Re: [gmx-users] Gromacs-5.1.2 Checkpoint/restart example

[Mark Abraham]

Hi,

On Tue, 26 Apr 2016 06:19 Husen R  wrote:

> Hi all,
>
> I tried to run this gromacs tutorial (
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html
> )
> in order to understand how checkpoint/restart works in Gromacs-5.1.2.
>
> Based on running that tutorial I found that mdrun automatically checkpoint
> even though I didn't specify -cpt option (based on mdrun manual page, by
> default checkpoint every 15 minutes)
>

Yes, as that webpage suggests.

1. What if I specify -cpt option with a value longer than or smaller than
> 15 minutes ? does -cpt value will automatically override the default ?
>

Yes, the default is used when you don't supply a value. But usually you
don't need to think about this.

2. I run the following command to restart production MD step (using SLURM)
> from checkpoint file. md_0_1_prev.cpt is .cpt file resulting from previous
> mdrun execution. is my command right ? I just want to make sure.
>

Not quite. From that webpage: "Note that mdrun will write state.cpt and
state_prev.cpt files. As you can see from their time stamps, one was
written approximately at the checkpoint interval before the other (15 mins
by default). Or you can use gmxcheck to see what is in them." You want to
follow the examples there and do your restart from the most recent file,
which is state.cpt. The older file is just kept for safety. Your command
will lead to wasting 15 minutes of simulation.

Mark

#!/bin/bash
> #SBATCH -J Lysozyme
> #SBATCH -o md-%j.out
> #SBATCH -A necis
> #SBATCH -N 3
> #SBATCH -n 24
> #SBATCH --time=144:00:00
> #SBATCH --mail-user=hus...@gmail.com
> #SBATCH --mail-type=begin
> #SBATCH --mail-type=end
>
> mpirun gmx_mpi mdrun -cpi md_0_1_prev.cpt -deffnm md_0_1
>
>
> Thank you in advance
>
> Regards,
>
>
> Husen
>
>
> On Sun, Apr 24, 2016 at 7:57 PM, Husen R  wrote:
>
> > Hi,
> >
> > Thanks a lot !
> > I'll try it,..
> >
> > Regards,
> >
> >
> > Husen
> >
> > On Sun, Apr 24, 2016 at 6:54 PM, Justin Lemkul  wrote:
> >
> >>
> >>
> >> On 4/24/16 12:04 AM, Husen R wrote:
> >>
> >>> Dear all,
> >>>
> >>> is there any complete documentation discussing checkpoint/restart in
> >>> Gromacs-5.1.2 ?
> >>> I found this link that discuss checkpoint (
> >>> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations)
> and
> >>> this link that discuss restart (
> >>> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts) but these
> >>> are
> >>> not specifically for gromacs 5.1.2.
> >>>
> >>>
> >> There are no differences for 5.1.2, so that information is all relevant.
> >>
> >> -Justin
> >>
> >> --
> >> ==
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>
> >> Department of Pharmaceutical Sciences
> >> School of Pharmacy
> >> Health Sciences Facility II, Room 629
> >> University of Maryland, Baltimore
> >> 20 Penn St.
> >> Baltimore, MD 21201
> >>
> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> >> http://mackerell.umaryland.edu/~jalemkul
> >>
> >> ==
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> >
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Gromacs-5.1.2 Checkpoint/restart example

[Husen R]

Hi all,

I tried to run this gromacs tutorial (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html)
in order to understand how checkpoint/restart works in Gromacs-5.1.2.

Based on running that tutorial I found that mdrun automatically checkpoint
even though I didn't specify -cpt option (based on mdrun manual page, by
default checkpoint every 15 minutes)

1. What if I specify -cpt option with a value longer than or smaller than
15 minutes ? does -cpt value will automatically override the default ?

2. I run the following command to restart production MD step (using SLURM)
from checkpoint file. md_0_1_prev.cpt is .cpt file resulting from previous
mdrun execution. is my command right ? I just want to make sure.

#!/bin/bash
#SBATCH -J Lysozyme
#SBATCH -o md-%j.out
#SBATCH -A necis
#SBATCH -N 3
#SBATCH -n 24
#SBATCH --time=144:00:00
#SBATCH --mail-user=hus...@gmail.com
#SBATCH --mail-type=begin
#SBATCH --mail-type=end

mpirun gmx_mpi mdrun -cpi md_0_1_prev.cpt -deffnm md_0_1


Thank you in advance

Regards,


Husen


On Sun, Apr 24, 2016 at 7:57 PM, Husen R  wrote:

> Hi,
>
> Thanks a lot !
> I'll try it,..
>
> Regards,
>
>
> Husen
>
> On Sun, Apr 24, 2016 at 6:54 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 4/24/16 12:04 AM, Husen R wrote:
>>
>>> Dear all,
>>>
>>> is there any complete documentation discussing checkpoint/restart in
>>> Gromacs-5.1.2 ?
>>> I found this link that discuss checkpoint (
>>> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations) and
>>> this link that discuss restart (
>>> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts) but these
>>> are
>>> not specifically for gromacs 5.1.2.
>>>
>>>
>> There are no differences for 5.1.2, so that information is all relevant.
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] [gmx-developers] MD Units

[Mark Abraham]

Hi,

I fixed the definition to be bar, and removed some other stuff I think is
unnecessary at https://gerrit.gromacs.org/#/c/5826/

Mark

On Mon, Apr 25, 2016 at 9:22 PM Erik Lindahl  wrote:

> Hi Adam,
>
> The stuff you get from the energy file should be bars. The first chapters
> is more about documenting the “natural” internal units, but we should
> probably clarify this.
>
> Cheers,
>
> Erik
>
>
> On 25 Apr 2016, at 21:17, Rigby, Adam  wrote:
>
> Dear All
>
> Are the MD Units at the beginning of the user manual correct, indicating
> that the pressure units are 16 bar (page 21 of manual-5.0.1) or are they 1
> bar (given by page 223 of the same manual). Because this variation is quite
> worrying and i have no clue what my actual units are.
>
> Regards
>
> Dr A. Rigby
> --
> Gromacs Developers mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers or
> send a mail to gmx-developers-requ...@gromacs.org.
>
>
> --
> Gromacs Developers mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers
> or send a mail to gmx-developers-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] how to convert CHARMM36 system into virtual site system?

[Justin Lemkul]

On 4/24/16 2:19 PM, Albert wrote:

Hello:

I've built a membrane system from CHARMM-GUI with CHARMM36 FF. I am just
wondering how can we convert the lipids molecule to virtual site lipids?



Presumably you'll have to create a .vsd file, but I've never validated such an 
approach with C36.  The C27 files distributed with GROMACS have a framework that 
you can probably use but I don't know if it's got anything useful for lipids.


-Justin

--
==

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

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

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

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Higher Density than Expected

[Justin Lemkul]

On 4/25/16 5:09 PM, Christopher Schlicksup wrote:

Hi, I am fairly new to simulation, and would like some input about whether
I have set up Gromacs correcly. I am using version 5.0.4 with the
CHARMM36-Jun2015 force field and the TIP3P water model. I am simulating a
35kDa protein in a dodecahedron box (-d 1.6) with 150mM NaCl plus
neutralizing ions.

I do a 200ps NVT equilibration followed by a 500ps NPT equilibration
followed by 230ps of production run where the protein is unrestrained. My
observations so far are that the density is higher than I would expect from
reading literature. I would appreciate any insight into whether I have a
problem, or if my density and pressure values look acceptable. Thanks in
advance



What value do you expect from the literature?  The density of such an 
inhomogeneous system is rather useless.  Everything looks fine to me.


