[gmx-users] re-weight Metadynamics trajectory from Plumed to make it canonical ensemble

[Christian Bope Domilongo]

Dear All,

I have run my Metadynamics simulation perfectly using plumed. I have check
in the tutorial and website to find if it is possible to reweigh my meta
trajectory as a function of FES and obtain a average trajectory which is a
canonical ensemble. Because the trajectory  obtained  from plumed is not a
Boltzmann distribution.

I have also us*e do *
HISTOGRAM

http://plumed.github.io/doc-master/user-doc/html/_h_i_s_t_o_g_r_a_m.html


with the REWEIGHT_BIAS option.


Regards,
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Re: [gmx-users] How to fix miising atoms in a pdb file?

[Tsjerk Wassenaar]

Hi,

If you install modeller, you can also use this simple python script to fix
side chains:

###

#!/usr/bin/env python

import sys
import modeller
import modeller.scripts

env = modeller.environ()
env.io.atom_files_directory = ['../atom_files']
env.libs.topology.read(file='$(LIB)/top_heav.lib')
env.libs.parameters.read(file='$(LIB)/par.lib')

modeller.scripts.complete_pdb(env,sys.argv[1]).write(sys.stdout)

##

Use as

./fix.py in.pdb > fixed.pdb


Hope it helps,

Tsjerk

On Wed, Jan 13, 2016 at 8:26 AM, Simone Bolognini 
wrote:

> For what I know, if you open the pdb file with SPDBV il will automatically
> fix the missing atoms. Then you should only take care of saving the new
> structure in a new pdb and you're done!
>
> Simone
> Il 13/gen/2016 08:13, "Seera Suryanarayana"  ha
> scritto:
>
> > Dear gromacs users,
> >
> > I have one pdb file which does not have one atom and I need to be fixed
> > that atom in the pdb to run MD simulations. Kindly suggest me to how to
> fix
> > it. Can I mutate the residue of my interest with the same residue by
> using
> > pymol or SPDBV to fix the missing atoms?
> >
> > Thanks in Advance
> > Surya
> > Graduate student
> > India.
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Re: [gmx-users] Installation of two versions of Gromacs on one system

[Szilárd Páll]

Install into two different location on your machine and source the GMXRC
script to get the right GROMACS version into your path. (
http://www.gromacs.org/Documentation/Installation_Instructions_4.6#4.11._Getting_access_to_GROMACS_after_installation
)

--
Szilárd

On Wed, Jan 13, 2016 at 8:56 AM, Indu Kumari 
wrote:

> Good afternoon sir/ma'am,
>
> I am using Gromacs-4.6.5 on my system (Ubuntu14.04LTS). I want to install
> Gromacs-4.5.6 on the same system. I have tried to install it as tutorial
> available on Gromcas site, but after sudo make install command, when I
> tried to run commands:
> g_rms_mod
>
> It give error: command not found.
>
> All the commands are there in the "build" directory, but they are not
> recognised.
>
> Please help.
>
>
> With regards,
> *Indu Kumari*
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[gmx-users] query on umbrella sampling of association of two plates

[Jagannath Mondal]

Dear Gromacs users

  I wanted to calculate PMF of association of two graphene plates using
umbrella sampling simulations. However, my concern is how we can maintain
the planer configuration of two plates along xy-planes while performing the
umbrella sampling along the separation along z direction. Does one need to
use any special restraint in gromacs ?

Thanks

jagannath
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Re: [gmx-users] Pull constrain makes simulation unstable

[Michail Palaiokostas Avramidis]

On 11/01/16 21:48, Justin Lemkul wrote:
>
>
> On 1/11/16 3:39 PM, Michail Palaiokostas Avramidis wrote:
>> Dear GMX users,
>>
>>
>> I am currently facing some stability issues when using the com
>> pulling to constrain the distance between two groups and I would
>> appreciate any help on the issue.
>>
>>
>> I am trying to simulate a lipid bilayer with a small molecule
>> introduced at several positions along the z-axis where I constrain
>> its z-movement but I allow the xy movement (z-constrain method). My
>> simulation protocol is:
>>
>>
>> 1) Run the lipid membrane with explicit water in a proper NPT
>> simulation until all properties converge
>>
>>
>> 2) Take the equilibrated gro file and by using VMD place the small
>> molecule in several different positions along the z-axis (from water
>> to bilayer core) of the bilayer (for each position I create a new gro
>> file)
>>
>>
>> 3) Then for each new gro file - position:
>>
>> 3.1) Run an energy minimization to relax any overlapping between the
>> old system and the new molecule.
>>
>> 3.2) Run the production simulation with the new molecule constrained
>> at a constant distance from the bilayer core
>>
>>
>> The problem is that I encounter inconsistent stability issues such as
>> "Water molecule xxx cannot be settled" and "LINCS WARNING
>> relative constraint deviation after LINCS ". The errors arise at
>> random positions and random setups (different molecule-membrane
>> combinations) and I cannot really identify a pattern. In all cases
>> however, the problem is not located on or around the newly introduced
>> molecule (as I would expect), but in irrelevant molecules that
>> previously worked fine.
>>
>>
>> So far I have tried:
>>
>> 1) Unconstrained simulations which run fine and indicate that the
>> system is stable on its own.
>>
>> 2) Add an extra step after 3.1 where I remove the constrain option
>> and I add a position restrain in the new molecule. Run for 1 ps to
>> basically let the system initiate. This always works flawlessly.
>> However, when I restart after the 1 ps with the COM pull constrain
>> activated and the restrain removed, the system shows me some or all
>> of the aforementioned errors.
>>
>>
>> Do you have any idea, what might be wrong? Are you aware of any
>> problems with the constrain algorithm?
>>
>>
>> The COM Pulling options I am using are:
>> pull = yes
>> pull-print-com1 = yes
>> pull-print-com2 = yes
>> pull-nstxout = 500
>> pull-nstfout = 500
>> pull-ngroups = 2
>> pull-ncoords  = 1
>> pull-group1-name = Permeant
>> pull-group2-name = Lipid
>> pull-coord1-type = constraint
>> pull-coord1-geometry = distance
>> pull-coord1-groups = 1 2
>> pull-coord1-dim = N N Y
>> pull-coord1-init = 0.01
>>
>>
>> I am sorry for the long e-mail and thank you in advance for any help
>> you can give me.
>>
>
> Your pull settings specify pull-coord1-init = 0.01, which indicates
> that the constraint distance is to be 0.01 nm separation from the
> bilayer ("Lipid" group).  This likely triggers an immediate crash
> because the constraint length at t=0 is much larger.  Remember that
> the constraint is rigid.  Probably what you want in the case of
> multiple locations along the reaction coordinate is:
>
> pull-coord1-start = yes; use starting coordinates to define length
> pull-coord1-init = 0.0
>

Hi Justin,

thanks a lot for your answer. Actually, the problem was on the
definition of the groups. I created the indexes from the PDB but until I
reached the after minimization gro, the atom numbers completely changed,
creating in that way huge distances that obviously crashed. Took some
time to discover this detail.

