[gmx-users] Fw: extremum value of rvdw rcoulomb rlist parameter

[Hamid]

 

 Hi

what is them extremum value of three parameters, rvdw,rlist and rcoulomb in mdp 
file
best of luck
  
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[gmx-users] 2nd CfP EuroVis 2019 Workshop on Molecular Graphics and Visual Analysis of Molecular Data

[Björn Sommer]

*

Workshop on Molecular Graphics and Visual Analysis of Molecular Data

(co-located with EuroVis 2019), June 3, 2019, Porto, Portugal

**



Molecular visualization is one of the oldest branches of scientific
visualization, which has been developing for over 50 years. Due to the
continuous advances in both computational biology and computer graphics
techniques, molecular graphics and visualization are still very active
areas of research. Not only the ever-increasing dataset sizes yield a
constant challenge for visual analysis, but also new technologies like
advances in web-based graphics or augmented and virtual reality open new
possibilities. In this half-day workshop, which is held for the second
time in conjunction with EuroVis, we would like to initiate a
multidisciplinary meeting which brings visualization researchers
together working with molecular data.


Whereas molecular graphics is an established topic for many years, the
hybrid-dimensional visual analysis of molecular structures is still a
quite new research field with a lot of potential. We would like to
encourage submissions especially using new technologies, such as
immersive analytics-related approaches.


We invite short papers as well as full papers (2-4 pages for short and
up to 8 pages for full papers, both with an additional page reserved for
references). All papers will undergo a single-stage, double-blind peer
review process. Accepted papers will be published in the EG digital
library. The workshop will be held in Porto, Portugal, June 3, 2019, as
part of EuroVis 2019.

 

Suggested topics include, but are not limited to:

- Molecular Graphics

- Visual Analysis of Molecular Data (e.g., molecular structures,
biological networks, and pathways, or omics data)

- Visualization of Dynamic Molecular Data

- Visualization of Large Molecular Systems

- Web-based Molecular Graphics and Visualization

- Immersive Analytics approaches using, e.g., VR/AR technologies

- Tools papers describing new molecular visualization tools or novel
features in existing tools

More info:

http://decibel.fi.muni.cz/~xbyska/molva/

Important Dates



Paper Submission Deadline:February 28, 2019

Notification of Acceptance:April 5, 2019

Camera-ready Deadline:April 15, 2019

Workshop Date:June 3, 2019

Organizers and Contact



- Jan Byska, University of Bergen, Norway

- Michael Krone, University of Tübingen, Germany

- Björn Sommer, University of Konstanz, Germany

If you have any question, please contact us:

mailto: molva.euro...@gmail.com 

Submission



Please submit your short and full papers via PCS (Deadline: February 28,
2019):

https://new.precisionconference.com/(EuroVis 2019 MolVA Workshop)  


Please follow the EG guidelines for writing the paper. You can find more
info and templates here:

https://www.eurovis.org/submission-guidelines/

https://www.eurovis.org/files/egPublStyle-EuroVis_full-short-stars-posters-2019.zip


Best regards,

  Jan Byška, Michael Krone, Björn Sommer

  MolVA 2019 Organizing Committee

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[gmx-users] Clustsize and -mol option

[Moir, Michael (MMoir)]

Although I have successfully used clustsize for identifying clusters of atoms, 
I am stymied by the -mol option for evaluating clusters of  molecules.  A 
command such as:

gmx clustsize -s system1.tpr -f system1.xtc -nc -n index.ndx

Works fine for obtaining information about clusters of atoms, but:

gmx clustsize -s system1.tpr -f system1.xtc -nc -n index.ndx -mol

gives a fatal error in Source file: src/gromacs/fileio/matio.cpp (line 681)

My index file consists of the list of atoms under headings like [HP6].

Any thoughts?

Mike Moir
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Re: [gmx-users] COM

[laura O.]

Hi,

I already used index.ndx at the line of code but the error kept the same. I
believe this is not the problem

Thanks
Laura

Em ter, 22 de jan de 2019 às 16:25, Joaquim Rui de Castro Rodrigues <
joaquim.rodrig...@ipleiria.pt> escreveu:

> Hi,
>
> Your command line specifies -n fix.ndx but you seem to be editing a file
> named "index.ndx".
>
> HTH,
> Rui Rodrigues
>
> 
> De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> em nome de laura O. <
> laura.o.vendr...@gmail.com>
> Enviado: 22 de janeiro de 2019 17:31
> Para: gromacs.org_gmx-users@maillist.sys.kth.se
> Assunto: [gmx-users] COM
>
> Dear Users.
>
> I'm trying to calculate the center of mass distance between cyclodextrine (
> HAGD) and a biological molecule (MTX).
> I've searched on gromacs documentation in gmx distance
>
> I use command line:
> gmx distance -f fixv1out.xtc -s bcd_mtx_solv_min.tpr -n fix.ndx -oav
> cmtransv1.xvg -select 'com of group "HAGD" plus com of group "MTX".
>
> On the index file (index.ndx) the names are correct (transcribed at the end
> of e-mail)
>
> However, I get the message bellow:
> Invalid index group reference(s)
>   Cannot match 'group "HAGD"', because no such index group can be found.
>   Cannot match 'group "MTX"', because no such index group can be found.
>
>
> Then, I used the index numbers for HAGD and MTX respectively. By doing so,
> I got the graphic but with wrong and unexpected results. I look the
> trajectory in VMD.
>
> What could I be doing wrong?
>
>
> What is the exact command for calculation of center of mass distance
> calculation between two groups A & B have in my index?
> Doing by the dist pair I manage to get a good result, but since
> cyclodextrine is cone shaped, I don't think that using the center of mass
> would be the best option.
>
>
> Index.ndx:
>
> [ HAGD ]
>123456789   10   11   12   13   14   15
>   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
>   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
>   46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
>   61   62   63   64   65   66   67   68   69   70   71   72   73   74   75
>   76   77   78   79   80   81   82   83   84   85   86   87   88   89   90
>   91   92   93   94   95   96   97   98
> [ MTX ]
>   99  100  101  102  103  104  105  106  107  108  109  110  111  112  113
>  114  115  116  117  118  119  120  121  122  123  124  125  126  127  128
>  129  130  131  132  133  134  135  136  137  138  139  140  141
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[gmx-users] Rotation matrix sequence

[Eugenio Gil]

 Dear all,

I´m using g_rotmat to calculate the angles and therefore orientation of a
protein after simulation. However, I cannot find any information on the
documentation regarding which rotation sequence does GROMACS use for
computing the rotation matrix. I´m assuming an RzRyRx sequence (first
around the x axis, then y, and last z), but a confirmation on this would be
much appreciated.

Many thanks,
Eugenio Gil
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Re: [gmx-users] COM

[Joaquim Rui de Castro Rodrigues]

Hi,

Your command line specifies -n fix.ndx but you seem to be editing a file named 
"index.ndx".

HTH,
Rui Rodrigues


De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 em nome de laura O. 

Enviado: 22 de janeiro de 2019 17:31
Para: gromacs.org_gmx-users@maillist.sys.kth.se
Assunto: [gmx-users] COM

Dear Users.

I'm trying to calculate the center of mass distance between cyclodextrine (
HAGD) and a biological molecule (MTX).
I've searched on gromacs documentation in gmx distance

I use command line:
gmx distance -f fixv1out.xtc -s bcd_mtx_solv_min.tpr -n fix.ndx -oav
cmtransv1.xvg -select 'com of group "HAGD" plus com of group "MTX".

On the index file (index.ndx) the names are correct (transcribed at the end
of e-mail)

However, I get the message bellow:
Invalid index group reference(s)
  Cannot match 'group "HAGD"', because no such index group can be found.
  Cannot match 'group "MTX"', because no such index group can be found.


Then, I used the index numbers for HAGD and MTX respectively. By doing so,
I got the graphic but with wrong and unexpected results. I look the
trajectory in VMD.

What could I be doing wrong?


What is the exact command for calculation of center of mass distance
calculation between two groups A & B have in my index?
Doing by the dist pair I manage to get a good result, but since
cyclodextrine is cone shaped, I don't think that using the center of mass
would be the best option.


Index.ndx:

[ HAGD ]
   123456789   10   11   12   13   14   15
  16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
  31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
  46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
  61   62   63   64   65   66   67   68   69   70   71   72   73   74   75
  76   77   78   79   80   81   82   83   84   85   86   87   88   89   90
  91   92   93   94   95   96   97   98
[ MTX ]
  99  100  101  102  103  104  105  106  107  108  109  110  111  112  113
 114  115  116  117  118  119  120  121  122  123  124  125  126  127  128
 129  130  131  132  133  134  135  136  137  138  139  140  141
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Re: [gmx-users] COM

[laura O.]

Hi,
Thanks
but I already tried without the double quotation marks but the result was
the same.

-
  Cannot match 'group "HAGD"', because no such index group can be found.
  Cannot match 'group "MTX"', because no such index group can be found.


Em ter, 22 de jan de 2019 às 16:01, Quyen VuVan 
escreveu:

> Hi,
> I don't think you need a double quote in your select HAGD
>
> On Tue, Jan 22, 2019 at 6:32 PM laura O. 
> wrote:
>
> > Dear Users.
> >
> > I'm trying to calculate the center of mass distance between
> cyclodextrine (
> > HAGD) and a biological molecule (MTX).
> > I've searched on gromacs documentation in gmx distance
> >
> > I use command line:
> > gmx distance -f fixv1out.xtc -s bcd_mtx_solv_min.tpr -n fix.ndx -oav
> > cmtransv1.xvg -select 'com of group "HAGD" plus com of group "MTX".
> >
> > On the index file (index.ndx) the names are correct (transcribed at the
> end
> > of e-mail)
> >
> > However, I get the message bellow:
> > Invalid index group reference(s)
> >   Cannot match 'group "HAGD"', because no such index group can be found.
> >   Cannot match 'group "MTX"', because no such index group can be found.
> >
> >
> > Then, I used the index numbers for HAGD and MTX respectively. By doing
> so,
> > I got the graphic but with wrong and unexpected results. I look the
> > trajectory in VMD.
> >
> > What could I be doing wrong?
> >
> >
> > What is the exact command for calculation of center of mass distance
> > calculation between two groups A & B have in my index?
> > Doing by the dist pair I manage to get a good result, but since
> > cyclodextrine is cone shaped, I don't think that using the center of mass
> > would be the best option.
> >
> >
> > Index.ndx:
> >
> > [ HAGD ]
> >123456789   10   11   12   13   14
>  15
> >   16   17   18   19   20   21   22   23   24   25   26   27   28   29
>  30
> >   31   32   33   34   35   36   37   38   39   40   41   42   43   44
>  45
> >   46   47   48   49   50   51   52   53   54   55   56   57   58   59
>  60
> >   61   62   63   64   65   66   67   68   69   70   71   72   73   74
>  75
> >   76   77   78   79   80   81   82   83   84   85   86   87   88   89
>  90
> >   91   92   93   94   95   96   97   98
> > [ MTX ]
> >   99  100  101  102  103  104  105  106  107  108  109  110  111  112
> 113
> >  114  115  116  117  118  119  120  121  122  123  124  125  126  127
> 128
> >  129  130  131  132  133  134  135  136  137  138  139  140  141
> > --
> > Gromacs Users mailing list
> >
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> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] COM

[laura O.]

Em ter, 22 de jan de 2019 às 16:01, Quyen VuVan 
escreveu:

> Hi,
> I don't think you need a double quote in your select HAGD
>
> On Tue, Jan 22, 2019 at 6:32 PM laura O. 
> wrote:
>
> > Dear Users.
> >
> > I'm trying to calculate the center of mass distance between
> cyclodextrine (
> > HAGD) and a biological molecule (MTX).
> > I've searched on gromacs documentation in gmx distance
> >
> > I use command line:
> > gmx distance -f fixv1out.xtc -s bcd_mtx_solv_min.tpr -n fix.ndx -oav
> > cmtransv1.xvg -select 'com of group "HAGD" plus com of group "MTX".
> >
> > On the index file (index.ndx) the names are correct (transcribed at the
> end
> > of e-mail)
> >
> > However, I get the message bellow:
> > Invalid index group reference(s)
> >   Cannot match 'group "HAGD"', because no such index group can be found.
> >   Cannot match 'group "MTX"', because no such index group can be found.
> >
> >
> > Then, I used the index numbers for HAGD and MTX respectively. By doing
> so,
> > I got the graphic but with wrong and unexpected results. I look the
> > trajectory in VMD.
> >
> > What could I be doing wrong?
> >
> >
> > What is the exact command for calculation of center of mass distance
> > calculation between two groups A & B have in my index?
> > Doing by the dist pair I manage to get a good result, but since
> > cyclodextrine is cone shaped, I don't think that using the center of mass
> > would be the best option.
> >
> >
> > Index.ndx:
> >
> > [ HAGD ]
> >123456789   10   11   12   13   14
>  15
> >   16   17   18   19   20   21   22   23   24   25   26   27   28   29
>  30
> >   31   32   33   34   35   36   37   38   39   40   41   42   43   44
>  45
> >   46   47   48   49   50   51   52   53   54   55   56   57   58   59
>  60
> >   61   62   63   64   65   66   67   68   69   70   71   72   73   74
>  75
> >   76   77   78   79   80   81   82   83   84   85   86   87   88   89
>  90
> >   91   92   93   94   95   96   97   98
> > [ MTX ]
> >   99  100  101  102  103  104  105  106  107  108  109  110  111  112
> 113
> >  114  115  116  117  118  119  120  121  122  123  124  125  126  127
> 128
> >  129  130  131  132  133  134  135  136  137  138  139  140  141
> > --
> > 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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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] COM

[Quyen VuVan]

Hi,
I don't think you need a double quote in your select HAGD

On Tue, Jan 22, 2019 at 6:32 PM laura O.  wrote:

> Dear Users.
>
> I'm trying to calculate the center of mass distance between cyclodextrine (
> HAGD) and a biological molecule (MTX).
> I've searched on gromacs documentation in gmx distance
>
> I use command line:
> gmx distance -f fixv1out.xtc -s bcd_mtx_solv_min.tpr -n fix.ndx -oav
> cmtransv1.xvg -select 'com of group "HAGD" plus com of group "MTX".
>
> On the index file (index.ndx) the names are correct (transcribed at the end
> of e-mail)
>
> However, I get the message bellow:
> Invalid index group reference(s)
>   Cannot match 'group "HAGD"', because no such index group can be found.
>   Cannot match 'group "MTX"', because no such index group can be found.
>
>
> Then, I used the index numbers for HAGD and MTX respectively. By doing so,
> I got the graphic but with wrong and unexpected results. I look the
> trajectory in VMD.
>
> What could I be doing wrong?
>
>
> What is the exact command for calculation of center of mass distance
> calculation between two groups A & B have in my index?
> Doing by the dist pair I manage to get a good result, but since
> cyclodextrine is cone shaped, I don't think that using the center of mass
> would be the best option.
>
>
> Index.ndx:
>
> [ HAGD ]
>123456789   10   11   12   13   14   15
>   16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
>   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
>   46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
>   61   62   63   64   65   66   67   68   69   70   71   72   73   74   75
>   76   77   78   79   80   81   82   83   84   85   86   87   88   89   90
>   91   92   93   94   95   96   97   98
> [ MTX ]
>   99  100  101  102  103  104  105  106  107  108  109  110  111  112  113
>  114  115  116  117  118  119  120  121  122  123  124  125  126  127  128
>  129  130  131  132  133  134  135  136  137  138  139  140  141
> --
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>
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> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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[gmx-users] COM

[laura O.]