-Justin


Here are my results from gmx energy:

*Energy minimization*

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Potential-1.93229e+06  2900077735.5-189748
(kJ/mol)


*NVT Equilibration 200ps*

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Temperature   299.9  0.0992.59846   0.560458  (K)


*NPT Equilibration 500ps*

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Pressure1.528921.781.007911.2974  (bar)
Density 1024.74  0.0571.70907 -0.0499058
(kg/m^3)
Volume  1168.76  0.0651.96293  0.0505822  (nm^3)


*Production Run 230ps*

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Pressure   0.450022   0.6575.3012   0.157248  (bar)
Density  1025.4  0.0481.39937  -0.209504
(kg/m^3)
Volume  1168.01  0.0551.59374   0.238338  (nm^3)



--
==

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

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

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

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Higher Density than Expected

[Christopher Schlicksup]

Hi, I am fairly new to simulation, and would like some input about whether
I have set up Gromacs correcly. I am using version 5.0.4 with the
CHARMM36-Jun2015 force field and the TIP3P water model. I am simulating a
35kDa protein in a dodecahedron box (-d 1.6) with 150mM NaCl plus
neutralizing ions.

I do a 200ps NVT equilibration followed by a 500ps NPT equilibration
followed by 230ps of production run where the protein is unrestrained. My
observations so far are that the density is higher than I would expect from
reading literature. I would appreciate any insight into whether I have a
problem, or if my density and pressure values look acceptable. Thanks in
advance

Here are my results from gmx energy:

*Energy minimization*

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Potential-1.93229e+06  2900077735.5-189748
(kJ/mol)


*NVT Equilibration 200ps*

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Temperature   299.9  0.0992.59846   0.560458  (K)


*NPT Equilibration 500ps*

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Pressure1.528921.781.007911.2974  (bar)
Density 1024.74  0.0571.70907 -0.0499058
(kg/m^3)
Volume  1168.76  0.0651.96293  0.0505822  (nm^3)


*Production Run 230ps*

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Pressure   0.450022   0.6575.3012   0.157248  (bar)
Density  1025.4  0.0481.39937  -0.209504
(kg/m^3)
Volume  1168.01  0.0551.59374   0.238338  (nm^3)
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] [gmx-developers] MD Units

[Erik Lindahl]

Hi Adam,

The stuff you get from the energy file should be bars. The first chapters is 
more about documenting the “natural” internal units, but we should probably 
clarify this.

Cheers,

Erik


> On 25 Apr 2016, at 21:17, Rigby, Adam  wrote:
> 
> Dear All
> 
> Are the MD Units at the beginning of the user manual correct, indicating that 
> the pressure units are 16 bar (page 21 of manual-5.0.1) or are they 1 bar 
> (given by page 223 of the same manual). Because this variation is quite 
> worrying and i have no clue what my actual units are.
> 
> Regards
> 
> Dr A. Rigby
> -- 
> Gromacs Developers mailing list
> 
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List 
>  before 
> posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists 
> 
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers 
>  or 
> send a mail to gmx-developers-requ...@gromacs.org 
> .

-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Problem in auto source

[Irem Altan]

Hi,

Can you try source /usr/local/gromacs/bin/GMXRC.bash ? I had the same problem 
and this works for me.

Best,
Irem

>> 
> On Apr 25, 2016, at 3:08 PM, Roshan Shrestha  wrote:
> 
> This is my .bashrc file and it looks like this-
> 
>> # ~/.bashrc: executed by bash(1) for non-login shells.
>> # see /usr/share/doc/bash/examples/startup-files (in the package bash-doc)
>> # for examples
>> 
>> # If not running interactively, don't do anything
>> case $- in
>>*i*) ;;
>>  *) return;;
>> esac
>> 
>> # don't put duplicate lines or lines starting with space in the history.
>> # See bash(1) for more options
>> HISTCONTROL=ignoreboth
>> 
>> # append to the history file, don't overwrite it
>> shopt -s histappend
>> 
>> # for setting history length see HISTSIZE and HISTFILESIZE in bash(1)
>> HISTSIZE=1000
>> HISTFILESIZE=2000
>> 
>> # check the window size after each command and, if necessary,
>> # update the values of LINES and COLUMNS.
>> shopt -s checkwinsize
>> 
>> # If set, the pattern "**" used in a pathname expansion context will
>> # match all files and zero or more directories and subdirectories.
>> #shopt -s globstar
>> 
>> # make less more friendly for non-text input files, see lesspipe(1)
>> [ -x /usr/bin/lesspipe ] && eval "$(SHELL=/bin/sh lesspipe)"
>> 
>> # set variable identifying the chroot you work in (used in the prompt
>> below)
>> if [ -z "${debian_chroot:-}" ] && [ -r /etc/debian_chroot ]; then
>>debian_chroot=$(cat /etc/debian_chroot)
>> fi
>> 
>> # set a fancy prompt (non-color, unless we know we "want" color)
>> case "$TERM" in
>>xterm-color|*-256color) color_prompt=yes;;
>> esac
>> 
>> # uncomment for a colored prompt, if the terminal has the capability;
>> turned
>> # off by default to not distract the user: the focus in a terminal window
>> # should be on the output of commands, not on the prompt
>> #force_color_prompt=yes
>> 
>> if [ -n "$force_color_prompt" ]; then
>>if [ -x /usr/bin/tput ] && tput setaf 1 >&/dev/null; then
>># We have color support; assume it's compliant with Ecma-48
>># (ISO/IEC-6429). (Lack of such support is extremely rare, and such
>># a case would tend to support setf rather than setaf.)
>>color_prompt=yes
>>else
>>color_prompt=
>>fi
>> fi
>> 
>> if [ "$color_prompt" = yes ]; then
>>
>> PS1='${debian_chroot:+($debian_chroot)}\[\033[01;32m\]\u@\h\[\033[00m\]:\[\033[01;34m\]\w\[\033[00m\]\$
>> '
>> else
>>PS1='${debian_chroot:+($debian_chroot)}\u@\h:\w\$ '
>> fi
>> unset color_prompt force_color_prompt
>> 
>> # If this is an xterm set the title to user@host:dir
>> case "$TERM" in
>> xterm*|rxvt*)
>>PS1="\[\e]0;${debian_chroot:+($debian_chroot)}\u@\h: \w\a\]$PS1"
>>;;
>> *)
>>;;
>> esac
>> 
>> # enable color support of ls and also add handy aliases
>> if [ -x /usr/bin/dircolors ]; then
>>test -r ~/.dircolors && eval "$(dircolors -b ~/.dircolors)" || eval
>> "$(dircolors -b)"
>>alias ls='ls --color=auto'
>>#alias dir='dir --color=auto'
>>#alias vdir='vdir --color=auto'
>> 
>>alias grep='grep --color=auto'
>>alias fgrep='fgrep --color=auto'
>>alias egrep='egrep --color=auto'
>> fi
>> 
>> # colored GCC warnings and errors
>> #export
>> GCC_COLORS='error=01;31:warning=01;35:note=01;36:caret=01;32:locus=01:quote=01'
>> 
>> # some more ls aliases
>> alias ll='ls -alF'
>> alias la='ls -A'
>> alias l='ls -CF'
>> 
>> # Add an "alert" alias for long running commands.  Use like so:
>> #   sleep 10; alert
>> alias alert='notify-send --urgency=low -i "$([ $? = 0 ] && echo terminal
>> || echo error)" "$(history|tail -n1|sed -e
>> '\''s/^\s*[0-9]\+\s*//;s/[;&|]\s*alert$//'\'')"'
>> 
>> # Alias definitions.
>> # You may want to put all your additions into a separate file like
>> # ~/.bash_aliases, instead of adding them here directly.
>> # See /usr/share/doc/bash-doc/examples in the bash-doc package.
>> 
>> if [ -f ~/.bash_aliases ]; then
>>. ~/.bash_aliases
>> fi
>> 
>> # enable programmable completion features (you don't need to enable
>> # this, if it's already enabled in /etc/bash.bashrc and /etc/profile
>> # sources /etc/bash.bashrc).
>> if ! shopt -oq posix; then
>>  if [ -f /usr/share/bash-completion/bash_completion ]; then
>>. /usr/share/bash-completion/bash_completion
>>  elif [ -f /etc/bash_completion ]; then
>>. /etc/bash_completion
>>  fi
>> fi
>> source /usr/local/gromacs/bin/GMXRC
>> 
>>> 
>>> So, there is this line *source /usr/local/gromacs/bin/GMXRC*  . But,
> gromacs is still not suto sourced whenever I open the new terminal. Thanks
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
> mail to gmx-users-requ...@gromacs.org.