Also, I had misunderstood how the above commands worked. I believe that
the documentation  needs a bit more explanation or at least some
examples, but anyway, thanks once again for your time and excellent
tutorials.

Best Regards,
Michail

> My tutorial may be helpful in explaining these settings:
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html
>
>
> -Justin
>

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[gmx-users] AMBER99SB and gaff X OS P X dihedral parameters

[tarak karmakar]

Dear All,
I have a confusion related to two dihedral parameters that are present in
ffbonded.itp file,
 X   OH  P   X 9   0.0  1.04600 3  ; JCC,7,(1986),230
 X   OS  P   X 9   0.0  1.04600 3  ; JCC,7,(1986),230

the similar dihedral parameters from parm99SBgaff.dat (GAFF) file,
X -oh-p5-X31.600 0.000   3.000
X -os-p5-X32.400 0.000   2.000

As you see, there is a mismatch between the periodicity (last column) of
the similar dihedral angle from AMBER99SB and gaff databases.

Would anybody like to comment on this?

I am currently simulating a protonated pyrophosphate ligand molecule in a
protein. During the heating step in NVT ensemble (within 150-200 ps, 200 K
temp), the atoms present in the phosphate groups (P,O and H) are showing
bizarre bonds and angles. I tried with the higher force constants (10 times
than the existing one) for the above mentioned dihedral angles, and then
the molecule was behaving fine.

Has anybody experienced this type of issue?
I appreciate any suggestions.

Regards,
Tarak
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Re: [gmx-users] Non-Integral Charges

[Justin Lemkul]

On 1/13/16 7:03 AM, sun wrote:

I am sorry i cudn't understand your question. After topology preparation and a 
few steps, i observe this note that system charge is non-integral. NVT and NPT 
run smoothly but final mdrun crashes. I have changed terminus from NH2,COOH to 
zwitterionic options but this reduced the charge from -5.0 to -4.9 only. I jave 
charged residues like Lys,Asp,Glu etc. Can you suggest something? Shall I add 
Na+ ions to my system? Actually i am a beginner. Would that affect my 
simulation?


Zwitterionic termini are for specific cases of single amino acids.  Reducing the 
charge from -5.0 to -4.9 is actually totally unphysical and even more wrong than 
what you were doing before.


Please do some simple tutorials; considerations like this are routine.

-Justin


Regards
Suniba

Sent from my iPhone


On 13-Jan-2016, at 3:03 am, "VITALY V. CHABAN"  wrote:

What is the charge of your infinite periodic system if your unit cell
charge is 5e?





On Tue, Jan 12, 2016 at 11:54 AM, sun  wrote:

Hello Everyone
I want to know how to change the non-integral charges? I am simulating a
pentameric model of protein in water and the net charge comes out to be
-5.0. Everything goes ok till final mdrun. As soon as its started, it
carshes. Is it dus to wring topology as the charges are non-integral?
Please reply
Suniba

Sent from my iPhone
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--
==

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

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

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

==
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Re: [gmx-users] re-weight Metadynamics trajectory from Plumed to make it canonical ensemble

[luigi]

Hi Christian,

It is not so clear why do you want to have a "reweighted trajectory", in
which you will likely lose all the maxima explored. However, if you want
to extract the frames, e.g. related to a MEP, for, e.g. a nice movie,
you could efficiently
1. evaluate the CVs values to extract analyzing the FES (and in case
chose the number of frames for each value proportionally to the free
energy of the system at those specific CVs),
2. select the frames based on the COLVAR files created by plumed and
eventually
3 extract those frames from the TRR trajectory files.

If you work in python I would suggest you to take a look at MDtraj
library for extracting the frames.

Cheers,
Luigi

On 13/01/16 12:23, Christian Bope Domilongo wrote:
> Dear All,
>
> I have run my Metadynamics simulation perfectly using plumed. I have check
> in the tutorial and website to find if it is possible to reweigh my meta
> trajectory as a function of FES and obtain a average trajectory which is a
> canonical ensemble. Because the trajectory  obtained  from plumed is not a
> Boltzmann distribution.
>
> I have also us*e do *
> HISTOGRAM
>
> http://plumed.github.io/doc-master/user-doc/html/_h_i_s_t_o_g_r_a_m.html
> 
>
> with the REWEIGHT_BIAS option.
>
>
> Regards,
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Re: [gmx-users] re-weight Metadynamics trajectory from Plumed to make it canonical ensemble

[Christian Bope Domilongo]

Thank you Luiji,



On 13 January 2016 at 20:51, luigi  wrote:

> Hi Christian,
>
> It is not so clear why do you want to have a "reweighted trajectory", in
> which you will likely lose all the maxima explored.


In other word I want to get average trajectory canonical ensemble. The main
objective  to run g_covar, obtain the modes (eigenvalue and eigenvec) of my
metadynamics trajectory and compare it with NMA. The  challenge is I can
not compare directly because the trajectory  obtained  from plumed is not a
Boltzmann distribution that why I need to re-weight it first.