Dear Users.

I'm trying to calculate the center of mass distance between cyclodextrine (
HAGD) and a biological molecule (MTX).
I've searched on gromacs documentation in gmx distance

I use command line:
gmx distance -f fixv1out.xtc -s bcd_mtx_solv_min.tpr -n fix.ndx -oav
cmtransv1.xvg -select 'com of group "HAGD" plus com of group "MTX".

On the index file (index.ndx) the names are correct (transcribed at the end
of e-mail)

However, I get the message bellow:
Invalid index group reference(s)
  Cannot match 'group "HAGD"', because no such index group can be found.
  Cannot match 'group "MTX"', because no such index group can be found.


Then, I used the index numbers for HAGD and MTX respectively. By doing so,
I got the graphic but with wrong and unexpected results. I look the
trajectory in VMD.

What could I be doing wrong?


What is the exact command for calculation of center of mass distance
calculation between two groups A & B have in my index?
Doing by the dist pair I manage to get a good result, but since
cyclodextrine is cone shaped, I don't think that using the center of mass
would be the best option.


Index.ndx:

[ HAGD ]
   123456789   10   11   12   13   14   15
  16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
  31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
  46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
  61   62   63   64   65   66   67   68   69   70   71   72   73   74   75
  76   77   78   79   80   81   82   83   84   85   86   87   88   89   90
  91   92   93   94   95   96   97   98
[ MTX ]
  99  100  101  102  103  104  105  106  107  108  109  110  111  112  113
 114  115  116  117  118  119  120  121  122  123  124  125  126  127  128
 129  130  131  132  133  134  135  136  137  138  139  140  141
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Re: [gmx-users] "Too many LINCS warnings" in a minimization after solvation with coarse-grained waters

[Fotis Baltoumas]

Hello Cheng,

The lines at the end of this mail are the extra parameters we usually 
define in our lab whenever we need to use soft potentials.


They are based on the parameters given by CHARMM-GUI for the Martini 
Maker.  However, you *may* need to make alterations if there are 
conflicts with your existing parameters.


Just remember to also run an additional, standard minimization after the 
"soft" one.



As for  constraints, you can control them through the relevant mdp options:

http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html#mdp-constraints


;soft-core-minimization so that single precision GROMACS works here
; Free energy parameters
free-energy  = yes
init-lambda  = 0.01
sc-alpha = 4
sc-power = 2
sc-coul  = yes
nstdhdl  = 0
couple-moltype   = system
; we are changing both the vdw and the charge. In the initial state, 
both are on

couple-lambda0   = vdw-q
; in the final state, both are off.
couple-lambda1   = none
couple-intramol  = yes


Good luck,

Fotis

--
Fotis A. Baltoumas, Bsc, Msc
Phd Candidate, Bioinformatics Postgraduate Programme
Section of Cell Biology and Biophysics
Department of Biology
National & Kapodistrian University of Athens
Panepistimiopolis, Athens 157 01, GREECE
   --

email : fbaltou...@biol.uoa.gr
http://biophysics.biol.uoa.gr
http://bioinformatics.biol.uoa.gr
Tel.: +30 2107274876
Mob.: +30 6979258570


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[gmx-users] COM

[laura O.]

Dear Users.

I'm trying to calculate the center of mass distance between cyclodextrine (
HAGD) and a biological molecule (MTX).
I've searched on gromacs documentation in gmx distance

I use command line:
gmx distance -f fixv1out.xtc -s bcd_mtx_solv_min.tpr -n fix.ndx -oav
cmtransv1.xvg -select 'com of group "HAGD" plus com of group "MTX".

On the index file (index.ndx) the names are correct (transcribed at the end
of e-mail)

However, I get the message bellow:
Invalid index group reference(s)
  Cannot match 'group "HAGD"', because no such index group can be found.
  Cannot match 'group "MTX"', because no such index group can be found.


Then, I used the index numbers for HAGD and MTX respectively. By doing so,
I got the graphic but with wrong and unexpected results. I look the
trajectory in VMD.

What could I be doing wrong?


What is the exact command for calculation of center of mass distance
calculation between two groups A & B have in my index?
Doing by the dist pair I manage to get a good result, but since
cyclodextrine is cone shaped, I don't think that using the center of mass
would be the best option.


Index.ndx:

[ HAGD ]
   123456789   10   11   12   13   14   15
  16   17   18   19   20   21   22   23   24   25   26   27   28   29   30
  31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
  46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
  61   62   63   64   65   66   67   68   69   70   71   72   73   74   75
  76   77   78   79   80   81   82   83   84   85   86   87   88   89   90
  91   92   93   94   95   96   97   98
[ MTX ]
  99  100  101  102  103  104  105  106  107  108  109  110  111  112  113
 114  115  116  117  118  119  120  121  122  123  124  125  126  127  128
 129  130  131  132  133  134  135  136  137  138  139  140  141
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[gmx-users] delay at start

[Michael Brunsteiner]

hi,
i notice that gromacs, when i start an MD simulation usuallyspends up to a few 
minutes using only one (out of several possible) threads.after a while it seems 
to have figured something out and then starts to runusing more threads. This is 
particularly conspicuous if also GPU is used.It is normally not a problem, but 
if you run a large number of very short simulations,as i do once in a while, 
this wastes a lot of time ... any remedy??
i should add that the delay i am talking about is NOT the one thatis caused by 
gromacs comparing different pme gird sizes, this comesAFTER the delay i 
mentioned and usually finishes much faster.

thanksMIchael


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Re: [gmx-users] turning off non-bonded terms

[Ali Khodayari]

Thank you Justin. 
Kind regards, Ali

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
 On Behalf Of Justin
Lemkul
Sent: dinsdag 22 januari 2019 15:59
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] turning off non-bonded terms



On 1/22/19 9:37 AM, Ali Khodayari wrote:
> Dear Users,
>
> Does it make sense if I use rcoulomb = 0 and rvdw = 0 in order to turn 
> off non-bonded term calculation during mdrun? If not, is there any 
> recommendations?

That does the opposite - setting cutoffs to zero calculates *all* nonbonded
interactions.

If you want to turn them off, you need to use the free energy settings with
a lambda state that specifies interactions are off.

-Justin

--
==

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

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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] seeking help for generating combined trajectory files and clusters

[Mark Abraham]

Hi,

I can't tell, because I don't know what you did with the xtc files
beforehand. But you should follow my earlier advice and visualize the
combined trajectory and observe that this may be your problem before
talking about it further. :-) Then see
http://manual.gromacs.org/documentation/current/user-guide/terminology.html#suggested-workflow

Mark

On Tue, 22 Jan 2019 at 16:06 MD  wrote:

