[gmx-users] NORMAL MODES analysis to compute specific heats

[Juan José Galano Frutos]

On 3/20/17 9:34 AM, Juan José Galano Frutos wrote:
>* Hi there:
*>>* I've been googled a bit about this issue (
*>* http://thread.gmane.org/gmane.science.biology.gromacs.user/49139,

*>* http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis,

*>* https://groups.google.com/forum/#!topic/archive-gmx-users/5C5Q8m9X21g
),
but
*>* I've not found answers to my doubts yet.
*>>* My situation is that I want to obtain specific heats (Cp) of my systems
*>* (protein solvated and neutralized) but, of course, at the Temperature and
*>* Pressure of my experiments. So, my idea here is carry out a Normal Modes
*>* analysis to extract the Hessian matrix but at least after the equilibration
*>* step of my system. I'm interested in doing it so because Cp values only
*>* make sense in relation with Temperature.
*>* My doubts come up, however, when I read through the posted discussion and I
*>* find that NM analyses apparently should be performed after minimization
*>* steps (Conjugate gradient and/or L-BFGS). Then, I would like to ask you if
*>* that is really so or if it is possible carry out this calculation after,
*>* for instance, an equilibration or a productive step in which, of course,
*>* some previous minimizations have already been performed as usual?
*>>* I've not understood also the suggestion made in one of the above referenced
*>* discussions in which David Van der Spoel recommended set all cut-offs to
*>* zero (=infinite), see below:
*>>>* You can use the g96 coordinate format instead of using the trr file
*>>* from the conjugate gradients energy minimization.
*>>* Set all cut-offs to zero (= infinite).
*>>* What's the reason for that?
*>* Where one should set to zero the cut-offs...? Just in the NM step or
*>* that is for the minimization steps?
*>
>NMA requires that you be in an energy minimum (and hence the requirement for
>exhaustive energy minimization, well below what is normally considered adequate
>for a standard MD simulation), is typically done in vacuo (hence "infinite"
>cutoffs/no PBC) and is only valid if the fundamental modes of motion are
>harmonic.  At elevated temperature (anything non-0 K) you have anharmonicity in
>many motions and the harmonic approximation fails.

>-Justin

Ok, now I'm more clear. Thank you very much Justin.

Best.


Juan José Galano Frutos

Department of Biochemistry and
Molecular and Cellular Biology,
Faculty of Sciences,
University of Zaragoza
Pedro Cerbuna # 12, 50009
Zaragoza (Spain)
+34 976 76 28 06

Institute for Biocomputation and
Physics of Complex Systems (BIFI)
Mariano Esquillor, Edificio I + D - 50018
Zaragoza (Spain)
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Re: [gmx-users] query about structural consistency

[Mark Abraham]

Hi,

On Tue, Mar 21, 2017 at 8:40 AM abhisek Mondal 
wrote:

> Hi,
>
> I just have a basic query.
>
> I'm working with a protein-ligand system with a goal of performing
> Umbrella sampling in gromacs. So first, after I build the complex, I'm
> going for NVT and followed by NPT equilibration of 20ns each. After
> equilibration, is it mandatory that my equilibrated protein-ligand complex
> matches exactly with the crystal structure used for equlibration (I mean
> before and after) ?
>

What is the purpose of doing an equilibration? Is that consistent with
requiring that nothing changes during the process of equilibration?

Mark


> Please be comprehensive. I just need to understand something.
>
>
> Thanks
>
> --
> Abhisek Mondal
>
> *Research Fellow*
>
> *Structural Biology and Bioinformatics Division*
> *CSIR-Indian Institute of Chemical Biology*
>
> *Kolkata 700032*
>
> *INDIA*
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Re: [gmx-users] mdp options for REMD

[Mark Abraham]

Sure. One takes longer.

Mark

On Tue, 21 Mar 2017 02:50 YanhuaOuyang <15901283...@163.com> wrote:

> Dear Mark,
> Do you mean that both  "generate at 300K but themostat at
> 500K"(gen-temp=300K,ref-t=500K) and "generate at 500K and thermostat at
> 500K"(gen-temp=500K, ref-t=500K)  are OK?
>
> And the latter one is recommended?
>
> Ouyang
>
>
>
>
>
>
>
>
> At 2017-03-20 21:56:35, "Mark Abraham"  wrote:
> >Hi,
> >
> >Will "generate at 300K but themostat at 500K" take more or less time to
> >equilibrate than "generate at 500K and thermostat at 500K"? Both have the
> >same desired end state when equilibration is over, so why not start closer
> >to it?
> >
> >Mark
> >
> >On Mon, Mar 20, 2017 at 2:01 PM YanhuaOuyang <15901283...@163.com> wrote:
> >
> >> Hi,
> >> I plan to run a REMD for a protein in explicit water. The
> temperature
> >> is 300k-500k and there are 40 replicas.
> >> I wander that are only the "ref-t" option in the equi_*.mdp files
> >> different when equilibration stage ? what about gen-temp option. should
> I
> >> make the gen-temp equal to ref-t (i.e. ref-t=gen-temp=500K)?
> >>
> >> Best regards,
> >> Ouyang
> >> --
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Re: [gmx-users] Regarding extending simulations

[Mark Abraham]

Hi,

Your first run used gmx mdrun -deffnm, and like the error message says, the
checkpoint file knows what the output filenames were in that case. But your
second mdrun doesn't specify -deffnm, so mdrun doesn't know whether you
meant to append to the old files, or not provide that checkpoint file, or
not append, or what. If you want to append to the old files, because the
run is logically equivalent to a single long run (which is a judgement you
can make, and mdrun should not make for you), then like the message
suggests, use -deffnm the same way you did the first time. Now mdrun knows
what output files you meant it to use, and that matches the checkpoint file
you gave, and so mdrun knows how to implement the default approach of file
appending. Alternatively, you can turn appending off, as the message
suggests.

Mark

On Tue, Mar 21, 2017 at 5:39 AM Dilip H N  wrote:

> Hello,
> I ran a md run of 20ns [1000*.002] and i got the files as md.edr,
> md.log, md.tpr, md.gro, md.xtc, md.cpt etc.,
> Now i want to extend/continue my simulation from 20 ns to again 20 ns
> (total 40 ns).
> So i gave the command as -
> gmx convert-tpr -s md.tpr - extend 2 -o md1.tpr
> gmx mdrun -v -s md1.tpr -cpi md.cpt -append
>
> But i am getting the following errors..
>
> Output file appending has been requested,
> but some output files listed in the checkpoint file md.cpt
> are not present or not named as the output files by the current program:
> Expect output files present:
>   md.log
>
> Expected output files not present or named differently:
>   md.xtc
>   md.trr
>   md.edr
>
> ---
> Program: gmx mdrun, version 2016.2
> Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 177)
>
> Fatal error:
> File appending requested, but 3 of the 4 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 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.
>
> why is this error coming in spite i have all the above files in my workin
> directory and i have not changed any names neither have edited any of
> those
>
> --
> With Best Regards,
>
> DILIP.H.N
> Research Scholar,
> Department of Chemistry, NITK.
>
>
>
>    Sent with Mailtrack
> <
> https://mailtrack.io/install?source=signature=en=cy16f01.di...@nitk.edu.in=22
> >
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[gmx-users] Fwd: CNT Water and DNA protein, Not working

[Abhishek Agrawal]

-- Forwarded message --
From: Abhishek Agrawal 
Date: Tue, Mar 21, 2017 at 2:25 PM
Subject: CNT Water and DNA protein, Not working
To: gmx-us...@gromacs.org


Hare Krishna Everyone!

OBJECITVE:
See I am aiming to make a system having
CNT
Water
DNA
to study the interaction of DNA with the CNT, when CNT has some charged
molecule attached to it or any one C be have some charge.

SPECIFICATIONS:
GROMACS 5.0.7
fftw
Python
VMD
i3 5005 2.0 GHz 4GB Ubuntu 16.04 LTS

PROBLEM:
Going through many tutorials, gromacs mailing list and Andre tutorial for
CNT on Gromacs site, I found that whatever I do, by making custom
forcefield or going by default forcefield with the GROMACS nothing is
working for me.
It gives error that residue "UNL" or whatever the PDB has, is not found in
the topolgy database,, this is for the default forcefield.
I make custom one, then CNT is accepted but then on solvating the Water is
not. Going forward DNA shall also be not accepted as it is not available in
the custom forcefield.

SUMMARY:
What to do to make a system having:
CNT Water and DNA, the FORCEFIELD is the major issue.
Please guide.

Regards,
Abhishek Agrawal
AMITY UNIVERSITY
Research Associate @ NIT Patna
NOIDA, INDIA
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[gmx-users] query about structural consistency

[abhisek Mondal]

Hi,

I just have a basic query.

I'm working with a protein-ligand system with a goal of performing
Umbrella sampling in gromacs. So first, after I build the complex, I'm
going for NVT and followed by NPT equilibration of 20ns each. After
equilibration, is it mandatory that my equilibrated protein-ligand complex
matches exactly with the crystal structure used for equlibration (I mean
before and after) ?

Please be comprehensive. I just need to understand something.


Thanks

-- 
Abhisek Mondal

*Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*
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[gmx-users] Topology for charmm

[RAHUL SURESH]

how to generate charmm topology file for gromacs using charmm2gmx python
script?

I have generated the stream file using cgenff.parachem server.?

I wish to have a comprehensive answer
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[gmx-users] DSSP

[Aishwarya Dhar]

Following procedure I have used
1. Downloaded  http://swift.cmbi.ru.nl/gv/dssp/
dssp-2.0.4-linux-i386 and renamed it dssp

2.made dssp  executable  and moved it to usr/local/bin

3.Then ran the command from the current location where the tpr and trr
files are present do_dssp -s  md.tpr -f md.trr -o ss.xpm  -ver 2.0

4.There are 91 residues in your selected group dssp cmd='/usr/local/bin/dssp
-i ddixopnV -o dd4YitS9 > /dev/null 2> /dev/null'
trn version: GMX_trn_file (single precision)
Reading frame   0 time0.000
Back Off! I just backed up ddixopnV to ./#ddixopnV.1#

It seems that the run is going on for two weeks and dssp analysis couldnt
be done
















Thanks




Sincerely

Aishwarya Dhar
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Re: [gmx-users] pdb2gmx generates very large .top for lipids with charmm36-nov2016.ff

[Jonathan Saboury]

So I found out why I didn't use charmm-gui initially, when using the
protein membrane builder it removes the ligand minocycline. I have found a
solution, on the unlikely chance what I have done will help someone, I'm
going to post what I did.

Since I used transformations on the protein (aligning to z axis, moving
along z axis) it made it difficult to align minocycline with the charmm-gui
protein as well as needing to fix hypervalent carbons.

I first aligned the xtal and charmm-gui proteins with uscf chimera. Then
outputted the minocycline coords and fixed the bonds with Spartan '08. Then
I used charmm-gui Ligand Reader & Modeler to output charmm36.itp and
MIY.itp. I renamed charmm36.itp to charmm36_2.itp and added both to the
charmm-gui directory and included them in .top. I combined the two pdbs
(protein/lipids/water and minicycline) and removed any TER/END's in the
middle. I also added minocycline to index.ndx.

Thanks for the help!

- Jonathan




On Mon, Mar 13, 2017 at 9:24 PM, Jonathan Saboury  wrote:

> I honestly forgot why (took too long, erred, or both) so I tried to do
> charm-gui again. From my current attempt it is taking a while. I'm on the
> last step and I'll keep checking the output.
>
> I'll keep you updated when something happens.
>
> Thanks again, your help is invaluable!
>
> - Jonathan
>
> P.S. I am seriously impressed on all the projects you are on and still
> have time to do user help XD
>
> On Sun, Mar 12, 2017 at 5:59 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 3/12/17 8:36 PM, Jonathan Saboury wrote:
>>
>>> Hello all,
>>>
>>> I generated a 3:1 POPE:POPG bilayer with charmm-gui, ran the
>>> minimization,
>>> equilibration, and production runs given. Then I copied the 10ns
>>> production
>>> run .gro to a different folder so that I can run it with
>>> charmm36-nov2016.ff instead of the ff given.
>>>
>>>
>> Why?  The topology CHARMM-GUI gives you still works, and that's sort of
>> the purpose - it gives you everything you need for the system.
>>
>> When running the command "gmx_mpi pdb2gmx -ff charmm36-nov2016 -f
>>> old_membrane_lipid_only.pdb -o old_membrane_pdb2gmx.pdb -p topol.top
>>> -water
>>> tip3p" it generates a very large .top file (26.8 MB) that has [ atoms ]
>>> and
>>> perhaps other headings.
>>>
>>> I was under the impression that the .top should have been small and just
>>> contained the include line for where the POPE and POPG .itps were in the
>>> charmm36-nov2016. Did I do something wrong? Would this give me a
>>> simulation
>>> that isn't accurate?
>>>
>>>
>> No, because pdb2gmx will generate an explicit copy of the topology for
>> every instance of every residue, which leads to an extremely redundant
>> topology with many copies of lipids and water.  As stated above, there is
>> no need to re-generate your topology.  Use what CHARMM-GUI gives you.  We
>> worked hard to make it easy for the end user :)
>>
>> -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
>>
>> ==
>> --
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>
>
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Re: [gmx-users] query about structural consistency

[abhisek Mondal]

Hello Mark,
I guess that's an endless question and will vary based on what kind of
ions used in equilibration. So how do I made a decision that I got the
correct equilibrated structure for my production run ? Is it pressure,
density, temperature convergence or I'm missing something?

On Tue, Mar 21, 2017 at 2:31 PM, Mark Abraham 
wrote:

> Hi,
>
> On Tue, Mar 21, 2017 at 8:40 AM abhisek Mondal 
> wrote:
>
> > Hi,
> >
> > I just have a basic query.
> >
> > I'm working with a protein-ligand system with a goal of performing
> > Umbrella sampling in gromacs. So first, after I build the complex, I'm
> > going for NVT and followed by NPT equilibration of 20ns each. After
> > equilibration, is it mandatory that my equilibrated protein-ligand
> complex
> > matches exactly with the crystal structure used for equlibration (I mean
> > before and after) ?
> >
>
> What is the purpose of doing an equilibration? Is that consistent with
> requiring that nothing changes during the process of equilibration?
>
> Mark
>
>
> > Please be comprehensive. I just need to understand something.
> >
> >
> > Thanks
> >
> > --
> > Abhisek Mondal
> >
> > *Research Fellow*
> >
> > *Structural Biology and Bioinformatics Division*
> > *CSIR-Indian Institute of Chemical Biology*
> >
> > *Kolkata 700032*
> >
> > *INDIA*
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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-- 
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*
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[gmx-users] NORMAL MODES analysis to compute specific heats

[Juan José Galano Frutos]

Sorry for insisting, but has no-one any idea of this?

Thanks

Juan José Galano Frutos

Department of Biochemistry and
Molecular and Cellular Biology,
Faculty of Sciences,
University of Zaragoza
Pedro Cerbuna # 12, 50009
Zaragoza (Spain)
+34 976 76 28 06

Institute for Biocomputation and
Physics of Complex Systems (BIFI)
Mariano Esquillor, Edificio I + D - 50018
Zaragoza (Spain)

-- Forwarded message --
From: Juan José Galano Frutos 
Date: 2017-03-20 14:34 GMT+01:00
Subject: NORMAL MODES analysis to compute specific heats
To: gmx-us...@gromacs.org


Hi there:

I've been googled a bit about this issue (http://thread.gmane.org/
gmane.science.biology.gromacs.user/49139, http://www.gromacs.org/
Documentation/How-tos/Normal_Mode_Analysis, https://groups.google.com/
forum/#!topic/archive-gmx-users/5C5Q8m9X21g), but I've not found answers to
my doubts yet.

My situation is that I want to obtain specific heats (Cp) of my systems
(protein solvated and neutralized) but, of course, at the Temperature and
Pressure of my experiments. So, my idea here is carry out a Normal Modes
analysis to extract the Hessian matrix but at least after the equilibration
step of my system. I'm interested in doing it so because Cp values only
make sense in relation with Temperature.
My doubts come up, however, when I read through the posted discussion and I
find that NM analyses apparently should be performed after minimization
steps (Conjugate gradient and/or L-BFGS). Then, I would like to ask you if
that is really so or if it is possible carry out this calculation after,
for instance, an equilibration or a productive step in which, of course,
some previous minimizations have already been performed as usual?

I've not understood also the suggestion made in one of the above referenced
discussions in which David Van der Spoel recommended set all cut-offs to
zero (=infinite), see below:

> You can use the g96 coordinate format instead of using the trr file
> from the conjugate gradients energy minimization.
> Set all cut-offs to zero (= infinite).

What's the reason for that?
Where one should set to zero the cut-offs...? Just in the NM step or
that is for the minimization steps?

Thank you very much for your help.



Juan José Galano Frutos

Department of Biochemistry and
Molecular and Cellular Biology,
Faculty of Sciences,
University of Zaragoza
Pedro Cerbuna # 12, 50009
Zaragoza (Spain)
+34 976 76 28 06 <+34%20976%2076%2028%2006>

Institute for Biocomputation and
Physics of Complex Systems (BIFI)
Mariano Esquillor, Edificio I + D - 50018
Zaragoza (Spain)
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Re: [gmx-users] Structure blowing up after increased the temperature

[Justin Lemkul]

On 3/21/17 12:39 PM, Sameer Edirisinghe wrote:

Dear users,

I'm trying to find the melting point and Tg of my polymer system using
Density vs temperature curve. I'm using all oplsaa forcefield and  I'm going
for NVT and followed by NPT equilibration ( Both at 523K) of 400ps each.
then after the production run (at 523K for 5ns) the system is blowing up
and can be observed broken molecules of the trajectory from VMD. But no
blowing up occurring at 300K temperature (200ns).



"Broken" molecules are a consequence of PBC, not instability.


But if I only did the production run (at 523K) up to 200ps it seems no
blowing up occurring until 200ps.



Systems simulated at higher temperature will naturally diffuse faster, therefore 
cross periodic boundaries more frequently or more quickly.



Note. used .mdp files has attached with the mail



The mailing list does not accept attachments.


1) I'm not sure if the .mdp files caused the blowing up or the topology
caused the blow up of the system.

2) Can use same .mdp files by only changing coupling temperature for any
temperature?



High-temperature simulations often require shorter time steps and perhaps a bit 
tighter regulation of temperature and pressure to be stable, but as of yet we 
have no evidence that your simulation was actually unstable.


-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

==
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[gmx-users] Water molecule starting at atom 39087 can not be settled

[liming_52]

Dear Gromacs users,I am trying to run a md using 4n6p.cif obtained from PDB 
with a ligand. I converted the file into pdb format using DS4.1, and got the 
file named lactoferrin.pdb. When I directly run
the command "gmx mdrun -v -deffnm em", the program runs and produces the 
information as follows:
:-) GROMACS - gmx mdrun, VERSION 5.1.2 (-:

GROMACS is written by:
 Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar Bjelkmar  
 Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian Fritsch
  Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent Hindriksen
 Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten Kutzner 
Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff
   Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk  
   Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers 
   Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf  
   and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:  gmx mdrun, VERSION 5.1.2
Executable:   /usr/bin/gmx
Data prefix:  /usr
Command line:
  gmx mdrun -v -deffnm em


Running on 1 node with total 12 cores, 24 logical cores
Hardware detected:
  CPU info:
Vendor: GenuineIntel
Brand:  Intel(R) Xeon(R) CPU E5-2620 v2 @ 2.10GHz
SIMD instructions most likely to fit this hardware: AVX_256
SIMD instructions selected at GROMACS compile time: SSE2

Compiled SIMD instructions: SSE2, GROMACS could use AVX_256 on this machine, 
which is better

Reading file em.tpr, VERSION 5.1.2 (single precision)

Will use 18 particle-particle and 6 PME only ranks
This is a guess, check the performance at the end of the log file
Using 24 MPI threads
Using 1 OpenMP thread per tMPI thread


Steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps=5
Step=0, Dmax= 1.0e-03 nm, Epot=  2.62236e+13 Fmax= 1.19534e+16, atom= 3295
Step=1, Dmax= 1.0e-03 nm, Epot=  1.08905e+13 Fmax= 4.61331e+15, atom= 3295
Step=2, Dmax= 1.2e-03 nm, Epot=  4.10454e+12 Fmax= 1.60266e+15, atom= 3295
Step=3, Dmax= 1.4e-03 nm, Epot=  1.40137e+12 Fmax= 5.00036e+14, atom= 3295
Step=4, Dmax= 1.7e-03 nm, Epot=  4.33654e+11 Fmax= 1.40069e+14, atom= 3295
Step=5, Dmax= 2.1e-03 nm, Epot=  1.22200e+11 Fmax= 3.52752e+13, atom= 3295
Step=6, Dmax= 2.5e-03 nm, Epot=  3.18990e+10 Fmax= 8.01234e+12, atom= 3295
Step=7, Dmax= 3.0e-03 nm, Epot=  8.21424e+09 Fmax= 1.64883e+12, atom= 3295
Step=8, Dmax= 3.6e-03 nm, Epot=  2.50045e+09 Fmax= 3.09257e+11, atom= 3295
Step=9, Dmax= 4.3e-03 nm, Epot=  9.40257e+08 Fmax= 6.82365e+10, atom= 3279
Step=   10, Dmax= 5.2e-03 nm, Epot=  2.72792e+08 Fmax= 1.39988e+10, atom= 3279
Step=   11, Dmax= 6.2e-03 nm, Epot=  5.92206e+07 Fmax= 2.62182e+09, atom= 3279
Step=   12, Dmax= 7.4e-03 nm, Epot=  1.69891e+07 Fmax= 4.55609e+08, atom= 3279
Step=   13, Dmax= 8.9e-03 nm, Epot=  4.88134e+06 Fmax= 1.13133e+08, atom= 3296
Step=   14, Dmax= 1.1e-02 nm, Epot=  1.86164e+06 Fmax= 3.65858e+07, atom= 3296
Step=   15, Dmax= 1.3e-02 nm, Epot=  6.44202e+05 Fmax= 1.40616e+07, atom= 3296
Step=   16, Dmax= 1.5e-02 nm, Epot=  2.16177e+05 Fmax= 4.49293e+06, atom= 3294
Step=   17, Dmax= 1.8e-02 nm, Epot=  2.88800e+04 Fmax= 2.99167e+06, atom= 134
Step=   18, Dmax= 2.2e-02 nm, Epot= -3.56134e+04 Fmax= 2.53958e+06, atom= 3296
Step=   19, Dmax= 2.7e-02 nm, Epot= -7.50786e+04 Fmax= 5.14618e+06, atom= 3296
Step=   20, Dmax= 3.2e-02 nm, Epot= -1.33736e+05 Fmax= 7.43406e+05, atom= 134
Step=   21, Dmax= 3.8e-02 nm, Epot= -1.68139e+05 Fmax= 6.44435e+06, atom= 3296
Step=   22, Dmax= 4.6e-02 nm, Epot= -2.39673e+05 Fmax= 3.99299e+05, atom= 3296
Step=   23, Dmax= 5.5e-02 nm, Epot= -3.07273e+05 Fmax= 1.60934e+06, atom= 3296
Step=   24, Dmax= 6.6e-02 nm, Epot= -3.25923e+05 Fmax= 2.64244e+05, atom= 3296
Step=   26, Dmax= 4.0e-02 nm, Epot= -3.66840e+05 Fmax= 1.58505e+05, atom= 1346
Step=   27, Dmax= 4.8e-02 nm, Epot= -3.98127e+05 Fmax= 6.82470e+05, atom= 134
Step=   28, Dmax= 5.7e-02 nm, Epot= -4.11327e+05 Fmax= 1.87577e+05, atom= 3297
Step=   29, Dmax= 6.9e-02 nm, Epot= -4.41304e+05 Fmax= 3.09908e+05, atom= 3297
Step=   30, Dmax= 8.2e-02 nm, Epot= -4.55118e+05 Fmax= 1.47622e+05, atom= 3297
Step=   31, Dmax= 9.9e-02 nm, Epot= -4.84124e+05 Fmax= 8.03024e+04, atom= 3296
Step=   32, Dmax= 1.2e-01 nm, Epot= -5.11472e+05 Fmax= 

Re: [gmx-users] Water molecule starting at atom 39087 can not be settled

[Justin Lemkul]

On 3/21/17 6:51 PM, liming_52 wrote:

Dear Gromacs users,I am trying to run a md using 4n6p.cif obtained from PDB 
with a ligand. I converted the file into pdb format using DS4.1, and got the 
file named lactoferrin.pdb. When I directly run
the command "gmx mdrun -v -deffnm em", the program runs and produces the 
information as follows:
:-) GROMACS - gmx mdrun, VERSION 5.1.2 (-:

GROMACS is written by:
 Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar Bjelkmar
 Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian Fritsch
  Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent Hindriksen
 Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten Kutzner
Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff
   Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk
   Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
   Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf
   and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:  gmx mdrun, VERSION 5.1.2
Executable:   /usr/bin/gmx
Data prefix:  /usr
Command line:
  gmx mdrun -v -deffnm em


Running on 1 node with total 12 cores, 24 logical cores
Hardware detected:
  CPU info:
Vendor: GenuineIntel
Brand:  Intel(R) Xeon(R) CPU E5-2620 v2 @ 2.10GHz
SIMD instructions most likely to fit this hardware: AVX_256
SIMD instructions selected at GROMACS compile time: SSE2

Compiled SIMD instructions: SSE2, GROMACS could use AVX_256 on this machine, 
which is better

Reading file em.tpr, VERSION 5.1.2 (single precision)

Will use 18 particle-particle and 6 PME only ranks
This is a guess, check the performance at the end of the log file
Using 24 MPI threads
Using 1 OpenMP thread per tMPI thread


Steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps=5
Step=0, Dmax= 1.0e-03 nm, Epot=  2.62236e+13 Fmax= 1.19534e+16, atom= 3295
Step=1, Dmax= 1.0e-03 nm, Epot=  1.08905e+13 Fmax= 4.61331e+15, atom= 3295
Step=2, Dmax= 1.2e-03 nm, Epot=  4.10454e+12 Fmax= 1.60266e+15, atom= 3295
Step=3, Dmax= 1.4e-03 nm, Epot=  1.40137e+12 Fmax= 5.00036e+14, atom= 3295
Step=4, Dmax= 1.7e-03 nm, Epot=  4.33654e+11 Fmax= 1.40069e+14, atom= 3295
Step=5, Dmax= 2.1e-03 nm, Epot=  1.22200e+11 Fmax= 3.52752e+13, atom= 3295
Step=6, Dmax= 2.5e-03 nm, Epot=  3.18990e+10 Fmax= 8.01234e+12, atom= 3295
Step=7, Dmax= 3.0e-03 nm, Epot=  8.21424e+09 Fmax= 1.64883e+12, atom= 3295
Step=8, Dmax= 3.6e-03 nm, Epot=  2.50045e+09 Fmax= 3.09257e+11, atom= 3295
Step=9, Dmax= 4.3e-03 nm, Epot=  9.40257e+08 Fmax= 6.82365e+10, atom= 3279
Step=   10, Dmax= 5.2e-03 nm, Epot=  2.72792e+08 Fmax= 1.39988e+10, atom= 3279
Step=   11, Dmax= 6.2e-03 nm, Epot=  5.92206e+07 Fmax= 2.62182e+09, atom= 3279
Step=   12, Dmax= 7.4e-03 nm, Epot=  1.69891e+07 Fmax= 4.55609e+08, atom= 3279
Step=   13, Dmax= 8.9e-03 nm, Epot=  4.88134e+06 Fmax= 1.13133e+08, atom= 3296
Step=   14, Dmax= 1.1e-02 nm, Epot=  1.86164e+06 Fmax= 3.65858e+07, atom= 3296
Step=   15, Dmax= 1.3e-02 nm, Epot=  6.44202e+05 Fmax= 1.40616e+07, atom= 3296
Step=   16, Dmax= 1.5e-02 nm, Epot=  2.16177e+05 Fmax= 4.49293e+06, atom= 3294
Step=   17, Dmax= 1.8e-02 nm, Epot=  2.88800e+04 Fmax= 2.99167e+06, atom= 134
Step=   18, Dmax= 2.2e-02 nm, Epot= -3.56134e+04 Fmax= 2.53958e+06, atom= 3296
Step=   19, Dmax= 2.7e-02 nm, Epot= -7.50786e+04 Fmax= 5.14618e+06, atom= 3296
Step=   20, Dmax= 3.2e-02 nm, Epot= -1.33736e+05 Fmax= 7.43406e+05, atom= 134
Step=   21, Dmax= 3.8e-02 nm, Epot= -1.68139e+05 Fmax= 6.44435e+06, atom= 3296
Step=   22, Dmax= 4.6e-02 nm, Epot= -2.39673e+05 Fmax= 3.99299e+05, atom= 3296
Step=   23, Dmax= 5.5e-02 nm, Epot= -3.07273e+05 Fmax= 1.60934e+06, atom= 3296
Step=   24, Dmax= 6.6e-02 nm, Epot= -3.25923e+05 Fmax= 2.64244e+05, atom= 3296
Step=   26, Dmax= 4.0e-02 nm, Epot= -3.66840e+05 Fmax= 1.58505e+05, atom= 1346
Step=   27, Dmax= 4.8e-02 nm, Epot= -3.98127e+05 Fmax= 6.82470e+05, atom= 134
Step=   28, Dmax= 5.7e-02 nm, Epot= -4.11327e+05 Fmax= 1.87577e+05, atom= 3297
Step=   29, Dmax= 6.9e-02 nm, Epot= -4.41304e+05 Fmax= 3.09908e+05, atom= 3297
Step=   30, Dmax= 8.2e-02 nm, Epot= -4.55118e+05 Fmax= 1.47622e+05, atom= 3297
Step=   31, Dmax= 9.9e-02 nm, Epot= -4.84124e+05 Fmax= 8.03024e+04, atom= 3296
Step=   32, Dmax= 1.2e-01 nm, 

Re: [gmx-users] Dihedral drivers and 2D Energy Plot in gromacs

[Justin Lemkul]

On 3/21/17 7:02 PM, Devashish_Das wrote:

Thanks for the solution.

So, Is it not possible to do 2D-energy plot of AIB-dipeptide with a water
box? or only the use of constant box is the problem?



You shouldn't be doing the calculations in water at all.  From our previous 
conversation, I understood that you wanted a 2-D energy plot as a function of 
(phi,psi) for AIB.  You do that in vacuo.  That gives you the relative 
conformational energy of the peptide as a function of the backbone geometry. 
You can then look at the sampling during an MD simulation to see where the 
configurations lie on that energy surface to understand if hydration causes a 
shift in the sampling from the "intrinsic" state.


-Justin


On Mon, Mar 20, 2017 at 5:26 PM, Justin Lemkul  wrote:




On 3/20/17 2:50 AM, Devashish_Das wrote:


Thanks for the reply.
The problem now I am facing is, the total energy ( 15960125.0 kJ/mol for
180-180
degree) and dihderal restraint (Its coming like 0.594114 for 180-180
degree).
What I am currently trying is:

1. Take the AIB dipeptide and do minimization in vacuum to get the nearly
angle
of Phi-Psi desired (I am doing it for every 10 degree)
2. Add water box manually to the minimized AIB.gro file (For keeping the
number
of water molecule exactly same?)
3. Minimize the system again with restraints.
4. remove the restraints from the .top file and use a normal .mdp file for
generating .tpr file
5. Use this tpr and minimized gro file with water to do mdrun -rerun
6. Use gmx energy to calculate "Total Energy" from the rerun.edr and
"Dihedral
Restraint" from AIB_water_minimized.edr file
7. Plot the final Energy (= (Total Energy - Dihedral Restraint Energy) -
minimum
of the list)

Am I doing this right?



No, you shouldn't be involving water at all, and the manual overlay of the
same water box on every system is undoubtedly going to cause atomic overlap
that leads to the bizarre energies.

What you care most about is the relative energetics in vacuum; balancing
intermolecular interactions is a totally separate issue.

-Justin



On Fri, Mar 17, 2017 at 7:16
PM, > wrote:

Message: 4
Date: Fri, 17 Mar 2017 09:45:21 -0400
From: Justin Lemkul >
To: gmx-us...@gromacs.org 
Subject: Re: [gmx-users] Dihedral drivers and 2D Energy Plot in
gromacs
Message-ID: <85061dd9-acaa-0b50-9eaf-4efb5081d...@vt.edu
>

Content-Type: text/plain; charset=windows-1252; format=flowed



On 3/17/17 1:40 AM, Devashish_Das wrote:
> Hello All,
>
> Presently we are working in generating dihedral drivers for AIB
dipeptide
> in gromacs. We would like to create energy contour maps for
different phi,
> psi angle for AIB in gromacs. We are unable to create the correct
energy
> map vs phi/psi angle of AIB dipeptide during energy minimization
step in
> Gromacs.
>
> Our MDP:
> #
> ; Parameters describing what to do, when to stop and what to save
> integrator = cg
> emtol = 1.0
> emstep= 0.01
> nsteps = 5
> #
>
> We retraining the dihedral angles using the following method:
> http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints

(*Is this
> the correct way to do this?*)
>
> As clarified Dr Justin Lemkul in a private mail, we need to do the
> following:
>
> * The 2-D energy surface requires several steps.  You need to
> assign dihedral restraints in the topology and relevant .mdp
options, and
> minimize the structures with those restrained phi/psi pairs.  You
then need
> to deactivate the restraints and use mdrun -rerun to recompute the
energy
> of the minimized conformation to eliminate the contribution from the
> restraint potential
> (http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy

> >).
Then
> you need to offset the surface to the global minimum (done
completely
> outside GROMACS)*
>
> But we are having following trouble:
>
> a)  "*You then need to deactivate the restraints and use mdrun
-rerun to
> recompute the energy of the minimized conformation to eliminate the
> contribution from the restraint potential*". How to do this? Which
.mdp
> file to be used for *mdrun -rerun*?
>

Anything that's not energy minimization.  Your topology also 

Re: [gmx-users] Dihedral drivers and 2D Energy Plot in gromacs

[Devashish_Das]

Thanks for the solution.

So, Is it not possible to do 2D-energy plot of AIB-dipeptide with a water
box? or only the use of constant box is the problem?

On Mon, Mar 20, 2017 at 5:26 PM, Justin Lemkul  wrote:

>
>
> On 3/20/17 2:50 AM, Devashish_Das wrote:
>
>> Thanks for the reply.
>> The problem now I am facing is, the total energy ( 15960125.0 kJ/mol for
>> 180-180
>> degree) and dihderal restraint (Its coming like 0.594114 for 180-180
>> degree).
>> What I am currently trying is:
>>
>> 1. Take the AIB dipeptide and do minimization in vacuum to get the nearly
>> angle
>> of Phi-Psi desired (I am doing it for every 10 degree)
>> 2. Add water box manually to the minimized AIB.gro file (For keeping the
>> number
>> of water molecule exactly same?)
>> 3. Minimize the system again with restraints.
>> 4. remove the restraints from the .top file and use a normal .mdp file for
>> generating .tpr file
>> 5. Use this tpr and minimized gro file with water to do mdrun -rerun
>> 6. Use gmx energy to calculate "Total Energy" from the rerun.edr and
>> "Dihedral
>> Restraint" from AIB_water_minimized.edr file
>> 7. Plot the final Energy (= (Total Energy - Dihedral Restraint Energy) -
>> minimum
>> of the list)
>>
>> Am I doing this right?
>>
>>
> No, you shouldn't be involving water at all, and the manual overlay of the
> same water box on every system is undoubtedly going to cause atomic overlap
> that leads to the bizarre energies.
>
> What you care most about is the relative energetics in vacuum; balancing
> intermolecular interactions is a totally separate issue.
>
> -Justin
>
>
>> On Fri, Mar 17, 2017 at 7:16
>> PM, > > wrote:
>>
>> Message: 4
>> Date: Fri, 17 Mar 2017 09:45:21 -0400
>> From: Justin Lemkul >
>> To: gmx-us...@gromacs.org 
>> Subject: Re: [gmx-users] Dihedral drivers and 2D Energy Plot in
>> gromacs
>> Message-ID: <85061dd9-acaa-0b50-9eaf-4efb5081d...@vt.edu
>> >
>>
>> Content-Type: text/plain; charset=windows-1252; format=flowed
>>
>>
>>
>> On 3/17/17 1:40 AM, Devashish_Das wrote:
>> > Hello All,
>> >
>> > Presently we are working in generating dihedral drivers for AIB
>> dipeptide
>> > in gromacs. We would like to create energy contour maps for
>> different phi,
>> > psi angle for AIB in gromacs. We are unable to create the correct
>> energy
>> > map vs phi/psi angle of AIB dipeptide during energy minimization
>> step in
>> > Gromacs.
>> >
>> > Our MDP:
>> > #
>> > ; Parameters describing what to do, when to stop and what to save
>> > integrator = cg
>> > emtol = 1.0
>> > emstep= 0.01
>> > nsteps = 5
>> > #
>> >
>> > We retraining the dihedral angles using the following method:
>> > http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints
>> 
>> (*Is this
>> > the correct way to do this?*)
>> >
>> > As clarified Dr Justin Lemkul in a private mail, we need to do the
>> > following:
>> >
>> > * The 2-D energy surface requires several steps.  You need to
>> > assign dihedral restraints in the topology and relevant .mdp
>> options, and
>> > minimize the structures with those restrained phi/psi pairs.  You
>> then need
>> > to deactivate the restraints and use mdrun -rerun to recompute the
>> energy
>> > of the minimized conformation to eliminate the contribution from the
>> > restraint potential
>> > (http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
>> 
>> > > >).
>> Then
>> > you need to offset the surface to the global minimum (done
>> completely
>> > outside GROMACS)*
>> >
>> > But we are having following trouble:
>> >
>> > a)  "*You then need to deactivate the restraints and use mdrun
>> -rerun to
>> > recompute the energy of the minimized conformation to eliminate the
>> > contribution from the restraint potential*". How to do this? Which
>> .mdp
>> > file to be used for *mdrun -rerun*?
>> >
>>
>> Anything that's not energy minimization.  Your topology also should
>> either not
>> include the dihedral restraint, or you should extract its
>> contribution from the
>> .edr file and subtract it from the total energy of the system.
>>
>> > b)  "Then you need to offset the surface to the global 

Re: [gmx-users] Water molecule starting at atom 39087 can not be settled

[Justin Lemkul]

On 3/21/17 7:08 PM, liming_52 wrote:

The position of the ligand was obtained using autodock vina. The gro file and 
ITP file were obtained from the PRODRG server 
(http://davapc1.bioch.dundee.ac.uk/prodrg). Anyway, I added the ions with 0.154 
M NaCl. Did these effect my md?



PRODRG topologies are of insufficient quality for MD simulations.  If you want 
to use GROMOS, try ATB instead.  Or investigate other parametrization tools for 
other force fields.  If you have a new topology and it's still not stable, 
follow 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System


-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

==
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Re: [gmx-users] Water molecule starting at atom 39087 can not be settled

[liming_52]

The position of the ligand was obtained using autodock vina. The gro file and 
ITP file were obtained from the PRODRG server 
(http://davapc1.bioch.dundee.ac.uk/prodrg). Anyway, I added the ions with 0.154 
M NaCl. Did these effect my md?




--

With my best wishes,
Ming Li, PhD
Chinese Academy of Agricultural Sciences, Beijing, China



At 2017-03-22 06:53:57, "Justin Lemkul"  wrote:
>
>
>On 3/21/17 6:51 PM, liming_52 wrote:
>> Dear Gromacs users,I am trying to run a md using 4n6p.cif obtained from PDB 
>> with a ligand. I converted the file into pdb format using DS4.1, and got the 
>> file named lactoferrin.pdb. When I directly run
>> the command "gmx mdrun -v -deffnm em", the program runs and produces the 
>> information as follows:
>> :-) GROMACS - gmx mdrun, VERSION 5.1.2 (-:
>>
>> GROMACS is written by:
>>  Emile Apol  Rossen Apostolov  Herman J.C. BerendsenPar Bjelkmar
>>  Aldert van Buuren   Rudi van Drunen Anton Feenstra   Sebastian Fritsch
>>   Gerrit Groenhof   Christoph Junghans   Anca HamuraruVincent Hindriksen
>>  Dimitrios KarkoulisPeter KassonJiri Kraus  Carsten Kutzner
>> Per Larsson  Justin A. Lemkul   Magnus Lundborg   Pieter Meulenhoff
>>Erik Marklund  Teemu Murtola   Szilard Pall   Sander Pronk
>>Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
>>Peter TielemanTeemu Virolainen  Christian WennbergMaarten Wolf
>>and the project leaders:
>> Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>>
>> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>> Copyright (c) 2001-2015, The GROMACS development team at
>> Uppsala University, Stockholm University and
>> the Royal Institute of Technology, Sweden.
>> check out http://www.gromacs.org for more information.
>>
>> GROMACS is free software; you can redistribute it and/or modify it
>> under the terms of the GNU Lesser General Public License
>> as published by the Free Software Foundation; either version 2.1
>> of the License, or (at your option) any later version.
>>
>> GROMACS:  gmx mdrun, VERSION 5.1.2
>> Executable:   /usr/bin/gmx
>> Data prefix:  /usr
>> Command line:
>>   gmx mdrun -v -deffnm em
>>
>>
>> Running on 1 node with total 12 cores, 24 logical cores
>> Hardware detected:
>>   CPU info:
>> Vendor: GenuineIntel
>> Brand:  Intel(R) Xeon(R) CPU E5-2620 v2 @ 2.10GHz
>> SIMD instructions most likely to fit this hardware: AVX_256
>> SIMD instructions selected at GROMACS compile time: SSE2
>>
>> Compiled SIMD instructions: SSE2, GROMACS could use AVX_256 on this machine, 
>> which is better
>>
>> Reading file em.tpr, VERSION 5.1.2 (single precision)
>>
>> Will use 18 particle-particle and 6 PME only ranks
>> This is a guess, check the performance at the end of the log file
>> Using 24 MPI threads
>> Using 1 OpenMP thread per tMPI thread
>>
>>
>> Steepest Descents:
>>Tolerance (Fmax)   =  1.0e+03
>>Number of steps=5
>> Step=0, Dmax= 1.0e-03 nm, Epot=  2.62236e+13 Fmax= 1.19534e+16, atom= 
>> 3295
>> Step=1, Dmax= 1.0e-03 nm, Epot=  1.08905e+13 Fmax= 4.61331e+15, atom= 
>> 3295
>> Step=2, Dmax= 1.2e-03 nm, Epot=  4.10454e+12 Fmax= 1.60266e+15, atom= 
>> 3295
>> Step=3, Dmax= 1.4e-03 nm, Epot=  1.40137e+12 Fmax= 5.00036e+14, atom= 
>> 3295
>> Step=4, Dmax= 1.7e-03 nm, Epot=  4.33654e+11 Fmax= 1.40069e+14, atom= 
>> 3295
>> Step=5, Dmax= 2.1e-03 nm, Epot=  1.22200e+11 Fmax= 3.52752e+13, atom= 
>> 3295
>> Step=6, Dmax= 2.5e-03 nm, Epot=  3.18990e+10 Fmax= 8.01234e+12, atom= 
>> 3295
>> Step=7, Dmax= 3.0e-03 nm, Epot=  8.21424e+09 Fmax= 1.64883e+12, atom= 
>> 3295
>> Step=8, Dmax= 3.6e-03 nm, Epot=  2.50045e+09 Fmax= 3.09257e+11, atom= 
>> 3295
>> Step=9, Dmax= 4.3e-03 nm, Epot=  9.40257e+08 Fmax= 6.82365e+10, atom= 
>> 3279
>> Step=   10, Dmax= 5.2e-03 nm, Epot=  2.72792e+08 Fmax= 1.39988e+10, atom= 
>> 3279
>> Step=   11, Dmax= 6.2e-03 nm, Epot=  5.92206e+07 Fmax= 2.62182e+09, atom= 
>> 3279
>> Step=   12, Dmax= 7.4e-03 nm, Epot=  1.69891e+07 Fmax= 4.55609e+08, atom= 
>> 3279
>> Step=   13, Dmax= 8.9e-03 nm, Epot=  4.88134e+06 Fmax= 1.13133e+08, atom= 
>> 3296
>> Step=   14, Dmax= 1.1e-02 nm, Epot=  1.86164e+06 Fmax= 3.65858e+07, atom= 
>> 3296
>> Step=   15, Dmax= 1.3e-02 nm, Epot=  6.44202e+05 Fmax= 1.40616e+07, atom= 
>> 3296
>> Step=   16, Dmax= 1.5e-02 nm, Epot=  2.16177e+05 Fmax= 4.49293e+06, atom= 
>> 3294
>> Step=   17, Dmax= 1.8e-02 nm, Epot=  2.88800e+04 Fmax= 2.99167e+06, atom= 134
>> Step=   18, Dmax= 2.2e-02 nm, Epot= -3.56134e+04 Fmax= 2.53958e+06, atom= 
>> 3296
>> Step=   19, Dmax= 2.7e-02 nm, Epot= -7.50786e+04 Fmax= 5.14618e+06, atom= 
>> 3296
>> Step=   20, Dmax= 3.2e-02 nm, Epot= -1.33736e+05 Fmax= 7.43406e+05, atom= 134
>> Step=   21, Dmax= 3.8e-02 nm, Epot= -1.68139e+05 Fmax= 6.44435e+06, atom= 
>> 3296
>> Step=   22, Dmax= 

Re: [gmx-users] