A   5   4.000   0.000   0.000  0.00  0.00   C
ATOM  6  B   BEA A   6   5.000   0.000   0.000  0.00  0.00   C
ATOM  7  B   BEA A   7   6.000   0.000   0.000  0.00  0.00   C
ATOM  8  B   BEA A   8   7.000   0.000   0.000  0.00  0.00   C
ATOM  9  B   BEA A   9   8.000   0.000   0.000  0.00  0.00   C
ATOM 10  B   BEA A  10   9.000   0.000   0.000  0.00  0.00   C
TER  11  BEA A  11
CONECT12
CONECT213
CONECT324
CONECT435
CONECT546
CONECT657
CONECT768
CONECT879
CONECT98   10
CONECT   109

And here is the output of command.

$ gmx pdb2gmx -f polimer10.pdb -o polimer10.gro
(...)

GROMACS:  gmx pdb2gmx, VERSION 5.0.6
Executable:   /usr/bin/gmx
Library dir:  /usr/share/gromacs/top
Command line:
   gmx pdb2gmx -f polimer10.pdb -o polimer10.gro


Select the Force Field:
 From '/usr/share/gromacs/top':
  1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 
1999-2012, 2003)
(...)
  8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
  9: MYFORCEFILDVery experimental forcefield
10: GROMOS96 43a1 force field
(...)
16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)

Using the myforcefield force field in directory myforcefield.ff

No file 'watermodels.dat' found, will not include a water model
Reading polimer10.pdb...
WARNING: all CONECT records are ignored
Read 10 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 10 residues with 10 atoms

   chain  #res #atoms
   1 'A'10 10

All occupancy fields zero. This is probably not an X-Ray structure
Opening force field file /usr/share/gromacs/top/chromatine1.ff/atomtypes.atp
Atomtype 2
Reading residue database... (chromatine1)
Opening force field file /usr/share/gromacs/top/chromatine1.ff/beads.rtp
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing proper dihedrals found on the same bond as a proper 
dihedral
Residue 1
Sorting it all out...

Processing chain 1 'A' (10 atoms, 10 residues)
Warning: Starting residue BEA1 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue BEA2 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue BEA3 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue BEA4 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue BEA5 in chain not identified as Protein/RNA/DNA.
More than 5 unidentified residues at start of chain - disabling further 
warnings.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
Checking for duplicate atoms
Generating any missing hydrogen atoms and/or adding termini.
Now there are 10 residues with 10 atoms
Making bonds...
No bonds
Generating angles, dihedrals and pairs...
Making cmap torsions...
There are0 dihedrals,0 impropers,0 angles
  0 pairs,0 bonds and 0 virtual 

[gmx-users] Own coarse-grained forcefield

[Michał Kadlof]

I would like to build my own coarse-grained forcefield for virtual 
beads-on-chain polymer. All I want for now is LJ Potential, and a spring 
between neighbours. Below are files that I have already have in my ff. The last 
file is my experimental structure in PDB format. When I run:

gmx pdb2gmx -f polimer10.pdb -o polimer10.gro

I got topol.top but there are no bonds.  What do I miss?





==> atomtypes.atp <==
B   1.0 ;   Simplest bead

==> beads.rtp <==
[ bondedtypes ]
; bonds angles  dihedrals   impropers
1 1 1 1

[ BEA ]

[ atoms ]
; name  type charge chargegroup
B   B   0.000   0

==> ffbonded.itp <==
[ bondtypes ]   
  
; i j   funcb0  kb
B B 1   1   1
[ angletypes ]
; i j k   functh0 cth ub0 cub
B B B 1 180 1

==> ffnonbonded.itp <==
[ atomtypes ]
;name   at.num  masscharge  ptype   sigma   epsilon
B   1   1.0 0.000   A   0.1 0.1

==> forcefield.doc <==
MYFORCEFIELDVery experimental forcefield

==> forcefield.itp <==

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
1   2   yes 1.0 1.0

#include "ffnonbonded.itp"
#include "ffbonded.itp"

==> polimer10.pdb <==
ATOM  1  B   BEA A   1   0.000   0.000   0.000  0.00  0.00   C
ATOM  2  B   BEA A   2   1.000   0.000   0.000  0.00  0.00   C
ATOM  3  B   BEA A   3   2.000   0.000   0.000  0.00  0.00   C
ATOM  4  B   BEA A   4   3.000   0.000   0.000  0.00  0.00   C
ATOM  5  B   BEA A   5   4.000   0.000   0.000  0.00  0.00   C
ATOM  6  B   BEA A   6   5.000   0.000   0.000  0.00  0.00   C
ATOM  7  B   BEA A   7   6.000   0.000   0.000  0.00  0.00   C
ATOM  8  B   BEA A   8   7.000   0.000   0.000  0.00  0.00   C
ATOM  9  B   BEA A   9   8.000   0.000   0.000  0.00  0.00   C
ATOM 10  B   BEA A  10   9.000   0.000   0.000  0.00  0.00   C
TER  11  BEA A  11
CONECT12
CONECT213
CONECT324
CONECT435
CONECT546
CONECT657
CONECT768
CONECT879
CONECT98   10
CONECT   109

And here is the output of command.

$ gmx pdb2gmx -f polimer10.pdb -o polimer10.gro
(...)

GROMACS:  gmx pdb2gmx, VERSION 5.0.6
Executable:   /usr/bin/gmx
Library dir:  /usr/share/gromacs/top
Command line:
  gmx pdb2gmx -f polimer10.pdb -o polimer10.gro


Select the Force Field:
>From '/usr/share/gromacs/top':
 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 
1999-2012, 2003)
(...)
 8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
 9: MYFORCEFILD Very experimental forcefield
10: GROMOS96 43a1 force field
(...)
16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)

Using the myforcefield force field in directory myforcefield.ff

No file 'watermodels.dat' found, will not include a water model
Reading polimer10.pdb...
WARNING: all CONECT records are ignored
Read 10 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 10 residues with 10 atoms

  chain  #res #atoms
  1 'A'10 10  

All occupancy fields zero. This is probably not an X-Ray structure
Opening force field file /usr/share/gromacs/top/chromatine1.ff/atomtypes.atp
Atomtype 2
Reading residue database... (chromatine1)
Opening force field file /usr/share/gromacs/top/chromatine1.ff/beads.rtp
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H--H interactions
Using default: removing proper dihedrals found on the same bond as a proper 
dihedral
Residue 1
Sorting it all out...

Processing chain 1 'A' (10 atoms, 10 residues)
Warning: Starting residue BEA1 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue BEA2 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue BEA3 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue BEA4 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue BEA5 in chain not identified as Protein/RNA/DNA.
More than 5 unidentified residues at start of chain - disabling further 
warnings.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
Checking for duplicate atoms
Generating any missing hydrogen atoms and/or adding termini.
Now there are 10 residues with 10 atoms
Making bonds...
No bonds
Generating angles, dihedrals and pairs...
Making cmap torsions...
There are0 dihedrals,0 impropers,0 angles
 0 pairs,0 bonds and 0 virtual sites
Total mass 10.000 a.m.u.
Total charge 

Re: [gmx-users] pdb2gmx & terminal residues

[Brett]

Dear Justin and All,

For terminal residue, regardless I select 0, 1, 2, the error messages always 
exist.

I have opened the pdb by swiss deep view and resaved it, the same error message 
still exist.


However if I choose force field 6: AMBER99SB-ILDN protein, the error message 
disappear.

Will you please give suggestions on getting rid of the warning messages for the 
terminal residues by pdb2gmx?