> Hi Mark, yes that makes sense. Then how can I make trjconv avoid from
> writing protein+ligand in different cells?
> Ming
>
> On Tue, Jan 22, 2019 at 9:59 AM Mark Abraham 
> wrote:
>
> > Hi,
> >
> > No, length has nothing to do with whether mdrun or trjconv may have
> written
> > different rounds in different representations (e.g. protein+ligand in the
> > same periodic cell, or different cells).
> >
> > Mark
> >
> > On Tue, 22 Jan 2019 at 15:40 MD  wrote:
> >
> > > Thanks Mark.
> > > When you said "mutually compatible periodic representation", did you
> mean
> > > they all have to have the same length of simulation? E.g. if one of
> them
> > > has a different length (91ns) and the rest all have 90 ns, the
> combining
> > > process will go wrong?
> > >
> > >
> > > On Tue, Jan 22, 2019 at 4:13 AM Mark Abraham  >
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > You're comparing to the configurations in -f2, but that will only
> make
> > > > sense if the contents of the files for each round have mutually
> > > compatible
> > > > periodic representation. I suggest you visualise the combined
> > trajectory
> > > > and observe the problem.
> > > >
> > > > Mark
> > > >
> > > > On Mon, 21 Jan 2019 at 17:30 MD  wrote:
> > > >
> > > > > Hi Gromacs folks,
> > > > >
> > > > > I am trying to simulate protein and ligand compound.
> > > > >
> > > > > I did several 200 ns simulations and combined them into one
> > trajectory
> > > > file
> > > > > with the commands:
> > > > > gmx trjcat -f md_round1_10-200ns.xtc
> > > > >  md_round2_10-200ns.xtcmd_round3_10-200ns.xtc -o md_combined.xtc
> -cat
> > > > > -settime
> > > > > I set the starting times to be: 10 ns, 190 ns, 380 ns
> > > > >
> > > > > Then I made a RMSD matrix with the command:
> > > > > gmx rms -f md_combined.xtc -f2 md_0_1_combined.xtc -s md.tpr -n
> > md.ndx
> > > -m
> > > > > md_RMSD-matrix.xpm
> > > > >
> > > > > Then I tried to build clusters with the command:
> > > > > gmx cluster -f md_combined.xtc -s md.tpr  -n md.ndx -dm
> > > > md_RMSD-matrix.xpm
> > > > > -method gromos -cl out.pdb -cutoff 0.2 -g out.log
> > > > >
> > > > > There were 120 clusters came back. Except for the first and largest
> > > > > cluster, all the rest of the clusters have a crazily far away
> ligand
> > > > > compared to where the protein is.
> > > > >
> > > > > I went back to look at each individual xtc from each round and
> > produced
> > > > > their own clusters and they all look good (no huge separation of
> > > protein
> > > > > and ligand).
> > > > >
> > > > > If all the xtc files are good on their own, how come the combined
> xtc
> > > is
> > > > > giving me this result?
> > > > >
> > > > > Best,
> > > > >
> > > > > MD
> > > > > --
> > > > > 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] seeking help for generating combined trajectory files and clusters

[MD]

Hi Mark, yes that makes sense. Then how can I make trjconv avoid from
writing protein+ligand in different cells?
Ming

On Tue, Jan 22, 2019 at 9:59 AM Mark Abraham 
wrote:

> Hi,
>
> No, length has nothing to do with whether mdrun or trjconv may have written
> different rounds in different representations (e.g. protein+ligand in the
> same periodic cell, or different cells).
>
> Mark
>
> On Tue, 22 Jan 2019 at 15:40 MD  wrote:
>
> > Thanks Mark.
> > When you said "mutually compatible periodic representation", did you mean
> > they all have to have the same length of simulation? E.g. if one of them
> > has a different length (91ns) and the rest all have 90 ns, the combining
> > process will go wrong?
> >
> >
> > On Tue, Jan 22, 2019 at 4:13 AM Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > You're comparing to the configurations in -f2, but that will only make
> > > sense if the contents of the files for each round have mutually
> > compatible
> > > periodic representation. I suggest you visualise the combined
> trajectory
> > > and observe the problem.
> > >
> > > Mark
> > >
> > > On Mon, 21 Jan 2019 at 17:30 MD  wrote:
> > >
> > > > Hi Gromacs folks,
> > > >
> > > > I am trying to simulate protein and ligand compound.
> > > >
> > > > I did several 200 ns simulations and combined them into one
> trajectory
> > > file
> > > > with the commands:
> > > > gmx trjcat -f md_round1_10-200ns.xtc
> > > >  md_round2_10-200ns.xtcmd_round3_10-200ns.xtc -o md_combined.xtc -cat
> > > > -settime
> > > > I set the starting times to be: 10 ns, 190 ns, 380 ns
> > > >
> > > > Then I made a RMSD matrix with the command:
> > > > gmx rms -f md_combined.xtc -f2 md_0_1_combined.xtc -s md.tpr -n
> md.ndx
> > -m
> > > > md_RMSD-matrix.xpm
> > > >
> > > > Then I tried to build clusters with the command:
> > > > gmx cluster -f md_combined.xtc -s md.tpr  -n md.ndx -dm
> > > md_RMSD-matrix.xpm
> > > > -method gromos -cl out.pdb -cutoff 0.2 -g out.log
> > > >
> > > > There were 120 clusters came back. Except for the first and largest
> > > > cluster, all the rest of the clusters have a crazily far away ligand
> > > > compared to where the protein is.
> > > >
> > > > I went back to look at each individual xtc from each round and
> produced
> > > > their own clusters and they all look good (no huge separation of
> > protein
> > > > and ligand).
> > > >
> > > > If all the xtc files are good on their own, how come the combined xtc
> > is
> > > > giving me this result?
> > > >
> > > > Best,
> > > >
> > > > MD
> > > > --
> > > > 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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> > > posting!
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Re: [gmx-users] turning off non-bonded terms

[Justin Lemkul]

On 1/22/19 9:37 AM, Ali Khodayari wrote:

Dear Users,

Does it make sense if I use rcoulomb = 0 and rvdw = 0 in order to turn off
non-bonded term calculation during mdrun? If not, is there any
recommendations?


That does the opposite - setting cutoffs to zero calculates *all* 
nonbonded interactions.


If you want to turn them off, you need to use the free energy settings 
with a lambda state that specifies interactions are off.


-Justin

--
==

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

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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] seeking help for generating combined trajectory files and clusters

[Mark Abraham]

Hi,

No, length has nothing to do with whether mdrun or trjconv may have written
different rounds in different representations (e.g. protein+ligand in the
same periodic cell, or different cells).

Mark

On Tue, 22 Jan 2019 at 15:40 MD  wrote:

> Thanks Mark.
> When you said "mutually compatible periodic representation", did you mean
> they all have to have the same length of simulation? E.g. if one of them
> has a different length (91ns) and the rest all have 90 ns, the combining
> process will go wrong?
>
>
> On Tue, Jan 22, 2019 at 4:13 AM Mark Abraham 
> wrote:
>
> > Hi,
> >
> > You're comparing to the configurations in -f2, but that will only make
> > sense if the contents of the files for each round have mutually
> compatible
> > periodic representation. I suggest you visualise the combined trajectory
> > and observe the problem.
> >
> > Mark
> >
> > On Mon, 21 Jan 2019 at 17:30 MD  wrote:
> >
> > > Hi Gromacs folks,
> > >
> > > I am trying to simulate protein and ligand compound.
> > >
> > > I did several 200 ns simulations and combined them into one trajectory
> > file
> > > with the commands:
> > > gmx trjcat -f md_round1_10-200ns.xtc
> > >  md_round2_10-200ns.xtcmd_round3_10-200ns.xtc -o md_combined.xtc -cat
> > > -settime
> > > I set the starting times to be: 10 ns, 190 ns, 380 ns
> > >
> > > Then I made a RMSD matrix with the command:
> > > gmx rms -f md_combined.xtc -f2 md_0_1_combined.xtc -s md.tpr -n md.ndx
> -m
> > > md_RMSD-matrix.xpm
> > >
> > > Then I tried to build clusters with the command:
> > > gmx cluster -f md_combined.xtc -s md.tpr  -n md.ndx -dm
> > md_RMSD-matrix.xpm
> > > -method gromos -cl out.pdb -cutoff 0.2 -g out.log
> > >
> > > There were 120 clusters came back. Except for the first and largest
> > > cluster, all the rest of the clusters have a crazily far away ligand
> > > compared to where the protein is.
> > >
> > > I went back to look at each individual xtc from each round and produced
> > > their own clusters and they all look good (no huge separation of
> protein
> > > and ligand).
> > >
> > > If all the xtc files are good on their own, how come the combined xtc
> is
> > > giving me this result?
> > >
> > > Best,
> > >
> > > MD
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
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Re: [gmx-users] "Too many LINCS warnings" in a minimization aftersolvation with coarse-grained waters

[P C Kroon]

Depends on your itp file. If you look in martini_v2.2P.itp at the definition of 
WP (polarized water) for example, you can see its constraints are wrapped as 
such:

#ifdef FLEXIBLE
; for minimization purposes constraints might be replaced by stiff bonds
[ bonds ]
1 2 1 0.14 1
1 3 1 0.14 1
#else
[ constraints ]
1 2 1 0.14
1 3 1 0.14
#endif

That means in that case you can just add a define = -DFLEXIBLE in your mdp 
file. Otherwise you’ll need to go through your itp by hand.