> However, if you want
> to extract the frames, e.g. related to a MEP, for, e.g. a nice movie,
> you could efficiently
> 1. evaluate the CVs values to extract analyzing the FES (and in case
> chose the number of frames for each value proportionally to the free
> energy of the system at those specific CVs),
> 2. select the frames based on the COLVAR files created by plumed and
> eventually
> 3 extract those frames from the TRR trajectory files.
>
> If you work in python I would suggest you to take a look at MDtraj
> library for extracting the frames.
>
> Cheers,
> Luigi
>
> On 13/01/16 12:23, Christian Bope Domilongo wrote:
> > Dear All,
> >
> > I have run my Metadynamics simulation perfectly using plumed. I have
> check
> > in the tutorial and website to find if it is possible to reweigh my meta
> > trajectory as a function of FES and obtain a average trajectory which is
> a
> > canonical ensemble. Because the trajectory  obtained  from plumed is not
> a
> > Boltzmann distribution.
> >
> > I have also us*e do *
> > HISTOGRAM
> >
> > http://plumed.github.io/doc-master/user-doc/html/_h_i_s_t_o_g_r_a_m.html
> > <
> http://www.google.com/url?q=http%3A%2F%2Fplumed.github.io%2Fdoc-master%2Fuser-doc%2Fhtml%2F_h_i_s_t_o_g_r_a_m.html=D=1=AFQjCNHvsK_WNA5VLHnvOijB6GKSrVOz7w
> >
> >
> > with the REWEIGHT_BIAS option.
> >
> >
> > Regards,
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>



-- 
Bope Domilongo Christian
Ph.D candidate in Computational Biology
Division of Structural Biology and Biochemistry
School of Biological Sciences
Nanyang Technological University
Singapore
+6590565804
http://www.ntu.edu.sg/
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[gmx-users] Help for gmx enemat

[valerio di giulio]

Hi,

I have a problem with the use of "gmx enemat". I'm trying to calculate
the contribution of SH-LJ to the potential that exists between two DNA
strands with GROMACS 5.1.1. I've already got a Potential of Mean Force
doing an umbrella sampling.
For this reason I have already many files .edr each one linked to a window,
from
which I would like to extract the SH-LJ contribution but every time I use
"enemat" this is the output:

..

GROMACS:  gmx enemat, VERSION 5.1.1
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Command line:
  gmx enemat umbrella1e.edr -ljsr

Opened ener.edr as single precision energy file
Will read groupnames from inputfile
Read 2 groups
group 0WARNING! could not find group Coul-SR:DNA1-DNA1 (0,0)in energy file
WARNING! could not find group LJ-SR:DNA1-DNA1 (0,0)in energy file
WARNING! could not find group Coul-SR:DNA1-DNA2 (0,1)in energy file
WARNING! could not find group LJ-SR:DNA1-DNA2 (0,1)in energy file
group 1WARNING! could not find group Coul-SR:DNA2-DNA2 (1,1)in energy file
WARNING! could not find group LJ-SR:DNA2-DNA2 (1,1)in energy file

Will select half-matrix of energies with 0 elements
Last energy frame read 500 time  500.000
Will build energy half-matrix of 2 groups, 0 elements, over 501 frames
Segmentation fault (core dumped)

...

Although I have written to the .mdp file:

energygrps = DNA1 DNA2

Thank you in advance,

Valerio Di Giulio
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Re: [gmx-users] Encountered with error after executing the command "gmx solvate"

[Mark Abraham]

Hi,

Please see the reference manual for discussion of the minimum image
convention.

Otherwise, your report sounds like a bug in gmx solvate. Please open an
issue at redmine.gromacs.org and attach a tarball of files that reproduce
the issue.

Mark

On Wed, 13 Jan 2016 13:15 Seera Suryanarayana  wrote:

> Dear gromacs users,
>
> I have been trying to simulate the xtal structure which is homo tetramer
> and each chain has more than 400 amino acids. after editconf where I have
> used the cubic box with -c -d 1.0. After this command I have executed the
> following command..
>
> gmx solvate -cp 4pv1.gro -cs spc216.gro -o 4cp1_solv.gro -p topal.top
>
> and I got the error as ..
>
> Fatal error:
> One of the box vectors has become shorter than twice the cut-off length or
> box_yy-|box_zy| or box_zz has become smaller than the cut-off.
>
> When I checked the gromacs archive somewhere mentioned that violating
> minimum image convention. I don't understand what does it mean. Kindly tell
> me why this error is encountered and how do I resolve it?
>
> Thanks in advance
> Surya
> Graduate student
> India.
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[gmx-users] Why GROMACS is generating so many output trajectory files?

[Swapnil Wagle]

Hi..!

I am having a system with 450 Protein atoms and ~9000 water atoms. When I am 
trying to do the energy minimization step, it gives me hundreds of trajectory 
files (all .pdb with names like Step**_**.pdb). I am using gromos 53a6 force 
field with TIP4P water model. The error message also says something like (one 
atom moved too far during the domain decomposition steps) which is not quite 
visible when I load the initial structure in VMD. The simulation completes 
sometimes but sometimes it also stops in the middle. Can you suggest me what 
can possibly be wrong, or any suggestion about how to remove this error?

Regards,
Swapnil Wagle
Department of Theory and Bio Systems
Max Planck Institute for Colloids and Interfaces
Potsdam-Golm, Germany D-14424
Tel.: +49-331 567-9607
Mail: swapnil.wa...@mpikg.mpg.de
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Re: [gmx-users] Help for gmx enemat

[Peter Stern]

I believe that you need to define which nucleotides are in each group DNA1 and 
DNA2 using make_ndx, since those are not "default" groups.  I think that you 
can do this and then do an Metin -rerun just to define the new groups.

