Re: [gmx-users] extending simulations

[Jernej Zidar]

Dear Yi,

The easiest way do this would by simply extending the first simulation for
a given number of steps:

- - - script - - -
# run the first simulation
gmx mdrun -v -deffnm md

# continuous running
for i in `seq 2 6`; do
let j=i-1
gmx mdrun -s md.tpr -deffnm md$i -nsteps 2 -cpi &> run"$i".out
done
- - - script - - -

This is probably the simplest way and will just append new data to existing
files.

Second option would be something like this:

- - - script - - -
# run the first simulation
gmx mdrun -v -deffnm md1

# continuous running
for i in `seq 2 6`; do
let j=i-1
gmx convert-tpr -s md"$j".tpr -o md"$i".tpr -extend 2.0
cp -a md"$j".log md"$i".log
cp -a md"$j".edr md"$i".edr
cp -a md"$j".trr md"$i".trr
cp -a md"$j".cpt md"$i".cpt
gmx mdrun -v -deffnm md"$i" -cpi
done
- - - script - - -

The above option is not the most efficient one because you end up using way
more disk space than necessary. It is also not as elegant as the first one.

One small note: The switch "-deffnm" sets all the input and output files to
the same basename (in your case md"$i"; note the lack of the ".tpr"). After
setting to "-deffnm md$i", Gromacs will expect the checkpoint file
(requested in your case by "-cpi md$j.cpt") to be called md"$i".cpt.

Cheers,
Jernej


> Message: 2
> Date: Mon, 29 Jan 2018 12:01:38 -0500
> From: Myunggi Yi 
> To: Discussion list for GROMACS users 
> Subject: Re: [gmx-users] extending simulations
> Message-ID:
>  fy0...@mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> The following is a part of my bash script to automate extended running.
> (not appending or not crashed simulations)
>
> script---
> # em
> ...
>
> # heating
> ...
>
> # npt equilibration
> gmx grompp -f npt.mdp -c nvt.gro -r ../mono.gro -t nvt.cpt -p ../mono.top
> -n ../index.ndx -o npt.tpr
> gmx mdrun -deffnm npt
>
> # md
> gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p ../mono.top -n ../index.ndx
> -o md1.tpr
> gmx mdrun -deffnm md1
>
> # continuous running
> for i in `seq 2 6`; do
> let j=i-1
> gmx convert-tpr -s md$j.tpr -o md$i.tpr -extend 2.0
> gmx mdrun -s md$i.tpr -cpi md$j.cpt -deffnm md$i
> done
> -script---
>
>
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Re: [gmx-users] Alignment algorithm

[Justin Lemkul]

On 1/29/18 3:46 PM, Simone Bolognini wrote:

Hi everyone,
I was wondering: what is the algorithm implemented by Gromacs for
structural alignment before RMSD calculation?


It's a simple least-squares fit.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] extending simulations

[Justin Lemkul]

On 1/29/18 12:01 PM, Myunggi Yi wrote:

Hi,

The following is a part of my bash script to automate extended running.
(not appending or not crashed simulations)

script---
# em
...

# heating
...

# npt equilibration
gmx grompp -f npt.mdp -c nvt.gro -r ../mono.gro -t nvt.cpt -p ../mono.top
-n ../index.ndx -o npt.tpr
gmx mdrun -deffnm npt

# md
gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p ../mono.top -n ../index.ndx
-o md1.tpr
gmx mdrun -deffnm md1

# continuous running
for i in `seq 2 6`; do
 let j=i-1
 gmx convert-tpr -s md$j.tpr -o md$i.tpr -extend 2.0
 gmx mdrun -s md$i.tpr -cpi md$j.cpt -deffnm md$i
done
-script---



The following is the error message.

--error 
Command line:
   gmx mdrun -s md2.tpr -cpi md1.cpt -deffnm md2

Output file appending has been requested,
but some output files listed in the checkpoint file md1.cpt
are not present or not named as the output files by the current program:
Expect output files present:

Expected output files not present or named differently:
   md1.log
   md1.xtc
   md1.edr


md1.cpt specifies that all your output files should have "md1" as their 
prefix. You're simultaneously trying to change names (via -deffnm md2) 
and append (because -append is default) to files named md.*  Those 
options are mutually exclusive. If you change file names, use -noappend 
and get a new set of output files that can be appended later.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] emtol value

[Justin Lemkul]

On 1/29/18 11:12 AM, Ahmed Mashaly wrote:

Hi,
What should be the emtol value for big proteins and system? speaking about 
+1500 residue and +50k water molecule.
Minimize as low as you can. I've never had an issue with an emtol 
between 100-1000. The goal is to get as close to the bottom of a 
potential energy well as you can, but there's no way to know if you're 
in the lowest anyway.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] Grompp warning about topology constrains

[Justin Lemkul]

On 1/29/18 11:03 AM, Ahmed Mashaly wrote:

Hi,
I have set up my parameters with tleap, converted to gromacs with Acpype, did 
the minimization.