-- 
Gromacs Users mailing list

[gmx-users] Problem in auto source

[Roshan Shrestha]

This is my .bashrc file and it looks like this-

> # ~/.bashrc: executed by bash(1) for non-login shells.
> # see /usr/share/doc/bash/examples/startup-files (in the package bash-doc)
> # for examples
>
> # If not running interactively, don't do anything
> case $- in
> *i*) ;;
>   *) return;;
> esac
>
> # don't put duplicate lines or lines starting with space in the history.
> # See bash(1) for more options
> HISTCONTROL=ignoreboth
>
> # append to the history file, don't overwrite it
> shopt -s histappend
>
> # for setting history length see HISTSIZE and HISTFILESIZE in bash(1)
> HISTSIZE=1000
> HISTFILESIZE=2000
>
> # check the window size after each command and, if necessary,
> # update the values of LINES and COLUMNS.
> shopt -s checkwinsize
>
> # If set, the pattern "**" used in a pathname expansion context will
> # match all files and zero or more directories and subdirectories.
> #shopt -s globstar
>
> # make less more friendly for non-text input files, see lesspipe(1)
> [ -x /usr/bin/lesspipe ] && eval "$(SHELL=/bin/sh lesspipe)"
>
> # set variable identifying the chroot you work in (used in the prompt
> below)
> if [ -z "${debian_chroot:-}" ] && [ -r /etc/debian_chroot ]; then
> debian_chroot=$(cat /etc/debian_chroot)
> fi
>
> # set a fancy prompt (non-color, unless we know we "want" color)
> case "$TERM" in
> xterm-color|*-256color) color_prompt=yes;;
> esac
>
> # uncomment for a colored prompt, if the terminal has the capability;
> turned
> # off by default to not distract the user: the focus in a terminal window
> # should be on the output of commands, not on the prompt
> #force_color_prompt=yes
>
> if [ -n "$force_color_prompt" ]; then
> if [ -x /usr/bin/tput ] && tput setaf 1 >&/dev/null; then
> # We have color support; assume it's compliant with Ecma-48
> # (ISO/IEC-6429). (Lack of such support is extremely rare, and such
> # a case would tend to support setf rather than setaf.)
> color_prompt=yes
> else
> color_prompt=
> fi
> fi
>
> if [ "$color_prompt" = yes ]; then
> 
> PS1='${debian_chroot:+($debian_chroot)}\[\033[01;32m\]\u@\h\[\033[00m\]:\[\033[01;34m\]\w\[\033[00m\]\$
> '
> else
> PS1='${debian_chroot:+($debian_chroot)}\u@\h:\w\$ '
> fi
> unset color_prompt force_color_prompt
>
> # If this is an xterm set the title to user@host:dir
> case "$TERM" in
> xterm*|rxvt*)
> PS1="\[\e]0;${debian_chroot:+($debian_chroot)}\u@\h: \w\a\]$PS1"
> ;;
> *)
> ;;
> esac
>
> # enable color support of ls and also add handy aliases
> if [ -x /usr/bin/dircolors ]; then
> test -r ~/.dircolors && eval "$(dircolors -b ~/.dircolors)" || eval
> "$(dircolors -b)"
> alias ls='ls --color=auto'
> #alias dir='dir --color=auto'
> #alias vdir='vdir --color=auto'
>
> alias grep='grep --color=auto'
> alias fgrep='fgrep --color=auto'
> alias egrep='egrep --color=auto'
> fi
>
> # colored GCC warnings and errors
> #export
> GCC_COLORS='error=01;31:warning=01;35:note=01;36:caret=01;32:locus=01:quote=01'
>
> # some more ls aliases
> alias ll='ls -alF'
> alias la='ls -A'
> alias l='ls -CF'
>
> # Add an "alert" alias for long running commands.  Use like so:
> #   sleep 10; alert
> alias alert='notify-send --urgency=low -i "$([ $? = 0 ] && echo terminal
> || echo error)" "$(history|tail -n1|sed -e
> '\''s/^\s*[0-9]\+\s*//;s/[;&|]\s*alert$//'\'')"'
>
> # Alias definitions.
> # You may want to put all your additions into a separate file like
> # ~/.bash_aliases, instead of adding them here directly.
> # See /usr/share/doc/bash-doc/examples in the bash-doc package.
>
> if [ -f ~/.bash_aliases ]; then
> . ~/.bash_aliases
> fi
>
> # enable programmable completion features (you don't need to enable
> # this, if it's already enabled in /etc/bash.bashrc and /etc/profile
> # sources /etc/bash.bashrc).
> if ! shopt -oq posix; then
>   if [ -f /usr/share/bash-completion/bash_completion ]; then
> . /usr/share/bash-completion/bash_completion
>   elif [ -f /etc/bash_completion ]; then
> . /etc/bash_completion
>   fi
> fi
> source /usr/local/gromacs/bin/GMXRC
>
>>
>> So, there is this line *source /usr/local/gromacs/bin/GMXRC*  . But,
gromacs is still not suto sourced whenever I open the new terminal. Thanks
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] REMD--how to determine the temperature distribution

[Christopher Neale]

There are many published approaches. Here is the one that I use: 
http://origami.phys.rpi.edu/racc/rate_of_acceptance.php
Another example is here: http://folding.bmc.uu.se/remd/


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of YanhuaOuyang 
<15901283...@163.com>
Sent: 25 April 2016 10:36
To: gmx-us...@gromacs.org
Subject: [gmx-users] REMD--how to determine the temperature distribution

Dear all,
I am going to run a REMD of a protein(explicit solvent) in NVT ensemble 
with gromacs, but I have trouble in determining a optimum temperature  
distribution.Can anybody know the ways to determine the temperature?
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] REMD--how to determine the temperature distribution

[YanhuaOuyang]

Dear all,
I am going to run a REMD of a protein(explicit solvent) in NVT ensemble 
with gromacs, but I have trouble in determining a optimum temperature  
distribution.Can anybody know the ways to determine the temperature?
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Potential shift

[Mark Abraham]

Hi,

It's often nice as a user to know that the program has agreed with your
intentions :-) You're using a tabulated interaction, so AFAICR mdrun just
does what you say. In some cases, mdrun will generate tables to implement
the user's short-ranged options, and it's important that mdrun says what
it's doing, and helpful if it always does so in similar ways.

Mark

On Mon, Apr 25, 2016 at 3:26 PM Alexander Alexander <
alexanderwie...@gmail.com> wrote:

> Dear GMX users,
>
> Does anybody know why the "Potential shift: LJ r^-12: 0.000e+00 r^-6:
> 0.000e+00" is written in my case.log file in spite of using LJ(6-9) in my
> calculations?
>
>
> Table routines are used for coulomb: TRUE
> Table routines are used for vdw: TRUE
> Cut-off's:   NS: 1   Coulomb: 1.26   LJ: 1.26
> System total charge: 0.000
> Read user tables from table.xvg with 1201 data points.
> Tabscale = 500 points/nm
> Potential shift: LJ r^-12: 0.000e+00 r^-6: 0.000e+00
>
>
> Best regards,
> Alex
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Potential shift

[Alexander Alexander]

Dear GMX users,

Does anybody know why the "Potential shift: LJ r^-12: 0.000e+00 r^-6:
0.000e+00" is written in my case.log file in spite of using LJ(6-9) in my
calculations?


Table routines are used for coulomb: TRUE
Table routines are used for vdw: TRUE
Cut-off's:   NS: 1   Coulomb: 1.26   LJ: 1.26
System total charge: 0.000
Read user tables from table.xvg with 1201 data points.
Tabscale = 500 points/nm
Potential shift: LJ r^-12: 0.000e+00 r^-6: 0.000e+00


Best regards,
Alex
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Fwd: how to convert CHARMM36 system into virtual site system?

[Albert]

Hello:

I've built a membrane system from CHARMM-GUI with CHARMM36 FF. I am just
wondering how can we convert the lipids molecule to virtual site lipids?

Thank you very much

Albert



--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.