Peter

From: ZHANG Cheng
Sent: 22 January 2019 15:23
To: gromacs.org_gmx-users
Subject: Re: [gmx-users] "Too many LINCS warnings" in a minimization 
aftersolvation with coarse-grained waters

Dear Fotis and Peter,


Thank you very much for the help.


Fotis, Can I modify the mdp file to use "soft" potential modifier, how to do 
that?


I think my problem is not the first reason (i.e. something wrong with the 
system structure or topology), because the potential is decreasing for the 
minimization step after inserting 10 protein molecules
https://github.com/lanselibai/martini/blob/master/20190121_LINCS/minimization%20after%20insert%2010%20proteins.jpg
$ Steepest Descents converged to machine precision in 4251 steps,
$ but did not reach the requested Fmax < 1.
$ Potential Energy  = -2.4130119e+05
$ Maximum force =  9.1535597e+00 on atom 2335
$ Norm of force =  7.1063030e-01





Peter, how to replace all constraints for stiff bonds?





-- Original --
From:  "ZHANG Cheng"<272699...@qq.com>;
Date:  Tue, Jan 22, 2019 05:58 AM
To:  "gromacs.org_gmx-users";

Subject:  Re: "Too many LINCS warnings" in a minimization after solvation with 
coarse-grained waters



I also tried to reduce the "emtol" gradually in the mdp file, i.e. from 1000 to 
100 to 10. It passed the "emtol = 1000" but it stopped again at "emtol = 100", 
i.e. outputting dozens of pdb files before the "LINCS warnings".


Then I looked at the edr files.
The potential in "emtol = 1000" and "emtol = 100" runs were actually converging
https://github.com/lanselibai/martini/blob/master/20190121_LINCS/emtol%201000%20then%20100.png


My understanding for the "LINCS warnings" is, the system is not stable. But why 
the potential is still converging?


Do I need to adjust the "lincs warning threshold", or "set the environment 
variable GMX_MAXCONSTRWARN to -1"? How to do that?


Is there a "standard" mdp file for minimization for a coarse-grained system 
with 10 proteins in water?
I am using this, but I do not know how to modify it.
https://github.com/lanselibai/martini/blob/master/20190121_LINCS/minimization_solvate.mdp




-- Original --
From:  "ZHANG Cheng"<272699...@qq.com>;
Date:  Tue, Jan 22, 2019 00:12 AM
To:  "gromacs.org_gmx-users";

Subject:  "Too many LINCS warnings" in a minimization after solvation with 
coarse-grained waters



I am doing coarse-grained (CG) modelling for 10 proteins in a box. I was told 
"Too many LINCS warnings" in the minimization after solvation with 
coarse-grained waters.


I try to diagnose the problems based on 
http://manual.gromacs.org/documentation/2018/user-guide/terminology.html#blowing-up


My procedure is


1) A single CG-protein was firstly minimized in vacuum, no problem


2) Then 10 of this protein were inserted to a box, followed by a minimization. 
It "stopped because the algorithm tried to make a new step whose size was too 
small, or there was no change in the energy since last step." So I think this 
minimization is also successful.


3) The system was then solvated by
$ gmx solvate -cp 10_noW_minimized.gro -cs water-box-CG_303K-1bar.gro -radius 
0.21 -o system-solvated.gro -p system.top


4) Then the solvated system is minimized by
$ gmx grompp -f minimization_solvate.mdp -c system-solvated.gro -p system.top 
-o system-min-solvent.tpr
$ gmx mdrun -deffnm system-min-solvent -v -c system-min-solvent.gro

PDB structures were outputted from step 327 to step 710, and it stopped due to 
the "LINCS warnings".


The "minimization_solvate.mdp" is here
https://github.com/lanselibai/martini/blob/master/20190121_LINCS/minimization_solvate.mdp


The "system-min-solvent.log" is here
https://github.com/lanselibai/martini/blob/master/20190121_LINCS/system-min-solvent.log


So I think the system with 10 proteins in vacuum is okay (right?). But when 
CG-water is added, it got problem? How to modify my system? Let me know if you 
need other information. Thank you.


Cheng
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Re: [gmx-users] seeking help for generating combined trajectory files and clusters

[MD]

Thanks Mark.
When you said "mutually compatible periodic representation", did you mean
they all have to have the same length of simulation? E.g. if one of them
has a different length (91ns) and the rest all have 90 ns, the combining
process will go wrong?


On Tue, Jan 22, 2019 at 4:13 AM Mark Abraham 
wrote:

> Hi,
>
> You're comparing to the configurations in -f2, but that will only make
> sense if the contents of the files for each round have mutually compatible
> periodic representation. I suggest you visualise the combined trajectory
> and observe the problem.
>
> Mark
>
> On Mon, 21 Jan 2019 at 17:30 MD  wrote:
>
> > Hi Gromacs folks,
> >
> > I am trying to simulate protein and ligand compound.
> >
> > I did several 200 ns simulations and combined them into one trajectory
> file
> > with the commands:
> > gmx trjcat -f md_round1_10-200ns.xtc
> >  md_round2_10-200ns.xtcmd_round3_10-200ns.xtc -o md_combined.xtc -cat
> > -settime
> > I set the starting times to be: 10 ns, 190 ns, 380 ns
> >
> > Then I made a RMSD matrix with the command:
> > gmx rms -f md_combined.xtc -f2 md_0_1_combined.xtc -s md.tpr -n md.ndx -m
> > md_RMSD-matrix.xpm
> >
> > Then I tried to build clusters with the command:
> > gmx cluster -f md_combined.xtc -s md.tpr  -n md.ndx -dm
> md_RMSD-matrix.xpm
> > -method gromos -cl out.pdb -cutoff 0.2 -g out.log
> >
> > There were 120 clusters came back. Except for the first and largest
> > cluster, all the rest of the clusters have a crazily far away ligand
> > compared to where the protein is.
> >
> > I went back to look at each individual xtc from each round and produced
> > their own clusters and they all look good (no huge separation of protein
> > and ligand).
> >
> > If all the xtc files are good on their own, how come the combined xtc is
> > giving me this result?
> >
> > Best,
> >
> > MD
> > --
> > 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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[gmx-users] turning off non-bonded terms

[Ali Khodayari]

Dear Users,

Does it make sense if I use rcoulomb = 0 and rvdw = 0 in order to turn off
non-bonded term calculation during mdrun? If not, is there any
recommendations?

Thank you for your responses in advanced.

Kind regards,

Ali

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Re: [gmx-users] "Too many LINCS warnings" in a minimization after solvation with coarse-grained waters

[ZHANG Cheng]

Dear Fotis and Peter,


Thank you very much for the help.


Fotis, Can I modify the mdp file to use "soft" potential modifier, how to do 
that?


I think my problem is not the first reason (i.e. something wrong with the 
system structure or topology), because the potential is decreasing for the 
minimization step after inserting 10 protein molecules
https://github.com/lanselibai/martini/blob/master/20190121_LINCS/minimization%20after%20insert%2010%20proteins.jpg
$ Steepest Descents converged to machine precision in 4251 steps,
$ but did not reach the requested Fmax < 1.
$ Potential Energy  = -2.4130119e+05
$ Maximum force =  9.1535597e+00 on atom 2335
$ Norm of force =  7.1063030e-01





Peter, how to replace all constraints for stiff bonds?