Brett









At 2016-03-31 19:12:38, "Justin Lemkul"  wrote:
>
>
>On 3/30/16 10:41 PM, Brett wrote:
>> Dear All,
>>
>> When I do "mx pdb2gmx -f practice.pdb -o target_processed.gro  -ignh" with 
>> force
>> field, it gave me the warning as following,
>>
>> "WARNING: WARNING: Residue 1 named ASP of a molecule in the input file was 
>> mapped
>> to an entry in the topology database, but the atom H used in
>> an interaction of type angle in that entry is not found in the
>> input file. Perhaps your atom and/or residue naming needs to be
>> fixed.
>>
>>
>>
>> WARNING: WARNING: Residue 42 named ILE of a molecule in the input file was 
>> mapped
>> to an entry in the topology database, but the atom O used in
>> an interaction of type angle in that entry is not found in the
>> input file. Perhaps your atom and/or residue naming needs to be
>> fixed.
>> "
>> I find Residue 1 (Asp) was exactly my N-terminal residue and Residue 42 was
>> exactly my C-terminal residue.
>>
>> Here I copied the coordinates part for the N- and C-terminal residues here:
>>
>> ATOM  17737  N   ASP N 288 177.107 183.312 121.044  1.00500.00   
>> N
>> ATOM  17738  CA  ASP N 288 177.038 182.924 122.484  1.00500.00   
>> C
>> ATOM  17739  CB  ASP N 288 176.431 184.048 123.329  1.00500.00   
>> C
>> ATOM  17740  CG  ASP N 288 177.329 185.261 123.401  1.00500.00   
>> C
>> ATOM  17741  OD1 ASP N 288 178.383 185.181 124.068  1.00500.00   
>> O
>> ATOM  17742  OD2 ASP N 288 176.982 186.286 122.782  1.00500.00   
>> O
>> ATOM  17743  C   ASP N 288 176.265 181.626 122.691  1.00500.00   
>> C
>> ATOM  17744  O   ASP N 288 176.684 180.791 123.483  1.00500.00   
>> O
>> ATOM  17745  N   ARG N 289 175.144 181.458 121.984  1.00500.00   
>> N
>> (Residue 1 named ASP by GROMACS)
>> .
>>
>> ATOM  18058  O   SER N 328 177.424 180.662 130.523  1.00500.00   
>> O
>> ATOM  18059  N   ILE N 329 176.478 178.748 129.872  1.00500.00   
>> N
>> ATOM  18060  CA  ILE N 329 175.525 179.385 128.948  1.00500.00   
>> C
>> ATOM  18061  CB  ILE N 329 174.867 178.368 127.980  1.00499.43   
>> C
>> ATOM  18062  CG1 ILE N 329 175.920 177.731 127.065  1.00498.96   
>> C
>> ATOM  18063  CD1 ILE N 329 175.462 176.450 126.400  1.00498.79   
>> C
>> ATOM  18064  CG2 ILE N 329 173.789 179.040 127.126  1.00498.79   
>> C
>> ATOM  18065  C   ILE N 329 174.437 180.100 129.753  1.00498.62   
>> C
>> ATOM  18066  O   ILE N 329 173.671 179.471 130.483  1.00498.27   
>> O
>> ATOM  18067  O   ILE N 329 174.302 181.322 129.689  1.00496.91   
>> O
>> (Residue 42 named ILE  by GROMACS)
>> TER
>> END
>>
>> I myself cannot find anything wrong for my 2 terminal residues.
>>
>> Will you please take a look to see how to modify the 2 terminal residues so 
>> that
>> the pdb2gmx will not give the warning messages?
>>
>> I am looking forward to getting a reply from you.
>>
>
>The only way the above errors would show up is if you chose "None" for your 
>termini; choosing an appropriate NH3+/COO- will correct this. Note you have 
>two 
>"O" in your C-terminal ILE, which is wrong as there should only be one, the 
>other should be OXT or whatever the force field wants (but again, the .tdb 
>patching mechanism takes care of this).
>
>-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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>Gromacs Users mailing list
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Re: [gmx-users] -pbc nojump failure

[Francesco Carbone]

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
> > --
> > Gromacs Users mailing list
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Re: [gmx-users] pdb2gmx & terminal residues

[Justin Lemkul]

On 3/30/16 10:41 PM, Brett wrote:

Dear All,

When I do "mx pdb2gmx -f practice.pdb -o target_processed.gro  -ignh" with force
field, it gave me the warning as following,

"WARNING: WARNING: Residue 1 named ASP of a molecule in the input file was 
mapped
to an entry in the topology database, but the atom H used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.