Peter

Sent from my iPad

> On 13 בינו׳ 2016, at 20:53, valerio di giulio  
> wrote:
> 
> Hi,
> 
> I have a problem with the use of "gmx enemat". I'm trying to calculate
> the contribution of SH-LJ to the potential that exists between two DNA
> strands with GROMACS 5.1.1. I've already got a Potential of Mean Force
> doing an umbrella sampling.
> For this reason I have already many files .edr each one linked to a window,
> from
> which I would like to extract the SH-LJ contribution but every time I use
> "enemat" this is the output:
> 
> ..
> 
> GROMACS:  gmx enemat, VERSION 5.1.1
> Executable:   /usr/local/gromacs/bin/gmx
> Data prefix:  /usr/local/gromacs
> Command line:
>  gmx enemat umbrella1e.edr -ljsr
> 
> Opened ener.edr as single precision energy file
> Will read groupnames from inputfile
> Read 2 groups
> group 0WARNING! could not find group Coul-SR:DNA1-DNA1 (0,0)in energy file
> WARNING! could not find group LJ-SR:DNA1-DNA1 (0,0)in energy file
> WARNING! could not find group Coul-SR:DNA1-DNA2 (0,1)in energy file
> WARNING! could not find group LJ-SR:DNA1-DNA2 (0,1)in energy file
> group 1WARNING! could not find group Coul-SR:DNA2-DNA2 (1,1)in energy file
> WARNING! could not find group LJ-SR:DNA2-DNA2 (1,1)in energy file
> 
> Will select half-matrix of energies with 0 elements
> Last energy frame read 500 time  500.000
> Will build energy half-matrix of 2 groups, 0 elements, over 501 frames
> Segmentation fault (core dumped)
> 
> ...
> 
> Although I have written to the .mdp file:
> 
> energygrps = DNA1 DNA2
> 
> Thank you in advance,
> 
> Valerio Di Giulio
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Re: [gmx-users] pdb2gmx, chain and segment names in the output pdb

[Mark Abraham]

Hi,

Unfortunately, pdb2gmx is only aware of chain ids, so you will not be able
to preserve segment id. If the atom ordering is unchanged then you don't
need the resulting PDB file, ie can use the original one. If not, then it's
straightforward to use some scripting tool to re-unite your segment id with
the output PDB.

Mark

On Wed, 13 Jan 2016 17:52 Maxim Igaev  wrote:

> Dear Gromacs users,
>
> I have a large molecular complex consisting of many identical monomers.
> I constructed a pdb file for it using VMD and assigned each monomer
> a segment name (A0, A1, A2 etc.). The chain name was however always
> the same - A. Then I created the topology for it using pdb2gmx.
>
> In the output pdb file, however, all segment names have disappeared
> and the chain names have changed - instead of A for each monomer, I
> now have A, B, C, D etc for the first ~20 monomers and then simply
> nothing for the rest of the monomers.
>
> Is there a way to make pdb2gmx preserve segment/chain names while
> creating a topology file?
>
> I need my initial naming since I want to postprocess my trajectories
> in VMD again.
>
> Thanks a lot in advance!
>
> Cheers,
> Maxim
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Re: [gmx-users] Help for gmx enemat

[valerio di giulio]

Hi Peter,

I have already created  an index file with make_ndx in which I specify
what atoms are in DNA1 and DNA2 groups. Moreover the two groups
are present in the file topol.top. Indeed GROMACS doesn't produce any
error about the declaration of them in the file .mdp. I send you also my
topol.top file
for clarity:
.

; GROMACS topology
;
; Include the force field
#include "/amber03.ff/forcefield.itp"

; Include chain topologies
#include "topol1.itp"
#include "topol2.itp"

; Include water topology
#include "amber03.ff/tip4p.itp"

; Include generic ion topology
#include "amber03.ff/ions.itp"

[ system ]
Two all-AT in water

[ molecules ]
DNA11
DNA21
SOL 39390
NA   190
CL   146

.

Thanks,

Valerio

2016-01-13 20:40 GMT+01:00 Peter Stern :

> I believe that you need to define which nucleotides are in each group DNA1
> and DNA2 using make_ndx, since those are not "default" groups.  I think
> that you can do this and then do an Metin -rerun just to define the new
> groups.
>
> Peter
>
> Sent from my iPad
>
> > On 13 בינו׳ 2016, at 20:53, valerio di giulio 
> wrote:
> >
> > Hi,
> >
> > I have a problem with the use of "gmx enemat". I'm trying to calculate
> > the contribution of SH-LJ to the potential that exists between two DNA
> > strands with GROMACS 5.1.1. I've already got a Potential of Mean Force
> > doing an umbrella sampling.
> > For this reason I have already many files .edr each one linked to a
> window,
> > from
> > which I would like to extract the SH-LJ contribution but every time I use
> > "enemat" this is the output:
> >
> > ..
> >
> > GROMACS:  gmx enemat, VERSION 5.1.1
> > Executable:   /usr/local/gromacs/bin/gmx
> > Data prefix:  /usr/local/gromacs
> > Command line:
> >  gmx enemat umbrella1e.edr -ljsr
> >
> > Opened ener.edr as single precision energy file
> > Will read groupnames from inputfile
> > Read 2 groups
> > group 0WARNING! could not find group Coul-SR:DNA1-DNA1 (0,0)in energy
> file
> > WARNING! could not find group LJ-SR:DNA1-DNA1 (0,0)in energy file
> > WARNING! could not find group Coul-SR:DNA1-DNA2 (0,1)in energy file
> > WARNING! could not find group LJ-SR:DNA1-DNA2 (0,1)in energy file
> > group 1WARNING! could not find group Coul-SR:DNA2-DNA2 (1,1)in energy
> file
> > WARNING! could not find group LJ-SR:DNA2-DNA2 (1,1)in energy file
> >
> > Will select half-matrix of energies with 0 elements
> > Last energy frame read 500 time  500.000
> > Will build energy half-matrix of 2 groups, 0 elements, over 501 frames
> > Segmentation fault (core dumped)
> >
> > ...
> >
> > Although I have written to the .mdp file:
> >
> > energygrps = DNA1 DNA2
> >
> > Thank you in advance,
> >
> > Valerio Di Giulio
> > --
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Re: [gmx-users] Why GROMACS is generating so many output trajectory files?

[Elton Carvalho]

Hello, Swapnil,

This usually means you have a problem with your topology and your
system may be in the verge of blowing up. If the simulation stops in
the middle, your system blew up.

Please read http://www.gromacs.org/Documentation/Terminology/Blowing_Up

Regards form an unusually cloudy Natal.

On Wed, Jan 13, 2016 at 3:30 PM, Swapnil Wagle
 wrote:
> Hi..!
>
> I am having a system with 450 Protein atoms and ~9000 water atoms. When I am 
> trying to do the energy minimization step, it gives me hundreds of trajectory 
> files (all .pdb with names like Step**_**.pdb). I am using gromos 53a6 force 
> field with TIP4P water model. The error message also says something like (one 
> atom moved too far during the domain decomposition steps) which is not quite 
> visible when I load the initial structure in VMD. The simulation completes 
> sometimes but sometimes it also stops in the middle. Can you suggest me what 
> can possibly be wrong, or any suggestion about how to remove this error?
>
> Regards,
> Swapnil Wagle
> Department of Theory and Bio Systems
> Max Planck Institute for Colloids and Interfaces
> Potsdam-Golm, Germany D-14424
> Tel.: +49-331 567-9607
> Mail: swapnil.wa...@mpikg.mpg.de
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Re: [gmx-users] problem with do_dssp

[Mark Abraham]

Hi,

If you have a working dssp and the correct environment variable that points
at it, things should work. Chances are you aren't doing something you think
you are doing, but with the available information, we can't tell what.

Mark

On Wed, 13 Jan 2016 15:35 Chiara Bello  wrote:

> Dear gromacs users,
>
> I am using gromacs 5.1.1 version and I have tried to perform secondary
> structure analysis using do_dssp, but I obtained a fatal error showing use
> -ver option . Even when I tried to use -ver 2 in the command line the same
> error appeared.
>
> I had this problem with both the 2.2.0 and 2.2.1 dssp versions. Note that
> in each cases I set an environment variable DSSP pointing to the dssp
> executable.
>
> Moreover I tried running dssp directly and it it run properly but I'd
> prefer to run it using gromacs to obtain the output in xpm format. How
> should I do?
>
> Regards,
>
> Chiara
>
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[gmx-users] necessary input files during simulation

[mah maz]

Dear users,

I deleted my input files(.gro,.mdp,.top,.ndx..) before the simulation is
over by mistake. However, it is still running. Which files should be
present to the end of a run?

Thank you.
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Re: [gmx-users] necessary input files during simulation

[Tsjerk Wassenaar]

Hi Mah Maz,

The run has everything it needs in memory. It writes .xtc/.tng/.trr .log
.edr and .cpt files as it goes.

Hope it helps,

Tsjerk

On Thu, Jan 14, 2016, 08:16 mah maz  wrote:

> Dear users,
>
> I deleted my input files(.gro,.mdp,.top,.ndx..) before the simulation is
> over by mistake. However, it is still running. Which files should be
> present to the end of a run?
>
> Thank you.
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[gmx-users] Electric field unit

[mah maz]

Dear users,

What is the electric field unit in gromacs? In the manual it is KJ/mol.nm.e
but in the source code I encountered V/nm which is about 100 times KJ/mol.nm.e.


Thank you.
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Re: [gmx-users] necessary input files during simulation

[mah maz]

Hi Tsjerk,

Thank you very much.


On Thu, Jan 14, 2016 at 10:46 AM, mah maz  wrote:

> Dear users,
>
> I deleted my input files(.gro,.mdp,.top,.ndx..) before the simulation is
> over by mistake. However, it is still running. Which files should be
> present to the end of a run?
>
> Thank you.
>
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Re: [gmx-users] genion with Na or Ca

[Turgay Cakmak]

Thank you for your useful replies.
Turgay

2016-01-12 23:38 GMT+02:00 VITALY V. CHABAN :

> Ca(2+) will block one of your binding sites, if you care.
>
>
>
>
>
> On Tue, Jan 12, 2016 at 6:19 AM, Turgay Cakmak 
> wrote:
>
> > Hi all,
> >
> >
> > I have a quick question about neutralizing the system. I have a solvated
> > system that contains a charged protein of -2q. Is there a major
> difference
> > betwen adding 2 Na ions and a single  Ca ion to neutralize the system
> > (using genion)?
> >
> >
> > Thanks in advance,
> >
> > Turgay
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Re: [gmx-users] re-weight Metadynamics trajectory from Plumed to make it canonical ensemble

[Tsjerk Wassenaar]

Hey :)


> I think I will just do PCA (g_covar), reweight the covariance matrix and
> obtain modes
>
>
Reweight the covariance matrix? Out of curiosity, how will you do that?

Cheers,

Tsjerk

>
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Re: [gmx-users] viscosity using green kubo relation for ionic liquids

[Shanmuga]

But in energy file we don't have stress tensor and some how we have to 
calculate stress tensor from pressure tensor. I am wondering how to get stress 
tensor from pressure tensor, in liquid md simulations. 

Regards, 
Shanu 

Sent from my iPhone

> On Jan 13, 2016, at 3:41 PM, David van der Spoel  wrote:
> 
>> On 13/01/16 18:11, Shanmuga wrote:
>> Hi all,
>> 
>> I am comparing viscosity calculation with eq md and non eq md. I want to 
>> calculate viscosity in eq md with green kubo equation. Can anyone suggest me 
>> how to get stress tensor from pressure tensor and its auto correction plot.
>> 
> Still gmx energy. Check all the options.
>> Thanks in advance.
>> 
>> Regards,
>> Shanu
>> 
>>> On Jan 12, 2016, at 3:35 PM, VITALY V. CHABAN  wrote:
>>> 
>>> EqMD methods work poorly for highly and moderate viscous liquids.
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> On Tue, Jan 12, 2016 at 5:19 PM, shanmuga sundaram 
>>> wrote:
>>> 
 I tried with g_energy -vis , but it calculates using einstein relation. I
 want to calculate using green kubo equation.
 
 
 regards,
 
 shanu
 
 On Tue, Jan 12, 2016 at 12:42 AM, David van der Spoel <
 sp...@xray.bmc.uu.se>
 wrote:
 
>> On 11/01/16 22:54, shanmuga sundaram wrote:
>> 
>> Hello all,
>> 
>> 
>> I am trying to find viscosity using green kubo relation for Ionic
 Liquids.
>> I got pressure tensor values (pxx, pyy, pzz, ….) from energy file .edr.
>> How
>> to get stress autocorrelation function (SACF) from pressure
>> autocorrelation
>> function in MD simulations? Also how to change ACF windows (10, 50,
 200ps)
>> in getting autocorrelation function from gromacs (usually from g_analyze
>> tool)?
>> 
>> try
> g_energy -vis
> 
> 
>> regards,
>> 
>> shanu
> 
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
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> 
> -- 
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> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205.
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Re: [gmx-users] viscosity using green kubo relation for ionic liquids

[David van der Spoel]

On 13/01/16 18:11, Shanmuga wrote:

Hi all,

I am comparing viscosity calculation with eq md and non eq md. I want to 
calculate viscosity in eq md with green kubo equation. Can anyone suggest me 
how to get stress tensor from pressure tensor and its auto correction plot.


Still gmx energy. Check all the options.

Thanks in advance.

Regards,
Shanu


On Jan 12, 2016, at 3:35 PM, VITALY V. CHABAN  wrote:

EqMD methods work poorly for highly and moderate viscous liquids.






On Tue, Jan 12, 2016 at 5:19 PM, shanmuga sundaram 
wrote:


I tried with g_energy -vis , but it calculates using einstein relation. I
want to calculate using green kubo equation.


regards,

shanu

On Tue, Jan 12, 2016 at 12:42 AM, David van der Spoel <
sp...@xray.bmc.uu.se>
wrote:


On 11/01/16 22:54, shanmuga sundaram wrote:

Hello all,


I am trying to find viscosity using green kubo relation for Ionic

Liquids.

I got pressure tensor values (pxx, pyy, pzz, ….) from energy file .edr.
How
to get stress autocorrelation function (SACF) from pressure
autocorrelation
function in MD simulations? Also how to change ACF windows (10, 50,

200ps)

in getting autocorrelation function from gromacs (usually from g_analyze
tool)?

try

g_energy -vis



regards,

shanu


--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] membed in mdrun VERSION 5.0.4

[Mark Abraham]

Hi,

You're right that mdrun -membed is only implemented for one rank - there's
a fatal error message that you doubtless have already seen.

On Sat, Jan 9, 2016 at 5:32 PM Nash, Anthony  wrote:

> My apologies that this hasn’t made it into one large message. I would like
> to add two further points. It appears as though mdrun (serial) does not
> output a .cpt file when -membed is specified. I just ran out of clock
> time, and the check point file is just not there.
>

Yeah, there's a message printed to stderr that this is deliberate, because
restart is not supported either.

Also, in response to your earlier comment about using gmx convert-tpr,
> -membed appears to remove some lipids and solvent molecules but it won’t
> tell you which ones until you have the final .gro file. Therefore, I don’t
> believe I can make a .ndx to use with gmx-convert-tpr.
>

It doesn't matter which molecules from a set of identical ones are removed,
so long as the atom ordering of the resulting system is the same.

Mark


> Thanks
> Anthony
>
> On 09/01/2016 09:28, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on
> behalf of Nash, Anthony"
>  a.n...@ucl.ac.uk> wrote:
>
> >Hi,
> >Just to add to my earlier message, I went through all release notes after
> >5.0.4, and besides a change in membed documentation, I can’t see a
> >reference to a parallelized version of mdrun -membed.
> >
> >
> >Thanks
> >Anthony
> >
> >On 08/01/2016 23:36, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> on
> >behalf of Nash, Anthony"
> > >a.n...@ucl.ac.uk> wrote:
> >
> >>Justin and Mark, many thanks for your help.
> >>
> >>With regards to the parallelization, when did parallel membed become
> >>supported? I¹ve just tried on 5.0.4 and I¹m getting the response:
> >>
> >>Reading file membed_NPT_B.tpr, VERSION 5.0.4 (double precision)
> >>
> >>---
> >>Program mdrun_mpi_d, VERSION 5.0.4
> >>Source code file:
> >>/dev/shm/tmp.3LEFQsSzrx/gromacs-5.0.4/src/programs/mdrun/membed.c, line:
> >>1056
> >>
> >>
> >>Input error or input inconsistency:
> >>Sorry, parallel g_membed is not yet fully functional.
> >>For more information and tips for troubleshooting, please check the
> >>GROMACS
> >>website at http://www.gromacs.org/Documentation/Errors
> >>---
> >>
> >>Error on rank 0, will try to stop all ranks
> >>Halting parallel program mdrun_mpi_d on CPU 0 out of 2
> >>
> >>
> >>
> >>Oh course, I understand this could be answered by installing the latest
> >>version, but I¹m ruling out anything I¹ve done wrong before asking
> >>central
> >>IT to put up a test module.
> >>
> >>Thanks for the help
> >>Anthony
> >>
> >>
> >>
> >>
> >>
> >>On 08/01/2016 13:24, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> >>on
> >>behalf of Mark Abraham"
> >> >>on behalf of mark.j.abra...@gmail.com> wrote:
> >>
> >>>Hi,
> >>>
> >>>The current implementation of membed is quite sane and should support
> >>>all
> >>>kinds of parallelization. (It is difficult to say much that is nice
> >>>about
> >>>the first implementation, though!)
> >>>
> >>>gmx trjconv and convert-tpr are good for making subsets from well chosen
> >>>index groups.
> >>>
> >>>Mark
> >>>
> >>>On Fri, 8 Jan 2016 13:35 Justin Lemkul  wrote:
> >>>
> 
> 
>  On 1/8/16 3:38 AM, Nash, Anthony wrote:
>  > Many thanks Justin, that¹s solved it.
>  >
>  > The simulation is now running, reporting that 8 POPC molecules and
> 12
> SOL
>  > molecules have been removed. However, I have a bit of a problem. I
> don¹t
>  > seem to be able to get the -membed option working on a parallel
>  > installation of gromacs, only serial. I assume parallel isn¹t
> supported?
>  >
> 
>  No idea, but the -membed incorporation into mdrun is currently a very
> big
>  hack
>  to make it work, so you should expect limited support for features.
> 
>  > Secondly, with my .tpr file very different from my running .trr (due
> to
>  > removed molecules), I don¹t know of a way of pulling out a single
> frame
>  > from the trajectory to see how the simulation is progressing. (I
> would
>  > have just taken the first frame as a .gro, downloaded the latest
> .trr,
>  and
>  > thrown them both into VMD). Any thoughts?
>  >
> 
>  Does the program report which residues were removed?  If so, you can
> just
>  remove
>  those from the coordinate file you had before.  Otherwise, no,
> probably
>  not.
>  Like I said, big hack to get it working in the present version.
> 
>  -Justin
> 
>  --
>  ==
> 
>  Justin A. 

Re: [gmx-users] re-weight Metadynamics trajectory from Plumed to make it canonical ensemble

[Christian Bope Domilongo]

On 13 January 2016 at 22:22, luigi  wrote:

> Hi,
>
> if your aim if to find out other conformational changes correlated to
> your CVs,
> you don't really need any reweighting of your trajectory: do a PCA on
> your trajectory and compare the projection of the frames with CV values
> of interest (according to your FES) on the new essential space.
>

I think I will just do PCA (g_covar), reweight the covariance matrix and
obtain modes


>
> If you well sampled your conformational space during the metadynamics
> you should probably discard the part in which the non-diffusive regime
> is reached: this would allow you to have a non-biased description of the
> possible conformational space along your CVs (no over-representation of
> the energy wells).


Technically, MDtraj can do that?


> You could also try to remove some noise and filter
> out frames with CV corresponding to high energietic conformations
> (keeping only relevant part of the FES).
> Then evaluate the projections of the frames with CVs of interest in the
> essential space obtained.
>
> How to do that technically.


> You should be able to obtain a fine description of what
> (conformationally) happen outside your explicitly defined collective
> variables.
>
> Cheers,
> Luigi
>
>
> On 13/01/16 14:09, Christian Bope Domilongo wrote:
> > Thank you Luiji,
> >
> >
> >
> > On 13 January 2016 at 20:51, luigi  wrote:
> >
> >> Hi Christian,
> >>
> >> It is not so clear why do you want to have a "reweighted trajectory", in
> >> which you will likely lose all the maxima explored.
> >
> > In other word I want to get average trajectory canonical ensemble. The
> main
> > objective  to run g_covar, obtain the modes (eigenvalue and eigenvec) of
> my
> > metadynamics trajectory and compare it with NMA. The  challenge is I can
> > not compare directly because the trajectory  obtained  from plumed is
> not a
> > Boltzmann distribution that why I need to re-weight it first.
> >
> >
> >> However, if you want
> >> to extract the frames, e.g. related to a MEP, for, e.g. a nice movie,
> >> you could efficiently
> >> 1. evaluate the CVs values to extract analyzing the FES (and in case
> >> chose the number of frames for each value proportionally to the free
> >> energy of the system at those specific CVs),
> >> 2. select the frames based on the COLVAR files created by plumed and
> >> eventually
> >> 3 extract those frames from the TRR trajectory files.
> >>
> >> If you work in python I would suggest you to take a look at MDtraj
> >> library for extracting the frames.
> >>
> >> Cheers,
> >> Luigi
> >>
> >> On 13/01/16 12:23, Christian Bope Domilongo wrote:
> >>> Dear All,
> >>>
> >>> I have run my Metadynamics simulation perfectly using plumed. I have
> >> check
> >>> in the tutorial and website to find if it is possible to reweigh my
> meta
> >>> trajectory as a function of FES and obtain a average trajectory which
> is
> >> a
> >>> canonical ensemble. Because the trajectory  obtained  from plumed is
> not
> >> a
> >>> Boltzmann distribution.
> >>>
> >>> I have also us*e do *
> >>> HISTOGRAM
> >>>
> >>>
> http://plumed.github.io/doc-master/user-doc/html/_h_i_s_t_o_g_r_a_m.html
> >>> <
> >>
> http://www.google.com/url?q=http%3A%2F%2Fplumed.github.io%2Fdoc-master%2Fuser-doc%2Fhtml%2F_h_i_s_t_o_g_r_a_m.html=D=1=AFQjCNHvsK_WNA5VLHnvOijB6GKSrVOz7w
> >>>
> >>> with the REWEIGHT_BIAS option.
> >>>
> >>>
> >>> Regards,
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
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> >>
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> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> >
> >
>
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-- 
Bope Domilongo Christian
Ph.D candidate in Computational Biology
Division of Structural Biology and Biochemistry
School of Biological Sciences
Nanyang Technological University
Singapore
+6590565804
http://www.ntu.edu.sg/
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[gmx-users] Regarding Umbrella Sampling Analysis Step

[Misa Banno]

Dear Gromacs users,

I've run the umbrella sampling. I could draw histograms with sufficient 
overlap, so I determined all of the simulations reached enough length of 
time. Now it's the analysis step.


When I chose tpr files and pullf.xvg (forces) files as the input to 
wham, I was able to analyze and draw PMF curve previously.


However, I chose tpr files and pullx.xvg (coordinates) files, I couldn't.
The command line is below.


gmx wham -it tpr-files.dat -ix pullx-files.dat  -o -hist -unit kCal -b 5 -e 
20


I got the profile.xvg but all PMF values are zero in that file.

While running gmx wham, I was getting warnings like below.
Warning, poor sampling bin 199 (z=-1.00185). Check your histograms!

I did simulation by using following COM pulling options:
; COM PULLING
pull = umbrella
pull_geometry= cylinder
pull_dim = N N Y
pull_r1  = 2
pull_r0  = 3
pull_constr_tol  = 1e-06
pull_start   = yes
pull_nstxout = 100
pull_nstfout = 100
pull_ngroups = 2
pull-ncoords = 1
pull-group1-name = zpopc
pull-group2-name = Protein
pull-coord1-groups   = 1 2
pull-coord1-origin   = 0 0 0
pull-coord1-vec  = 0 0 -1.0
pull-coord1-init = 0
pull-coord1-rate = 0
pull-coord1-k= 1000
pull-coord1-kB   = 0


Please help me in this regard.

Many Thanks
Misa Banno

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Re: [gmx-users] re-weight Metadynamics trajectory from Plumed to make it canonical ensemble

[luigi]

Hi,

if your aim if to find out other conformational changes correlated to
your CVs,
you don't really need any reweighting of your trajectory: do a PCA on
your trajectory and compare the projection of the frames with CV values
of interest (according to your FES) on the new essential space.

If you well sampled your conformational space during the metadynamics
you should probably discard the part in which the non-diffusive regime
is reached: this would allow you to have a non-biased description of the
possible conformational space along your CVs (no over-representation of
the energy wells). You could also try to remove some noise and filter
out frames with CV corresponding to high energietic conformations
(keeping only relevant part of the FES).
Then evaluate the projections of the frames with CVs of interest in the
essential space obtained.

You should be able to obtain a fine description of what
(conformationally) happen outside your explicitly defined collective
variables.

Cheers,
Luigi


On 13/01/16 14:09, Christian Bope Domilongo wrote:
> Thank you Luiji,
>
>
>
> On 13 January 2016 at 20:51, luigi  wrote:
>
>> Hi Christian,
>>
>> It is not so clear why do you want to have a "reweighted trajectory", in
>> which you will likely lose all the maxima explored.
>
> In other word I want to get average trajectory canonical ensemble. The main
> objective  to run g_covar, obtain the modes (eigenvalue and eigenvec) of my
> metadynamics trajectory and compare it with NMA. The  challenge is I can
> not compare directly because the trajectory  obtained  from plumed is not a
> Boltzmann distribution that why I need to re-weight it first.
>
>
>> However, if you want
>> to extract the frames, e.g. related to a MEP, for, e.g. a nice movie,
>> you could efficiently
>> 1. evaluate the CVs values to extract analyzing the FES (and in case
>> chose the number of frames for each value proportionally to the free
>> energy of the system at those specific CVs),
>> 2. select the frames based on the COLVAR files created by plumed and
>> eventually
>> 3 extract those frames from the TRR trajectory files.
>>
>> If you work in python I would suggest you to take a look at MDtraj
>> library for extracting the frames.
>>
>> Cheers,
>> Luigi
>>
>> On 13/01/16 12:23, Christian Bope Domilongo wrote:
>>> Dear All,
>>>
>>> I have run my Metadynamics simulation perfectly using plumed. I have
>> check
>>> in the tutorial and website to find if it is possible to reweigh my meta
>>> trajectory as a function of FES and obtain a average trajectory which is
>> a
>>> canonical ensemble. Because the trajectory  obtained  from plumed is not
>> a
>>> Boltzmann distribution.
>>>
>>> I have also us*e do *
>>> HISTOGRAM
>>>
>>> http://plumed.github.io/doc-master/user-doc/html/_h_i_s_t_o_g_r_a_m.html
>>> <
>> http://www.google.com/url?q=http%3A%2F%2Fplumed.github.io%2Fdoc-master%2Fuser-doc%2Fhtml%2F_h_i_s_t_o_g_r_a_m.html=D=1=AFQjCNHvsK_WNA5VLHnvOijB6GKSrVOz7w
>>>
>>> with the REWEIGHT_BIAS option.
>>>
>>>
>>> Regards,
>> --
>> 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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[gmx-users] problem with do_dssp

[Chiara Bello]

Dear gromacs users,

I am using gromacs 5.1.1 version and I have tried to perform secondary 
structure analysis using do_dssp, but I obtained a fatal error showing use -ver 
option . Even when I tried to use -ver 2 in the command line the same error 
appeared.

I had this problem with both the 2.2.0 and 2.2.1 dssp versions. Note that in 
each cases I set an environment variable DSSP pointing to the dssp executable.

Moreover I tried running dssp directly and it it run properly but I'd prefer to 
run it using gromacs to obtain the output in xpm format. How should I do?

Regards,

Chiara

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Re: [gmx-users] viscosity using green kubo relation for ionic liquids

[Shanmuga]

Hi all, 

I am comparing viscosity calculation with eq md and non eq md. I want to 
calculate viscosity in eq md with green kubo equation. Can anyone suggest me 
how to get stress tensor from pressure tensor and its auto correction plot. 

Thanks in advance. 

Regards, 
Shanu

> On Jan 12, 2016, at 3:35 PM, VITALY V. CHABAN  wrote:
> 
> EqMD methods work poorly for highly and moderate viscous liquids.
> 
> 
> 
> 
> 
> 
> On Tue, Jan 12, 2016 at 5:19 PM, shanmuga sundaram 
> wrote:
> 
>> I tried with g_energy -vis , but it calculates using einstein relation. I
>> want to calculate using green kubo equation.
>> 
>> 
>> regards,
>> 
>> shanu
>> 
>> On Tue, Jan 12, 2016 at 12:42 AM, David van der Spoel <
>> sp...@xray.bmc.uu.se>
>> wrote:
>> 
 On 11/01/16 22:54, shanmuga sundaram wrote:
 
 Hello all,
 
 
 I am trying to find viscosity using green kubo relation for Ionic
>> Liquids.
 I got pressure tensor values (pxx, pyy, pzz, ….) from energy file .edr.
 How
 to get stress autocorrelation function (SACF) from pressure
 autocorrelation
 function in MD simulations? Also how to change ACF windows (10, 50,
>> 200ps)
 in getting autocorrelation function from gromacs (usually from g_analyze
 tool)?
 
 try
>>> g_energy -vis
>>> 
>>> 
 regards,
 
 shanu
>>> 
>>> --
>>> David van der Spoel, Ph.D., Professor of Biology
>>> Dept. of Cell & Molec. Biol., Uppsala University.
>>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>>> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
>>> --
>>> 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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>>> 
>>> * 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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>> posting!
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[gmx-users] pdb2gmx, chain and segment names in the output pdb

[Maxim Igaev]

Dear Gromacs users,

I have a large molecular complex consisting of many identical monomers.
I constructed a pdb file for it using VMD and assigned each monomer
a segment name (A0, A1, A2 etc.). The chain name was however always
the same - A. Then I created the topology for it using pdb2gmx.

In the output pdb file, however, all segment names have disappeared
and the chain names have changed - instead of A for each monomer, I
now have A, B, C, D etc for the first ~20 monomers and then simply
nothing for the rest of the monomers.

Is there a way to make pdb2gmx preserve segment/chain names while
creating a topology file?

I need my initial naming since I want to postprocess my trajectories
in VMD again.

Thanks a lot in advance!

Cheers,
Maxim
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