-- Original --
From:  "ZHANG Cheng"<272699...@qq.com>;
Date:  Tue, Jan 22, 2019 05:58 AM
To:  "gromacs.org_gmx-users";

Subject:  Re: "Too many LINCS warnings" in a minimization after solvation with 
coarse-grained waters



I also tried to reduce the "emtol" gradually in the mdp file, i.e. from 1000 to 
100 to 10. It passed the "emtol = 1000" but it stopped again at "emtol = 100", 
i.e. outputting dozens of pdb files before the "LINCS warnings".


Then I looked at the edr files.
The potential in "emtol = 1000" and "emtol = 100" runs were actually converging
https://github.com/lanselibai/martini/blob/master/20190121_LINCS/emtol%201000%20then%20100.png


My understanding for the "LINCS warnings" is, the system is not stable. But why 
the potential is still converging?


Do I need to adjust the "lincs warning threshold", or "set the environment 
variable GMX_MAXCONSTRWARN to -1"? How to do that?


Is there a "standard" mdp file for minimization for a coarse-grained system 
with 10 proteins in water?
I am using this, but I do not know how to modify it.
https://github.com/lanselibai/martini/blob/master/20190121_LINCS/minimization_solvate.mdp




-- Original --
From:  "ZHANG Cheng"<272699...@qq.com>;
Date:  Tue, Jan 22, 2019 00:12 AM
To:  "gromacs.org_gmx-users";

Subject:  "Too many LINCS warnings" in a minimization after solvation with 
coarse-grained waters



I am doing coarse-grained (CG) modelling for 10 proteins in a box. I was told 
"Too many LINCS warnings" in the minimization after solvation with 
coarse-grained waters.


I try to diagnose the problems based on 
http://manual.gromacs.org/documentation/2018/user-guide/terminology.html#blowing-up


My procedure is


1) A single CG-protein was firstly minimized in vacuum, no problem


2) Then 10 of this protein were inserted to a box, followed by a minimization. 
It "stopped because the algorithm tried to make a new step whose size was too 
small, or there was no change in the energy since last step." So I think this 
minimization is also successful.


3) The system was then solvated by
$ gmx solvate -cp 10_noW_minimized.gro -cs water-box-CG_303K-1bar.gro -radius 
0.21 -o system-solvated.gro -p system.top


4) Then the solvated system is minimized by
$ gmx grompp -f minimization_solvate.mdp -c system-solvated.gro -p system.top 
-o system-min-solvent.tpr
$ gmx mdrun -deffnm system-min-solvent -v -c system-min-solvent.gro

PDB structures were outputted from step 327 to step 710, and it stopped due to 
the "LINCS warnings".


The "minimization_solvate.mdp" is here
https://github.com/lanselibai/martini/blob/master/20190121_LINCS/minimization_solvate.mdp


The "system-min-solvent.log" is here
https://github.com/lanselibai/martini/blob/master/20190121_LINCS/system-min-solvent.log


So I think the system with 10 proteins in vacuum is okay (right?). But when 
CG-water is added, it got problem? How to modify my system? Let me know if you 
need other information. Thank you.


Cheng
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Re: [gmx-users] Error Found by Equilibration

[Lianxin Xin]

Thank you very much.

Lianxin
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Re: [gmx-users] "Too many LINCS warnings" in a minimization after solvation with coarse-grained waters

[Peter Kroon]

Hi all,


@Fotis, the softcore potential for minimization sounds interesting, I'll
remember that!

Alternatively, something we also occasionally do in the lab, is replace
all constraints for stiff bonds during minimization and if needed the
first bit of equilibration.


Peter

On 22-01-19 13:24, Fotis Baltoumas wrote:
> Hello all,
>
> I would like to point out step 2 of the original poster's message:
>
>>> /2) Then 10 of this protein were inserted to a box, followed by a
>>> />>/minimization. It "stopped because the algorithm tried to make a
>>> new step />>/whose size was too small, or there was no change in the
>>> energy since last />>/step." So I think this minimization is also
>>> successful./
>
> I've found, from personal experience, that this message ("stopped
> because the algorithm tried to make a new step, whose size was too
> small, or there was no change in the energy since last step") means that:
>
> 1. either there is something wrong with the system structure or
> topology (a fact shown at almost the first step of an equilibration
> following the minimization with this message).
>
> 2. or that single precision GROMACS cannot perform minimization
> properly.  The latter often applies to MARTINI systems, especially if
> they are large or have too many protein subunits (I can't say whether
> the application of ELNEDYN plays a part).
>
> If, hopefully, the latter case applies, the solution is to either use
> double precision GROMACS for minimization (gmx_d mdrun) or, since this
> is MARTINI, use "soft" potential modifiers like those they apply in
> the mdp files given by the CHARMM-GUI Martini Maker.  In any case, the
> initial minimization should be followed by a second, "standard" one
> (i.e. standard mdp options and single precision GROMACS).
>
> Hope this helps in some manner,
>
> Fotis Baltoumas
>
>  --
> Fotis A. Baltoumas, Bsc, Msc
> Phd Candidate, Bioinformatics Postgraduate Programme
> Section of Cell Biology and Biophysics
> Department of Biology
> National & Kapodistrian University of Athens
> Panepistimiopolis, Athens 157 01, GREECE
>    --
>
> email : fbaltou...@biol.uoa.gr
> http://biophysics.biol.uoa.gr
> http://bioinformatics.biol.uoa.gr
> Tel.: +30 2107274876
> Mob.: +30 6979258570
>
>
>
> ---
> This email has been checked for viruses by Avast antivirus software.
> https://www.avast.com/antivirus
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Re: [gmx-users] "Too many LINCS warnings" in a minimization after solvation with coarse-grained waters

[Fotis Baltoumas]

Hello all,

I would like to point out step 2 of the original poster's message:


/2) Then 10 of this protein were inserted to a box, followed by a />>/minimization. It "stopped 
because the algorithm tried to make a new step />>/whose size was too small, or there was no change 
in the energy since last />>/step." So I think this minimization is also successful./


I've found, from personal experience, that this message ("stopped 
because the algorithm tried to make a new step, whose size was too 
small, or there was no change in the energy since last step") means that:


1. either there is something wrong with the system structure or topology 
(a fact shown at almost the first step of an equilibration following the 
minimization with this message).


2. or that single precision GROMACS cannot perform minimization 
properly.  The latter often applies to MARTINI systems, especially if 
they are large or have too many protein subunits (I can't say whether 
the application of ELNEDYN plays a part).


If, hopefully, the latter case applies, the solution is to either use 
double precision GROMACS for minimization (gmx_d mdrun) or, since this 
is MARTINI, use "soft" potential modifiers like those they apply in the 
mdp files given by the CHARMM-GUI Martini Maker.  In any case, the 
initial minimization should be followed by a second, "standard" one 
(i.e. standard mdp options and single precision GROMACS).


Hope this helps in some manner,

Fotis Baltoumas

 --
Fotis A. Baltoumas, Bsc, Msc
Phd Candidate, Bioinformatics Postgraduate Programme
Section of Cell Biology and Biophysics
Department of Biology
National & Kapodistrian University of Athens
Panepistimiopolis, Athens 157 01, GREECE
   --

email : fbaltou...@biol.uoa.gr
http://biophysics.biol.uoa.gr
http://bioinformatics.biol.uoa.gr
Tel.: +30 2107274876
Mob.: +30 6979258570



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[gmx-users] GROMACS 2018.5 patch release available

[Paul bauer]

Hi GROMACS users,

The official release of GROMACS 2018.5 is available!

This release fixes several issues found since 2018.4. We encourage all 
users of the 2018

series to update to 2018.5. Please see the link to the release notes below
for more details.

You can find the code, documentation, release notes, and test suite at the
links below.

Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2018.5.tar.gz
Documentation: http://manual.gromacs.org/2018.5/index.html
(including release notes, install guide, user guide, reference manual)
Test Suite: http://gerrit.gromacs.org/download/regressiontests-2018.5.tar.gz

Happy simulating!

Paul

--

Paul Bauer, PhD
GROMACS Release Manager
KTH Stockholm, SciLifeLab
0046737308594

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Re: [gmx-users] "Too many LINCS warnings" in a minimization after solvation with coarse-grained waters

[Peter Kroon]

Hi,


You can reduce the timestep during equilibrations to e.g. 10 fs, or 5
when you have a really bad starting configuration. Bring it back up to
20 (in steps if needed) before starting your actual
equilibration/production though.

In addition, you can raise the lincs_order to 8.

And yes, the cgmartini.nl forum is currently unavailable due to
technical issues. We're working on it.


Peter

On 22-01-19 10:07, Mark Abraham wrote:
> Hi,
>
> I don't have any experience of coarse-grained systems, but everything looks
> OK from this level. It is normal to troubleshoot by visualizing your input
> and progress result. Minimizers are local, so if you start from something
> that has a frustration that can't be resolved, you are stuck. Generally
> this can be seen.
>
> Mark
>
> On Mon, 21 Jan 2019 at 22:59 ZHANG Cheng <272699...@qq.com> wrote:
>
>> I also tried to reduce the "emtol" gradually in the mdp file, i.e. from
>> 1000 to 100 to 10. It passed the "emtol = 1000" but it stopped again at
>> "emtol = 100", i.e. outputting dozens of pdb files before the "LINCS
>> warnings".
>>
>>
>> Then I looked at the edr files.
>> The potential in "emtol = 1000" and "emtol = 100" runs were actually
>> converging
>>
>> https://github.com/lanselibai/martini/blob/master/20190121_LINCS/emtol%201000%20then%20100.png
>>
>>
>> My understanding for the "LINCS warnings" is, the system is not stable.
>> But why the potential is still converging?
>>
>>
>> Do I need to adjust the "lincs warning threshold", or "set the environment
>> variable GMX_MAXCONSTRWARN to -1"? How to do that?
>>
>>
>> Is there a "standard" mdp file for minimization for a coarse-grained
>> system with 10 proteins in water?
>> I am using this, but I do not know how to modify it.
>>
>> https://github.com/lanselibai/martini/blob/master/20190121_LINCS/minimization_solvate.mdp
>>
>>
>>
>>
>> -- Original --
>> From:  "ZHANG Cheng"<272699...@qq.com>;
>> Date:  Tue, Jan 22, 2019 00:12 AM
>> To:  "gromacs.org_gmx-users";
>>
>> Subject:  "Too many LINCS warnings" in a minimization after solvation with
>> coarse-grained waters
>>
>>
>>
>> I am doing coarse-grained (CG) modelling for 10 proteins in a box. I was
>> told "Too many LINCS warnings" in the minimization after solvation with
>> coarse-grained waters.
>>
>>
>> I try to diagnose the problems based on
>>
>> http://manual.gromacs.org/documentation/2018/user-guide/terminology.html#blowing-up
>>
>>
>> My procedure is
>>
>>
>> 1) A single CG-protein was firstly minimized in vacuum, no problem
>>
>>
>> 2) Then 10 of this protein were inserted to a box, followed by a
>> minimization. It "stopped because the algorithm tried to make a new step
>> whose size was too small, or there was no change in the energy since last
>> step." So I think this minimization is also successful.
>>
>>
>> 3) The system was then solvated by
>> $ gmx solvate -cp 10_noW_minimized.gro -cs water-box-CG_303K-1bar.gro
>> -radius 0.21 -o system-solvated.gro -p system.top
>>
>>
>> 4) Then the solvated system is minimized by
>> $ gmx grompp -f minimization_solvate.mdp -c system-solvated.gro -p
>> system.top -o system-min-solvent.tpr
>> $ gmx mdrun -deffnm system-min-solvent -v -c system-min-solvent.gro
>>
>> PDB structures were outputted from step 327 to step 710, and it stopped
>> due to the "LINCS warnings".
>>
>>
>> The "minimization_solvate.mdp" is here
>>
>> https://github.com/lanselibai/martini/blob/master/20190121_LINCS/minimization_solvate.mdp
>>
>>
>> The "system-min-solvent.log" is here
>>
>> https://github.com/lanselibai/martini/blob/master/20190121_LINCS/system-min-solvent.log
>>
>>
>> So I think the system with 10 proteins in vacuum is okay (right?). But
>> when CG-water is added, it got problem? How to modify my system? Let me
>> know if you need other information. Thank you.
>>
>>
>> Cheng
>> --
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>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
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Re: [gmx-users] Error Found by Equilibration

[Mark Abraham]

Hi,

Minimization is sometimes not enough to stop
http://manual.gromacs.org/current/user-guide/terminology.html#blowing-up.
Start with a smaller timestep while you let the large forces relax. Then
move to your production setup.

Mark

On Tue, 22 Jan 2019 at 01:02 Lianxin Xin  wrote:

> Hi, everyone,
>
> We are simulating a pure DPPC bilayer with 128 lipids.
>
> Now, we defined a box around the bilayer, and solvated, after solvating, we
> removed water molecular between the bilayer.
> Then, we did energy minimization for the system. However, when we got our
> nvt.tpr file, and did NVT equilibration, there are errors found. Our input
> file are adjusted by the Tutorial 2: KALP15 in DPPC.
>
> Some Important Command we applied:
>
> *Solvate:*
>
>
> gmx grompp -f ions.mdp -c dppc128_solv_fix.gro -p topol_dppc.top -o
> ions.tpr
>
>
> gmx genion -s ions.tpr -o dppc128_solv_ions.gro -p topol_dppc.top -pname NA
> -nname CL -neutral
>
>
>
> *Energy Minimization*
>
>
> gmx grompp -f minim.mdp -c dppc128_solv_ions.gro -p topol_dppc.top -o
> em.tpr
>
>
> gmx mdrun -v -deffnm em
>
>
>
> *Equilibration (here found errors)*
>
>
> gmx grompp -f nvt.mdp -c dppc128_solv_ions.gro -r dppc128_solv_ions.gro -p
> topol_dppc.top -n index.ndx -o nvt.tpr
>
>
> gmx mdrun -deffnm nvt
>
>
>  *ERROR for Equilibration *:
>
> step 198: Water molecule starting at atom 11939 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 200: Water molecule starting at atom 11939 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
>
>
> step 200: Water molecule starting at atom 11939 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Wrote pdb files with previous and current coordinates
>
> Wrote pdb files with previous and current coordinates
>
>
>
> step 201: Water molecule starting at atom 14015 can not be settled.
>
>
>
> .
>
> .
>
> .
>
>
>
> Fatal error:
>
> 1 particles communicated to PME rank 2 are more than 2/3 times the cut-off
> out of the domain decomposition cell of their charge group in dimension x.
>
> This usually means that your system is not well equilibrated.
>
>
> link are including these files.
>
> 1. dppc128_solv_fix.groRemoved water molecular
>
> 2. dppc128_solv_ions.gro Energy Minimization
>
> 3. topol_dppc.top   Input topol file
>
> 4. nvt.mdp  NVT  input file
>
>
> https://drive.google.com/file/d/0B1E3Ulh4cGv7azhqejk1VmhHbW1QTS12bF9zTE5KQl9kb1Rv/view?usp=sharing
>
> https://drive.google.com/file/d/0B1E3Ulh4cGv7MGZNQ1Zoc183X3N5djhYVncxSThRcmdhTkQ4/view?usp=sharing
>
> https://drive.google.com/file/d/0B1E3Ulh4cGv7ejBkUkg2d1pIR0lGOVI4Yjg5ZXk4WG8wOTFN/view?usp=sharing
>
> https://drive.google.com/file/d/0B1E3Ulh4cGv7YTB0d21HUnRZZHhjQ3AyYXplU1c3ejhGVU5R/view?usp=sharing
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Re: [gmx-users] seeking help for generating combined trajectory files and clusters

[Mark Abraham]

Hi,

You're comparing to the configurations in -f2, but that will only make
sense if the contents of the files for each round have mutually compatible
periodic representation. I suggest you visualise the combined trajectory
and observe the problem.

Mark

On Mon, 21 Jan 2019 at 17:30 MD  wrote:

> Hi Gromacs folks,
>
> I am trying to simulate protein and ligand compound.
>
> I did several 200 ns simulations and combined them into one trajectory file
> with the commands:
> gmx trjcat -f md_round1_10-200ns.xtc
>  md_round2_10-200ns.xtcmd_round3_10-200ns.xtc -o md_combined.xtc -cat
> -settime
> I set the starting times to be: 10 ns, 190 ns, 380 ns
>
> Then I made a RMSD matrix with the command:
> gmx rms -f md_combined.xtc -f2 md_0_1_combined.xtc -s md.tpr -n md.ndx -m
> md_RMSD-matrix.xpm
>
> Then I tried to build clusters with the command:
> gmx cluster -f md_combined.xtc -s md.tpr  -n md.ndx -dm md_RMSD-matrix.xpm
> -method gromos -cl out.pdb -cutoff 0.2 -g out.log
>
> There were 120 clusters came back. Except for the first and largest
> cluster, all the rest of the clusters have a crazily far away ligand
> compared to where the protein is.
>
> I went back to look at each individual xtc from each round and produced
> their own clusters and they all look good (no huge separation of protein
> and ligand).
>
> If all the xtc files are good on their own, how come the combined xtc is
> giving me this result?
>
> Best,
>
> MD
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Re: [gmx-users] "Too many LINCS warnings" in a minimization after solvation with coarse-grained waters

[Mark Abraham]

Hi,

I don't have any experience of coarse-grained systems, but everything looks
OK from this level. It is normal to troubleshoot by visualizing your input
and progress result. Minimizers are local, so if you start from something
that has a frustration that can't be resolved, you are stuck. Generally
this can be seen.

Mark

On Mon, 21 Jan 2019 at 22:59 ZHANG Cheng <272699...@qq.com> wrote:

> I also tried to reduce the "emtol" gradually in the mdp file, i.e. from
> 1000 to 100 to 10. It passed the "emtol = 1000" but it stopped again at
> "emtol = 100", i.e. outputting dozens of pdb files before the "LINCS
> warnings".
>
>
> Then I looked at the edr files.
> The potential in "emtol = 1000" and "emtol = 100" runs were actually
> converging
>
> https://github.com/lanselibai/martini/blob/master/20190121_LINCS/emtol%201000%20then%20100.png
>
>
> My understanding for the "LINCS warnings" is, the system is not stable.
> But why the potential is still converging?
>
>
> Do I need to adjust the "lincs warning threshold", or "set the environment
> variable GMX_MAXCONSTRWARN to -1"? How to do that?
>
>
> Is there a "standard" mdp file for minimization for a coarse-grained
> system with 10 proteins in water?
> I am using this, but I do not know how to modify it.
>
> https://github.com/lanselibai/martini/blob/master/20190121_LINCS/minimization_solvate.mdp
>
>
>
>
> -- Original --
> From:  "ZHANG Cheng"<272699...@qq.com>;
> Date:  Tue, Jan 22, 2019 00:12 AM
> To:  "gromacs.org_gmx-users";
>
> Subject:  "Too many LINCS warnings" in a minimization after solvation with
> coarse-grained waters
>
>
>
> I am doing coarse-grained (CG) modelling for 10 proteins in a box. I was
> told "Too many LINCS warnings" in the minimization after solvation with
> coarse-grained waters.
>
>
> I try to diagnose the problems based on
>
> http://manual.gromacs.org/documentation/2018/user-guide/terminology.html#blowing-up
>
>
> My procedure is
>
>
> 1) A single CG-protein was firstly minimized in vacuum, no problem
>
>
> 2) Then 10 of this protein were inserted to a box, followed by a
> minimization. It "stopped because the algorithm tried to make a new step
> whose size was too small, or there was no change in the energy since last
> step." So I think this minimization is also successful.
>
>
> 3) The system was then solvated by
> $ gmx solvate -cp 10_noW_minimized.gro -cs water-box-CG_303K-1bar.gro
> -radius 0.21 -o system-solvated.gro -p system.top
>
>
> 4) Then the solvated system is minimized by
> $ gmx grompp -f minimization_solvate.mdp -c system-solvated.gro -p
> system.top -o system-min-solvent.tpr
> $ gmx mdrun -deffnm system-min-solvent -v -c system-min-solvent.gro
>
> PDB structures were outputted from step 327 to step 710, and it stopped
> due to the "LINCS warnings".
>
>
> The "minimization_solvate.mdp" is here
>
> https://github.com/lanselibai/martini/blob/master/20190121_LINCS/minimization_solvate.mdp
>
>
> The "system-min-solvent.log" is here
>
> https://github.com/lanselibai/martini/blob/master/20190121_LINCS/system-min-solvent.log
>
>
> So I think the system with 10 proteins in vacuum is okay (right?). But
> when CG-water is added, it got problem? How to modify my system? Let me
> know if you need other information. Thank you.
>
>
> Cheng
> --
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Re: [gmx-users] npt equlibration without position restrain

[Olga Press]

Thank you very much for your help.

Olga

‫בתאריך יום א׳, 20 בינו׳ 2019 ב-22:35 מאת ‪Mark Abraham‬‏ <‪
mark.j.abra...@gmail.com‬‏>:‬

> Hi,
>
> They're inactive so whether they have any value or are present does not
> matter.
>
> Mark
>
> On Sun., 20 Jan. 2019, 10:34 Olga Press,  wrote:
>
> >  Dr. Mark Abraham, thank you so much for your help.
> > That meaning that in the NPT equilibration without position restrains
> > the refcoord_scaling should not be present at all in the mdp file*?*
> >
> > Thank you in advance.
> > Olga
> >
> > ‫בתאריך יום א׳, 20 בינו׳ 2019 ב-11:06 מאת ‪Mark Abraham‬‏ <‪
> > mark.j.abra...@gmail.com‬‏>:‬
> >
> > > Hi,
> > >
> > > If you're not using position restraints then options that affect how
> they
> > > work are inactive.
> > >
> > > Mark
> > >
> > > On Sun., 20 Jan. 2019, 09:46 Olga Press, 
> wrote:
> > >
> > > > Dear gromacs users,
> > > >
> > > >  I perform membrane-protein simulation and used the same mdp files as
> > > > suggested by the tutorial of Dr. Justin Lemkul with one exception of
> > > > changing the correct parameters for charmm36ff as suggested
> > > > by gromacs manual.
> > > >
> > > > I performed 10ns of *NVT equilibration with position restrained* on
> the
> > > > protein and found a convergence of the temperature to the desired
> > > > temperature. Followed by 50ns of *NPT equilibration with position
> > > > restrained *on the protein, and after that,  I performed 100ns of
> *NPT
> > > > equilibration without position restraint*.
> > > > My question is, in the *NPT equilibration without the position
> > restrain,*
> > > > what should I put in the category of   *refcoord_scaling? com? *or
> > > should I
> > > > delete it as I found in the MD.mdp file in the tutorial?
> > > >
> > > > Thanks in advance,
> > > > Olga
> > > > --
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> > > >
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