WARNING: WARNING: Residue 42 named ILE of a molecule in the input file was 
mapped
to an entry in the topology database, but the atom O used in
an interaction of type angle in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.
"
I find Residue 1 (Asp) was exactly my N-terminal residue and Residue 42 was
exactly my C-terminal residue.

Here I copied the coordinates part for the N- and C-terminal residues here:

ATOM  17737  N   ASP N 288 177.107 183.312 121.044  1.00500.00   N
ATOM  17738  CA  ASP N 288 177.038 182.924 122.484  1.00500.00   C
ATOM  17739  CB  ASP N 288 176.431 184.048 123.329  1.00500.00   C
ATOM  17740  CG  ASP N 288 177.329 185.261 123.401  1.00500.00   C
ATOM  17741  OD1 ASP N 288 178.383 185.181 124.068  1.00500.00   O
ATOM  17742  OD2 ASP N 288 176.982 186.286 122.782  1.00500.00   O
ATOM  17743  C   ASP N 288 176.265 181.626 122.691  1.00500.00   C
ATOM  17744  O   ASP N 288 176.684 180.791 123.483  1.00500.00   O
ATOM  17745  N   ARG N 289 175.144 181.458 121.984  1.00500.00   N
(Residue 1 named ASP by GROMACS)
.

ATOM  18058  O   SER N 328 177.424 180.662 130.523  1.00500.00   O
ATOM  18059  N   ILE N 329 176.478 178.748 129.872  1.00500.00   N
ATOM  18060  CA  ILE N 329 175.525 179.385 128.948  1.00500.00   C
ATOM  18061  CB  ILE N 329 174.867 178.368 127.980  1.00499.43   C
ATOM  18062  CG1 ILE N 329 175.920 177.731 127.065  1.00498.96   C
ATOM  18063  CD1 ILE N 329 175.462 176.450 126.400  1.00498.79   C
ATOM  18064  CG2 ILE N 329 173.789 179.040 127.126  1.00498.79   C
ATOM  18065  C   ILE N 329 174.437 180.100 129.753  1.00498.62   C
ATOM  18066  O   ILE N 329 173.671 179.471 130.483  1.00498.27   O
ATOM  18067  O   ILE N 329 174.302 181.322 129.689  1.00496.91   O
(Residue 42 named ILE  by GROMACS)
TER
END

I myself cannot find anything wrong for my 2 terminal residues.

Will you please take a look to see how to modify the 2 terminal residues so that
the pdb2gmx will not give the warning messages?

I am looking forward to getting a reply from you.



The only way the above errors would show up is if you chose "None" for your 
termini; choosing an appropriate NH3+/COO- will correct this. Note you have two 
"O" in your C-terminal ILE, which is wrong as there should only be one, the 
other should be OXT or whatever the force field wants (but again, the .tdb 
patching mechanism takes care of this).


-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] QM calculation

[Justin Lemkul]

On 3/31/16 12:19 AM, mohammad r wrote:

Thank you Justin, I want to do QM calculationbefore running equilibration
then run the MD simulation by GROMACS. Do you knowwhich software is
appropriate and compatible with GROMACS that after QM calculation I can run
the rest of simulation?


Again, for a pure QM calculation (geometry optimization, I presume) there is no 
interaction with GROMACS or any other software.  You do your optimization, 
output the coordinates, and then move on.  If I'm missing some critical detail, 
please describe exactly what you want to do.


-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] virtual site - algorithmic reasons

[Justin Lemkul]

On 3/31/16 6:06 AM, Samith Rathnayake wrote:

Hi everyone,

Recently i was used to started Bevan Lab tutorial  and gone through
specially with virtual site tutorial.In this tutorial Dr.Justin emphasized
that co2 cannot effectively build in traditional sense  because of
  algorithmic reasons. And cant hold 180 degree during a simulation.Could
any one elaborate what are this "algorithmic reasons" ? any publication
upon this virtual site techniques in any gromos force field? and also about
this algorithmic reasons ? And if it is okey to used this virtual site
techniques in gromacs 4.6.5 version ?