For NVT, when I use grompp, this warning appears:
WARNING 1 [file gromacs.top, line 79147]:  There are atoms at both ends of an angle, 
connected by constraints and  with masses that differ by more than a factor of 13. This 
means that  there are likely dynamic modes that are only very weakly coupled. To  ensure 
good equipartitioning, you need to either not use constraints on  all bonds (but, if 
possible, only on bonds involving hydrogens) or use  integrator = sd or decrease one or 
more tolerances:  verlet-buffer-tolerance <= 0.0001, LINCS iterations >= 2, LINCS 
order >=  4 or SHAKE tolerance <= 1e-05

But in .top file there in this line (the last one) there is no such a thing.


The error appears at the end of topology parsing, so it reports the last 
line as being the source, but that's not correct. It's just a reflection 
of the fact that you're doing something unstable somewhere in the topology.



It worked when I changed the integrator to sd or when I changed the constraints to only 
h-bonds and not with LINCS iterations >= 2, LINCS order >= 4 or SHAKE tolerance 
<= 1e-05


I even deleteddefine                  = -DPOSRES
from the .mdp file and got the same warning


Position restraints have nothing to do with bond constraints.

The text below is basically unintelligible. Please use proper line 
wrapping in your email client.


-Justin



this is my input file:itle                   = NVT define                  = 
-DPOSRES ; Run parametersintegrator              = md       dt                  
    = 0.002    nsteps                  = 25   ; Output controlnstlog        
          = 500     nstxout                 = 500    nstvout                 = 
500     nstfout                 = 500     nstcalcenergy           = 10  
nstenergy               = 500    ; Bond parameterscontinuation            = no  
     constraint_algorithm    = lincs       constraints             = all-bonds  
   lincs_iter              = 2           lincs_order             = 4          
shake-tol = 1e-05  ; Neighborsearchingcutoff-scheme           = Verletns_type   
              = grid           nstlist                 = 10            rlist    
               = 1.0            rvdw                    = 1.0            
vdwtype                 = Cut-offrcoulomb                = 1.0            ; 
Electrostaticscoulombtype             = pme            pme_order               
= 4              fourierspacing          = 0.16
; Temperature couplingtcoupl                  = V-rescaletc_grps                
 = Protein Non-Protein tau_t                   = 0.1    0.1ref_t                
   = 300    300
; Pressure couplingpcoupl                  = no        ; Periodic boundary 
conditionspbc                     = xyz       ; Dispersion correctionDispCorr   
             = EnerPres  ;gen_vel                 = yes       gen_temp          
      = 300       gen_seed                = -1



And these are the last lines of .top with line numbers (starting 79101)  79101 
[ moleculetype ]  79102 ; Name            nrexcl  79103 SOL          3  79104   
79105 [ atoms ]  79106 ;   nr       type  resnr residue  atom   cgnr    charge  
     mass  typeB    chargeB      massB  79107 ; residue    1 WAT rtp WAT q 0.0  
79108     1         OW      1    SOL     OW      1  -0.834000    16.   ; 
qtot -0.8340  79109     2         HW      1    SOL    HW1      2   0.417000     
1.0080   ; qtot -0.4170  79110     3         HW      1    SOL    HW2      3   
0.417000     1.0080   ; qtot 0.  79111   79112 #ifdef FLEXIBLE  79113   
79114 [ bonds ]  79115 ;    ai     aj funct         c0         c1         c2    
     c3  79116       2      3     1   0.15136 462750.40  79117       1      
2     1   0.09572 462750.40  79118       1      3     1   0.09572 
462750.40  79119   79120   79121 #else  79122   79123 [ settles ]  79124 ; 
i     funct   doh     dhh  79125 1     1   0.09572   0.15136  79126   79127 
#endif  79128   79129 [ exclusions ]  79130 1  2  3  79131 2  1  3  79132 3  1  
2  79133   79134 [ system ]  79135 ; Name  79136 Generic title  79137   79138 [ 
molecules ]  79139 ; Compound       #mols  79140 system1              1  79141 
system2              1  79142 system1              1  79143 system2             
 1  79144 system1              1  79145 system2              1  79146 NA        
           3  79147 SOL              49664
Thanks,Ahmed


