Re: [gmx-users] Energy drift combining tabulated potentials and group cut-off.

[serpercon]

Hello, 

Thank you very much for your thoughtfull response. The structural
properties seem to be represented correctly so I guess it should work. I
know that drifts are something we must live with but since it appeared
when changing the system to a tabulated potential+a group cutoff I was
not sure if I was making some mistake.  

Sergio 

El 01/09/2017 12:48, Mark Abraham escribió:

> Hi,
> 
> There's not easy answers to such questions. A practical implementation of
> MD that can actually do most relevant kinds of science in relevant time
> frames can't have bitwise conservation. Drift accumulates from multiple
> aspects of the implementation, too, including the system size, and
> constraint algorithm, which can dominate over the effects of missing
> interactions over the lifetime of pair lists. See the discussion in the
> GROMACS reference manual, e.g. figure 3.5.
> 
> One proper question to ask is at what point your protocol correctly models
> whatever relevant physical data exists that is relevant to what you want to
> observe. Drift that is too large is likely to affect observables, but will
> affect different ones differently.
> 
> Mark
> 
> On Fri, Sep 1, 2017 at 12:12 PM  wrote:
> 
>> Dear GROMACS Community,
>> 
>> I am trying to do a simulation using a tabulated potential which forces
>> me to use the group cut-off. I get a drift in the conserved quantity of
>> -600KJ/mol/ns. My system consists of 1000 rigid TIP4P water molecules
>> and a Na+ ion. I imagine that eventhough it will soon be deprecated the
>> group cutoff scheme still works correctly. I have tryed to change the
>> parameters without success and in any case the ones I use seem
>> reasonable (in my experience using other programs). The rdfs of the
>> system look normal so I ruled out topology problems.
>> 
>> It seems that the problem is in the group cut-off since
>> when I change the tabulated potential for a regular vdw the problem
>> persists. I have followed the instructions of:
>> 
>> http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf
>> 
>> to implement the tabulated potentials.
>> 
>> Is this the kind of energy drift acceptable? I have pasted a copy .mdp
>> 
>> Thanks for your help,
>> 
>> Sergio Perez-Conesa
>> 
>> integrator = md
>> dt = 0.001
>> nsteps = 10
>> init-step = 0
>> cutoff-scheme = group
>> nst-list = 1
>> verlet-buffer-tolerance = 0.0005
>> ns-type = grid
>> rlist = 1.3
>> pbc = xyz
>> coulombtype = PME-switch
>> rcoulomb = 1.
>> rcoulomb-switch = 0.95
>> pme-order = 4
>> fourierspacing = 0.1
>> ewald-rtol = 1.e-5
>> vdwtype = user
>> rvdw = 1.0
>> DispCorr = No
>> tcoupl = v-rescale
>> tc-grps = System
>> ;nsttcouple = 1
>> tau-t = ref-t = 300.0
>> constraints = all-angles
>> constraint-algorithm = LINCS
>> lincs_iter = 1
>> lincs_order = 4
>> energygrps = NA OW
>> energygrp_table = NA OW
>> comm-mode = linear
>> --
>> Gromacs Users mailing list
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[gmx-users] Calculating hydrogen bonds along the length of the Bilayer

[atb files]

Hi Experts,How can we calculate hydrogen bonds as a function of 
distance from the Bilayer centre.ThanksYogi








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Re: [gmx-users] Error while running perl distances.pl

[Vytautas Rakeviius]

Script assumes that variable $distance is the second row separated by space in 
the file dist{number}.xvg which appears after execution of system call 
gmx distance -s md_pull.tpr -f conf${i}.gro -n index.ndx -oall dist${i}.xvg 
-select \'com of group \"lig\" plus com of group \"protein\"\'I just think that 
dist{number}.xvg creation fails for you in first place because "gmx distance" 
in the script is not adjusted according to your system.You use _mpi_d in your 
post.

 

On Monday, September 4, 2017, 5:48:43 AM GMT+3, 가디 장데부 고라크스나트 
 wrote:  
 
 
Hello Gmx user,


I would like to transport solute molecule from the ion channel (intracellular 
to extracellular site) using steered MD and umbrella sampling method to 
calculate the energy.

I followed Dr. Lemkul's tutorial and it works fine upto equilibration step but 
in distance.pl it shows some errors.

I used the distance of pulling along the Z-axis but still it do not work. I 
found when I use distance as a pull-geometry, solute moves away from the 
channel rather transporting through channel. Then I tried direction as a 
pull-geoetry, then solute transported from the chanel,and generated pullf.xvg 
but not pullx.xvg file.

I separated the trajectory using trjconv command

gmx_mpi_d -f recenter_traj.xtc -s md_pull.tpr -n pro-lig.ndx -o conf.gro -sep

It generated conformations.




Now I would like to calculate the COM distance between ion channel (protein) 
and solute (lig) using perl distance.pl but I received following error.

Error

readline() on closed filehandle IN at distances.pl line 16

Use of uminitialized value $distance in concatanation (.) or string at 
distances.pl line 30.




Here is the distance.pl file which I used for this purpose which was downloaded 
from Dr. Lemkul's tutorial file.

-
#!/usr/bin/perl -w

use strict;

# loop g_dist command - measure distance in each frame, write to a file
for (my $i=0; $i<=800; $i++) {
    print "Processing configuration $i...\n";
    system("gmx distance -s md_pull.tpr -f conf${i}.gro -n index.ndx -oall 
dist${i}.xvg -select \'com of group \"lig\" plus com of group \"protein\"\' 
&>/dev/null");
}

# write output to single file
open(OUT, ">>summary_distances.dat");

for (my $j=0; $j<=800; $j++) {
    open(IN, "

Re: [gmx-users] Regarding position restraining in nvt.mdp and npt.mdp files

[Mark Abraham]

Hi,

See http://www.gromacs.org/Documentation/How-tos/Position_Restraints. And
do manage the spelling of the abbreviation correctly!

Mark

On Mon, 4 Sep 2017 06:27 Dilip H N  wrote:

> Hello,
> I am running a peptide simulation, i have done an energy minimization , now
> going to do nvt/npt simulation...
> My doubts are:-
> 1] Why is the position restrained (-DPORSE)in the nvt/npt mdp files..??
> 2] If i remove the -DPORSE than i can see the molecules moving , but with
> option -DPORSE, the molecules have restricted movement...
> So, Doesn't it affect the Dynamics of the system..?? Is there any
> consequences of it..??
> What is the significance of keeping the -DPORSE option..??
>
> Any suggestions..?? or references from where i can get knowledge about
> it...
>
> Thank you...
>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
>  Sent with Mailtrack
> <
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