There are mailing list posts about it; I forget the details but the long and 
short of it was that the fluctuations around a 180-degree angle lead to 
numerical instability in the code.  IIRC that was fixed some time ago, but I 
would not expect 4.6.5 to work.  Try the newest version and see if you can get 
away with a linear angle without any fancy work.


-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] Generate diagram/figure with information about protein-ligand interactions

[Justin Lemkul]

On 3/31/16 6:58 AM, bio hpc wrote:

My problem is not excel or whatever graphical program. I just need the data,
in an automatic way. Then I can use either matplotlib or similar to get the
plots automatically. But my question is if there is somewhere a repository of
gromacs scripts with a script doing an analysis of the protein-ligand
itneractions during trajectory. I do not think to be the only one requesting
this



I doubt you can do something like this "automatically," though of course it 
could be done.  My hesitation comes from the fact that the terminology used is 
quite generic and could be defined several ways.  Without knowing the context of 
the figure (which I assume is pulled from a paper, in which case your questions 
should be directed to the authors, not here...) then it's hard to say.  Of 
course GROMACS tools will do analysis like this (gmx hbond, gmx mindist -on, gmx 
saltbr) but you'll have to mine those data appropriately to pull out whatever is 
useful to you.


-Justin




El 30/3/2016, a las 6:46, Sun Iba  escribió:

i am sorry, i replied prior to looking at your figure. Actually, i have
never came across plotting data in this matter. However, I believe you
have tabulated data, so you can use Origin or excel for generating similar
images. You need little effort to arrange the data in desired manner. Best
Wishes

On Wed, Mar 30, 2016 at 3:15 AM, bio hpc  wrote:


Hi,

after a protein-ligand simulation with gromacs, I would like to be able
to generate a diagram/figure with information about protein-ligand
interactions, something like this:

https://dl.dropboxusercontent.com/u/2012631/Figure7.jpg <
https://dl.dropboxusercontent.com/u/2012631/Figure7.jpg>

I had a look to all gromacs tools but found nothing similar to this.
Where can I start from?

Thanks,

biohpc

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--
==

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] Generate diagram/figure with information about protein-ligand interactions

[Tsjerk Wassenaar]

Hi biohpc,

For this you need to combine output from gmx hbond, gmx sasa, and gmx
saltbr.

Cheers,

Tsjerk
On Mar 31, 2016 12:58, "bio hpc"  wrote:

> My problem is not excel or whatever graphical program. I just need the
> data, in an automatic way. Then I can use either matplotlib or similar to
> get the plots automatically. But my question is if there is somewhere a
> repository of gromacs scripts with a script doing an analysis of the
> protein-ligand itneractions during trajectory. I do not think to be the
> only one requesting this
>
>
> > El 30/3/2016, a las 6:46, Sun Iba  escribió:
> >
> > i am sorry, i replied prior to looking at your figure. Actually, i have
> > never came across plotting data in this matter. However, I believe you
> have
> > tabulated data, so you can use Origin or excel for generating similar
> > images. You need little effort to arrange the data in desired manner.
> > Best Wishes
> >
> > On Wed, Mar 30, 2016 at 3:15 AM, bio hpc  wrote:
> >
> >> Hi,
> >>
> >> after a protein-ligand simulation with gromacs, I would like to be able
> to
> >> generate a diagram/figure with information about protein-ligand
> >> interactions, something like this:
> >>
> >> https://dl.dropboxusercontent.com/u/2012631/Figure7.jpg <
> >> https://dl.dropboxusercontent.com/u/2012631/Figure7.jpg>
> >>
> >> I had a look to all gromacs tools but found nothing similar to this.
> Where
> >> can I start from?
> >>
> >> Thanks,
> >>
> >> biohpc
> >>
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Re: [gmx-users] Use pdb file generated with Maestro, in Gromacs

[Justin Lemkul]

On 3/31/16 6:55 AM, bio hpc wrote:

Thanks.
Apart from this, is is there some script that keeps my original hydrogens from 
Maestro?



Rename with sed according to what the force field expects.