--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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[gmx-users] constant surface tension in gormacs

[Ali Shomali]

Dear Justin and all GROMACS users,



I'm simulating a monolayer system using the surface tension command in
gromacs to set the surface tension and obtain the area( per molecule).
Although my system is 2d and uniform : a slab of water covered with
surfactant molecules and the surface tension reaches the desired value
without problem, pxx and pyy are different and they don’t converge to a
similar value. Is this an error or non physical problem? should I use a
barostat with proper values  for each direction instead of surface tension
command  to make pxx=pyy?


Thank you for any help,

Ali
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[gmx-users] Alignment algorithm

[Simone Bolognini]

Hi everyone,
I was wondering: what is the algorithm implemented by Gromacs for
structural alignment before RMSD calculation?

Best
Simone

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Simone
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Re: [gmx-users] extending simulations

[Myunggi Yi]

Hi,

The following is a part of my bash script to automate extended running.
(not appending or not crashed simulations)

script---
# em
...

# heating
...

# npt equilibration
gmx grompp -f npt.mdp -c nvt.gro -r ../mono.gro -t nvt.cpt -p ../mono.top
-n ../index.ndx -o npt.tpr
gmx mdrun -deffnm npt

# md
gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p ../mono.top -n ../index.ndx
-o md1.tpr
gmx mdrun -deffnm md1

# continuous running
for i in `seq 2 6`; do
let j=i-1
gmx convert-tpr -s md$j.tpr -o md$i.tpr -extend 2.0
gmx mdrun -s md$i.tpr -cpi md$j.cpt -deffnm md$i
done
-script---



The following is the error message.

--error 
Command line:
  gmx mdrun -s md2.tpr -cpi md1.cpt -deffnm md2

Output file appending has been requested,
but some output files listed in the checkpoint file md1.cpt
are not present or not named as the output files by the current program:
Expect output files present:

Expected output files not present or named differently:
  md1.log
  md1.xtc
  md1.edr

---
Program: gmx mdrun, version 2018
Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 179)

Fatal error:
File appending requested, but 3 of the 3 output files are not present or are
named differently. For safety reasons, GROMACS-2016 and later only allows
file
appending to be used when all files have the same names as they had in the
original run. Checkpointing is merely intended for plain continuation of
runs.
For safety reasons you must specify all file names (e.g. with -deffnm), and
all these files must match the names used in the run prior to checkpointing
since we will append to them by default. If you used -deffnm and the files
listed above as not present are in fact present, try explicitly specifying
them in respective mdrun options. If the files are not available, you can
add
the -noappend flag to mdrun and write separate new parts. For mere
concatenation of files, you should use the gmx trjcat tool instead.
--- error 


I did read the manual, but complicated for me.
which is input? which is output options? unclear manual for me.


I don't want appending of crashed simulation.

Previous simulation stopped regularly.

I want to run continuous md running with separate out files like md1, md2,
md3, etc

How can I achieve this goal?


Thank you.



On Mon, Jan 29, 2018 at 9:40 AM, Mark Abraham 
wrote:

> Hi,
>
> See
> http://manual.gromacs.org/documentation/2018-latest/user-guide/managing-
> simulations.html#extending-a-tpr-file
>
> Mark
>
> On Mon, Jan 29, 2018 at 3:37 PM Myunggi Yi  wrote:
>
> > Thank you for your help.
> >
> > Then how can the simulation be continued without previous cpt file
> > (information)?
> >
> > Or, should I use another way to extend the simulations?
> >
> >
> > Myunggi
> >
> >
> > On Mon, Jan 29, 2018 at 9:10 AM, Justin Lemkul  wrote:
> >
> > >
> > >
> > > On 1/29/18 9:07 AM, Myunggi Yi wrote:
> > >
> > >> Dear users,
> > >>
> > >> I am using gromacs2018
> > >>
> > >> I've got the following error message.
> > >>
> > >>
> > >>
> > >>
> > >> Command line:
> > >>gmx convert-tpr -s md1.tpr -f md1.cpt -n ../index.ndx -o md2.tpr
> > >> -extend
> > >> 2.0
> > >>
> > >>
> > >> ---
> > >> Program: gmx convert-tpr, version 2018
> > >> Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276)
> > >> Function:void gmx::CommandLineParser::parse(int*, char**)
> > >>
> > >> Error in user input:
> > >> Invalid command-line options
> > >>  Unknown command-line option -f
> > >>
> > >>
> > >>
> > >>
> > >> The option is valid.
> > >>
> > >> http://manual.gromacs.org/programs/gmx-convert-tpr.html
> > >>
> > >>
> > >> Is this a bug?
> > >>
> > >
> > > No, because you're looking at the wrong version of the manual.
> > >
> > > http://manual.gromacs.org/documentation/2018-latest/onlinehe
> > > lp/gmx-convert-tpr.html
> > >
> > > -Justin
> > >
> > > --
> > > ==
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Assistant Professor
> > > Virginia Tech Department of Biochemistry
> > >
> > > 303 Engel Hall
> > > 340 West Campus Dr.
> > > Blacksburg, VA 24061
> > >
> > > jalem...@vt.edu | (540) 231-3129
> > > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> > >
> > > ==
> > >
> > > --
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> > > /Mailing_Lists/GMX-Users_List before posting!
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> > > send a mail to 

[gmx-users] emtol value

[Ahmed Mashaly]

Hi,
What should be the emtol value for big proteins and system? speaking about 
+1500 residue and +50k water molecule. 
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[gmx-users] Grompp warning about topology constrains

[Ahmed Mashaly]

Hi,
I have set up my parameters with tleap, converted to gromacs with Acpype, did 
the minimization.


For NVT, when I use grompp, this warning appears:
WARNING 1 [file gromacs.top, line 79147]:  There are atoms at both ends of an 
angle, connected by constraints and  with masses that differ by more than a 
factor of 13. This means that  there are likely dynamic modes that are only 
very weakly coupled. To  ensure good equipartitioning, you need to either not 
use constraints on  all bonds (but, if possible, only on bonds involving 
hydrogens) or use  integrator = sd or decrease one or more tolerances:  
verlet-buffer-tolerance <= 0.0001, LINCS iterations >= 2, LINCS order >=  4 or 
SHAKE tolerance <= 1e-05

But in .top file there in this line (the last one) there is no such a thing.

It worked when I changed the integrator to sd or when I changed the constraints 
to only h-bonds and not with LINCS iterations >= 2, LINCS order >= 4 or SHAKE 
tolerance <= 1e-05


I even deleteddefine                  = -DPOSRES
from the .mdp file and got the same warning


this is my input file:itle                   = NVT define                  = 
-DPOSRES ; Run parametersintegrator              = md       dt                  
    = 0.002    nsteps                  = 25   ; Output controlnstlog        
          = 500     nstxout                 = 500    nstvout                 = 
500     nstfout                 = 500     nstcalcenergy           = 10  
nstenergy               = 500    ; Bond parameterscontinuation            = no  
     constraint_algorithm    = lincs       constraints             = all-bonds  
   lincs_iter              = 2           lincs_order             = 4          
shake-tol = 1e-05  ; Neighborsearchingcutoff-scheme           = Verletns_type   
              = grid           nstlist                 = 10            rlist    
               = 1.0            rvdw                    = 1.0            
vdwtype                 = Cut-offrcoulomb                = 1.0            ; 
Electrostaticscoulombtype             = pme            pme_order               
= 4              fourierspacing          = 0.16           
; Temperature couplingtcoupl                  = V-rescaletc_grps                
 = Protein Non-Protein tau_t                   = 0.1    0.1ref_t                
   = 300    300
; Pressure couplingpcoupl                  = no        ; Periodic boundary 
conditionspbc                     = xyz       ; Dispersion correctionDispCorr   
             = EnerPres  ;gen_vel                 = yes       gen_temp          
      = 300       gen_seed                = -1  



And these are the last lines of .top with line numbers (starting 79101)  79101 
[ moleculetype ]  79102 ; Name            nrexcl  79103 SOL          3  79104   
79105 [ atoms ]  79106 ;   nr       type  resnr residue  atom   cgnr    charge  
     mass  typeB    chargeB      massB  79107 ; residue    1 WAT rtp WAT q 0.0  
79108     1         OW      1    SOL     OW      1  -0.834000    16.   ; 
qtot -0.8340  79109     2         HW      1    SOL    HW1      2   0.417000     
1.0080   ; qtot -0.4170  79110     3         HW      1    SOL    HW2      3   
0.417000     1.0080   ; qtot 0.  79111   79112 #ifdef FLEXIBLE  79113   
79114 [ bonds ]  79115 ;    ai     aj funct         c0         c1         c2    
     c3  79116       2      3     1   0.15136 462750.40  79117       1      
2     1   0.09572 462750.40  79118       1      3     1   0.09572 
462750.40  79119   79120   79121 #else  79122   79123 [ settles ]  79124 ; 
i     funct   doh     dhh  79125 1     1   0.09572   0.15136  79126   79127 
#endif  79128   79129 [ exclusions ]  79130 1  2  3  79131 2  1  3  79132 3  1  
2  79133   79134 [ system ]  79135 ; Name  79136 Generic title  79137   79138 [ 
molecules ]  79139 ; Compound       #mols  79140 system1              1  79141 
system2              1  79142 system1              1  79143 system2             
 1  79144 system1              1  79145 system2              1  79146 NA        
           3  79147 SOL              49664
Thanks,Ahmed
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Re: [gmx-users] extending simulations

[Myunggi Yi]

Thank you all.

Have a great day.


Myunggi

On Mon, Jan 29, 2018 at 9:40 AM, Mark Abraham 
wrote:

> Hi,
>
> See
> http://manual.gromacs.org/documentation/2018-latest/user-guide/managing-
> simulations.html#extending-a-tpr-file
>
> Mark
>
> On Mon, Jan 29, 2018 at 3:37 PM Myunggi Yi  wrote:
>
> > Thank you for your help.
> >
> > Then how can the simulation be continued without previous cpt file
> > (information)?
> >
> > Or, should I use another way to extend the simulations?
> >
> >
> > Myunggi
> >
> >
> > On Mon, Jan 29, 2018 at 9:10 AM, Justin Lemkul  wrote:
> >
> > >
> > >
> > > On 1/29/18 9:07 AM, Myunggi Yi wrote:
> > >
> > >> Dear users,
> > >>
> > >> I am using gromacs2018
> > >>
> > >> I've got the following error message.
> > >>
> > >>
> > >>
> > >>
> > >> Command line:
> > >>gmx convert-tpr -s md1.tpr -f md1.cpt -n ../index.ndx -o md2.tpr
> > >> -extend
> > >> 2.0
> > >>
> > >>
> > >> ---
> > >> Program: gmx convert-tpr, version 2018
> > >> Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276)
> > >> Function:void gmx::CommandLineParser::parse(int*, char**)
> > >>
> > >> Error in user input:
> > >> Invalid command-line options
> > >>  Unknown command-line option -f
> > >>
> > >>
> > >>
> > >>
> > >> The option is valid.
> > >>
> > >> http://manual.gromacs.org/programs/gmx-convert-tpr.html
> > >>
> > >>
> > >> Is this a bug?
> > >>
> > >
> > > No, because you're looking at the wrong version of the manual.
> > >
> > > http://manual.gromacs.org/documentation/2018-latest/onlinehe
> > > lp/gmx-convert-tpr.html
> > >
> > > -Justin
> > >
> > > --
> > > ==
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Assistant Professor
> > > Virginia Tech Department of Biochemistry
> > >
> > > 303 Engel Hall
> > > 340 West Campus Dr.
> > > Blacksburg, VA 24061
> > >
> > > jalem...@vt.edu | (540) 231-3129
> > > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> > >
> > > ==
> > >
> > > --
> > > 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.
> > >
> > --
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Re: [gmx-users] extending simulations

[Mark Abraham]

Hi,

See
http://manual.gromacs.org/documentation/2018-latest/user-guide/managing-simulations.html#extending-a-tpr-file

Mark

On Mon, Jan 29, 2018 at 3:37 PM Myunggi Yi  wrote:

> Thank you for your help.
>
> Then how can the simulation be continued without previous cpt file
> (information)?
>
> Or, should I use another way to extend the simulations?
>
>
> Myunggi
>
>
> On Mon, Jan 29, 2018 at 9:10 AM, Justin Lemkul  wrote:
>
> >
> >
> > On 1/29/18 9:07 AM, Myunggi Yi wrote:
> >
> >> Dear users,
> >>
> >> I am using gromacs2018
> >>
> >> I've got the following error message.
> >>
> >>
> >>
> >>
> >> Command line:
> >>gmx convert-tpr -s md1.tpr -f md1.cpt -n ../index.ndx -o md2.tpr
> >> -extend
> >> 2.0
> >>
> >>
> >> ---
> >> Program: gmx convert-tpr, version 2018
> >> Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276)
> >> Function:void gmx::CommandLineParser::parse(int*, char**)
> >>
> >> Error in user input:
> >> Invalid command-line options
> >>  Unknown command-line option -f
> >>
> >>
> >>
> >>
> >> The option is valid.
> >>
> >> http://manual.gromacs.org/programs/gmx-convert-tpr.html
> >>
> >>
> >> Is this a bug?
> >>
> >
> > No, because you're looking at the wrong version of the manual.
> >
> > http://manual.gromacs.org/documentation/2018-latest/onlinehe
> > lp/gmx-convert-tpr.html
> >
> > -Justin
> >
> > --
> > ==
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Virginia Tech Department of Biochemistry
> >
> > 303 Engel Hall
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalem...@vt.edu | (540) 231-3129
> > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> >
> > ==
> >
> > --
> > 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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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] extending simulations

[Myunggi Yi]

Thank you for your help.

Then how can the simulation be continued without previous cpt file
(information)?

Or, should I use another way to extend the simulations?


Myunggi


On Mon, Jan 29, 2018 at 9:10 AM, Justin Lemkul  wrote:

>
>
> On 1/29/18 9:07 AM, Myunggi Yi wrote:
>
>> Dear users,
>>
>> I am using gromacs2018
>>
>> I've got the following error message.
>>
>>
>>
>>
>> Command line:
>>gmx convert-tpr -s md1.tpr -f md1.cpt -n ../index.ndx -o md2.tpr
>> -extend
>> 2.0
>>
>>
>> ---
>> Program: gmx convert-tpr, version 2018
>> Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276)
>> Function:void gmx::CommandLineParser::parse(int*, char**)
>>
>> Error in user input:
>> Invalid command-line options
>>  Unknown command-line option -f
>>
>>
>>
>>
>> The option is valid.
>>
>> http://manual.gromacs.org/programs/gmx-convert-tpr.html
>>
>>
>> Is this a bug?
>>
>
> No, because you're looking at the wrong version of the manual.
>
> http://manual.gromacs.org/documentation/2018-latest/onlinehe
> lp/gmx-convert-tpr.html
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
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>
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Re: [gmx-users] KALP15 in DPPC

[Justin Lemkul]

On 1/28/18 3:22 PM, negar habibzadeh wrote:

my peptide is a cpp (cell penetrating peptide) . i am going to simulation
this peptide in dopc bilayer , i did lots of methods to build the system
but in nvt step i saw water inside dopc (i used posre for water but when i
removed it to run npt or md ,my problem was not solved ).Is it true that my
peptide causes water to enter into the membrane because it is a cpp???


Water leaking in immediately at the end of equilibration is almost 
certainly spurious. Again, I suggest you build your system a different 
way or find a better method of equilibration. It shouldn't be hard to 
keep waters out if the system is built properly. If they then leak in 
over (long) simulations, it might be relevant.


-Justin


On Thu, Jan 25, 2018 at 11:14 PM, Justin Lemkul  wrote:



On 1/25/18 12:17 PM, negar habibzadeh wrote:


How much time is needed to run ? i changed from 100 ps ( restrained
equilibration run ( nvt)) to 1 ns(1000ps) . but when i did npt (without
water and lipids restraints) again i saw water inside membrane.


I don't know. Such protocols are usually not necessary for a properly
prepared membrane. If you've got a huge amount of void space, I suggest
trying a different method to build the system, because perhaps the starting
coordinates are simply poor.


-Justin



On Wed, Jan 24, 2018 at 10:51 PM, Justin Lemkul  wrote:



On 1/24/18 11:16 AM, negar habibzadeh wrote:

i did it  but when i removed the restraints from water to equilibrate

again
,(after new equilibration ) i saw some water molecules  inside the
membrane
again. what can i do ?

Let the restrained equilibration run longer. Make sure you're not

restraining the lipids in any way.

-Justin



On Wed, Jan 24, 2018 at 4:24 PM, Justin Lemkul  wrote:


On 1/24/18 5:02 AM, negar habibzadeh wrote:

hi . i am doing simulation of peptide in DOPC bilayer. i have dopc.itp
,


dopc.pdb, dopc.gro , peptide.itp , sample.top for dopc ,
peptide.pdb,topol.top. i used below commands.

gmx editconf -f peptide.gro -o pep.gro -box 6.35172   6.80701
  7.49241
-c
(it corresponds to the x/y/z box vectors of the DOPC unit cell)
i merg peptide and dopc:
cat pep.gro DOPC_323K.gro > tot1.gro
(I remove unnecessary lines)
i add ions :
gmx grompp -f ions.mdp -c tot1.gro -p mem.top -o ions.tpr
gmx genion -s ions.tpr -o tot.gro -p mem.top -pname NA -nname CL -nn 8
i get tpr file  (in mem.mdp i add some line to freeze protein )
gmx grompp -f mem.mdp -c tot.gro -p mem.top -o mem.tpr -n index.ndx
and i use g-membed command:
g_membed -f mem.tpr -dat mem.dat -c final.gro -n index.ndx -xyinit 0.1
(in
mem.dat i include the place of protein in the center of box)
in final.gro there were a few stray water molecules, i deleted them
manually and
i did energy minimization :
gmx grompp -f minim.mdp -c final.gro -p mem.top -o em.tpr
gmx mdrun -v -deffnm em
i checked em.gro , every thing is ok . but when i run nvt
in nvt.gro , A large number of water molecules are inside the
membrane.
how can i solve this problem ?

If there's lots of void space around the protein in the membrane, then


you'll either need to prepare the system more carefully to prevent such
voids, or do an equilibration with water molecules restrained in the
z-dimension only, to prevent them from diffusing into the membrane.
Then,
remove the restraints and equilibrate again.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West 

[gmx-users] extending simulations

[Myunggi Yi]

Dear users,

I am using gromacs2018

I've got the following error message.




Command line:
  gmx convert-tpr -s md1.tpr -f md1.cpt -n ../index.ndx -o md2.tpr -extend
2.0


---
Program: gmx convert-tpr, version 2018
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276)
Function:void gmx::CommandLineParser::parse(int*, char**)

Error in user input:
Invalid command-line options
Unknown command-line option -f




The option is valid.

http://manual.gromacs.org/programs/gmx-convert-tpr.html


Is this a bug?

Thank you for any help, in advance.



Myunggi Yi
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Re: [gmx-users] Heat capacity of the system

[Mark Abraham]

Hi,

Rerun should not be doing anything with the velocities, because a
trajectory file does not have all the necessary state to reproduce what the
original mdrun did. (I forget whether we've actually stopped mdrun -rerun
from pretending to, but that's at least the plan.) Calculate your heat
capacities from the data in the original .edr files.

Mark

On Mon, Jan 29, 2018 at 6:13 AM Malvika K  wrote:

> Dear Gromacs Users,
>
> I used mdrun -rerun to recalculate energies of the system (protein in
> water). However, I notice that the temperature in these regenerated .edr
> files is not the same as the the simulation temperature. So if I were to
> calculate the heat capacity (Cp) of the system using this edr file,
> wouldn't it be incorrect since the temperature used is not at which the
> simulation was performed?
>
> Any help would be appreciated. Thank-you!
>
> Best,
> Malvika
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[gmx-users] RMSF

[YanhuaOuyang]

Dear gromacs users,
I have run a MD of 2 short peptides respectively, I want to compare the 
flexibility between these two peptides along the full sequence via the 
per-residue RMSF.
I understand that gmx rmsf computes the root mean square fluctuation of atomic 
positions in the trajectory (supplied with -f) after(optionally) fitting to a 
reference frame (supplied with -s), namely using "fit" option. Well, I am 
confused that if we add "nofit" option when calculating RMSF, does gmx rmsf 
still fit before computing rms flucuation? If so, what structure does gmx rmsf 
fit to since no fitting to reference structure(supplied with -s)?

Best regards,
Ouyang
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[gmx-users] Questions on residue RMSF

[YanhuaOuyang]

Dear gromacs users,
I have run a MD of 2 short peptides respectively, I want to compare the 
flexibility between these two peptides along the full sequence via the 
per-residue RMSF.

I wonder that should I use "nofit" of "fit" option when I calculate the 
per-residue RMSF of a trajectory using gmx rmsf ? What is the difference 
between using "fit" and "nofit" option?


Best regards,
Ouyang
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