-Justin


El 30/3/2016, a las 19:43, Tsjerk Wassenaar  escribió:

Hey :)

-ignh does ignore the hydrogens in the input file. It builds those
hydrogens that are specified in the force field. For histidines, the
protonation state is determined from the possible hydrogen-bonded network,
but it is possible to assign specific states interactively, using the
option -his, or by specifying the residue name in the input file.

Hope it helps,

Tsjerk

On Wed, Mar 30, 2016 at 4:42 PM, sun  wrote:


I think using -ignh does not "remove" hydrogens. Hence, you can use it.

Sent from my iPhone


On 30-Mar-2016, at 6:04 pm, rajendra kumar  wrote:

Hi,

As suggested above, use -ignh to ignore hydrogen atoms. To use a specific
Histidine, you may change residue name HIS to

HIP(Amber)/HSP(Charmm)/HISH(

​OPLS​
) or HID(Amber)/HSD(Charmm)/HISD(
​OPLS​
) or HIE(Amber)/HSE(Charmm)/HISE(
​OPLS​
) either in PDB file or interactively through pdb2gmx usng -his command.



On Wed, Mar 30, 2016 at 12:27 PM, bio hpc  wrote:

Hi,

we have created some protein pdb files with Maestro. When we try to un

an

MD simulation with gromacs, we get errors like:


Atom HD11 in residue ASN 5 was not found in rtp entry ASN with 14

atoms


I tried to find a solution and it seems that internal gromacs dictionary
for hydrogens is different from the one from Maestro and other formats.

It

seems, from what I read, that one must convert all hydrogen types to
Gromacs format. Is is there any script that can do this automatically?

Of course, there is the option “ignore hydrogens”, but this would be bad
for us, since we need some histidines in the binding site, and so on.

Thanks,
BIO-HPC



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--
==

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] Generate diagram/figure with information about protein-ligand interactions

[bio hpc]

My problem is not excel or whatever graphical program. I just need the data, in 
an automatic way. Then I can use either matplotlib or similar to get the plots 
automatically. But my question is if there is somewhere a repository of gromacs 
scripts with a script doing an analysis of the protein-ligand itneractions 
during trajectory. I do not think to be the only one requesting this


> El 30/3/2016, a las 6:46, Sun Iba  escribió:
> 
> i am sorry, i replied prior to looking at your figure. Actually, i have
> never came across plotting data in this matter. However, I believe you have
> tabulated data, so you can use Origin or excel for generating similar
> images. You need little effort to arrange the data in desired manner.
> Best Wishes
> 
> On Wed, Mar 30, 2016 at 3:15 AM, bio hpc  wrote:
> 
>> Hi,
>> 
>> after a protein-ligand simulation with gromacs, I would like to be able to
>> generate a diagram/figure with information about protein-ligand
>> interactions, something like this:
>> 
>> https://dl.dropboxusercontent.com/u/2012631/Figure7.jpg <
>> https://dl.dropboxusercontent.com/u/2012631/Figure7.jpg>
>> 
>> I had a look to all gromacs tools but found nothing similar to this. Where
>> can I start from?
>> 
>> Thanks,
>> 
>> biohpc
>> 
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Re: [gmx-users] Use pdb file generated with Maestro, in Gromacs

[bio hpc]

Thanks. 
Apart from this, is is there some script that keeps my original hydrogens from 
Maestro?

> El 30/3/2016, a las 19:43, Tsjerk Wassenaar  escribió:
> 
> Hey :)
> 
> -ignh does ignore the hydrogens in the input file. It builds those
> hydrogens that are specified in the force field. For histidines, the
> protonation state is determined from the possible hydrogen-bonded network,
> but it is possible to assign specific states interactively, using the
> option -his, or by specifying the residue name in the input file.
> 
> Hope it helps,
> 
> Tsjerk
> 
> On Wed, Mar 30, 2016 at 4:42 PM, sun  wrote:
> 
>> I think using -ignh does not "remove" hydrogens. Hence, you can use it.
>> 
>> Sent from my iPhone
>> 
>>> On 30-Mar-2016, at 6:04 pm, rajendra kumar  wrote:
>>> 
>>> Hi,
>>> 
>>> As suggested above, use -ignh to ignore hydrogen atoms. To use a specific
>>> Histidine, you may change residue name HIS to
>> HIP(Amber)/HSP(Charmm)/HISH(
>>> ​OPLS​
>>> ) or HID(Amber)/HSD(Charmm)/HISD(
>>> ​OPLS​
>>> ) or HIE(Amber)/HSE(Charmm)/HISE(
>>> ​OPLS​
>>> ) either in PDB file or interactively through pdb2gmx usng -his command.
>>> 
>>> 
 On Wed, Mar 30, 2016 at 12:27 PM, bio hpc  wrote:
 
 Hi,
 
 we have created some protein pdb files with Maestro. When we try to un
>> an
 MD simulation with gromacs, we get errors like:
 
>> Atom HD11 in residue ASN 5 was not found in rtp entry ASN with 14
>> atoms
 
 I tried to find a solution and it seems that internal gromacs dictionary
 for hydrogens is different from the one from Maestro and other formats.
>> It
 seems, from what I read, that one must convert all hydrogen types to
 Gromacs format. Is is there any script that can do this automatically?
 
 Of course, there is the option “ignore hydrogens”, but this would be bad
 for us, since we need some histidines in the binding site, and so on.
 
 Thanks,
 BIO-HPC
 
 
 
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> 
> 
> 
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[gmx-users] virtual site - algorithmic reasons

[Samith Rathnayake]

Hi everyone,

Recently i was used to started Bevan Lab tutorial  and gone through
specially with virtual site tutorial.In this tutorial Dr.Justin emphasized
that co2 cannot effectively build in traditional sense  because of
 algorithmic reasons. And cant hold 180 degree during a simulation.Could
any one elaborate what are this "algorithmic reasons" ? any publication
upon this virtual site techniques in any gromos force field? and also about
this algorithmic reasons ? And if it is okey to used this virtual site
techniques in gromacs 4.6.5 version ?

thank you in advance
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Re: [gmx-users] Umbrella sampling along PCA eigenvector using make_edi

[Kutzner, Carsten]

Dear Hendrik,

that indeed looks a bit strange. If you provide the necessary input
files for a test, I could have a look at what might be wrong.
You can put them somewhere for download or email them directly
to me (not to the list, they will not be accepted).

Carsten


> On 30 Mar 2016, at 16:11, Hendrik Goeddeke  wrote:
> 
> Hi everyone,
> 
> I want to do umbrella sampling along a PCA eigenvector using 'gmx
> make_edi'. The eigenvectors of the protein backbone atoms were computed
> using 'gmx covar'. The command for generating the 'sam.edi' file looks
> like the following:
> 
> gmx make_edi -s topol.tpr -f eigenvec.trr -eig eigenval.xvg -restrain
> yes -harmonic yes -ori window1_backbone.gro -flood 1 -tau 0 -Eflnull 1000
> 
> The file 'window1_backbone.gro' just contains the backbone atoms of a
> snapshot called 'window1.gro', which was used for generating
> 'topol.tpr'. I changed the eigenvalue of the first eigenvector in
> 'eigenval.xvg' to 1 to get a force constant of 1000 kJ/(mol*nm^2). When
> I then start 'gmx mdrun -ei sam.edi' the output states that the initial
> RMSD from the reference structure is not zero:
> 
> ...
> ED: Flooding 1 eigenvector.
> ED: Initial RMSD from reference after fit = 0.371082 nm
> ...
> 
> But when I compute the RMSD to the reference structure ('topol.tpr')
> manually by using 'gmx rms', the RMSD is zero as expected. This excludes
> a possibly wrong PBC representaion of the ED group (backbone atoms). I
> looked at the code ('edsam.c') but it seems that the RMSD is also
> computed from 'topol.tpr', which was specified in 'gmx make_edi'. I
> repeated the procedure many times but could not find any mistake.
> 
> Any help is highly appreciated.
> 
> Thank you very much in advance!
> 
> All the best,
> Hendrik
> 
> 
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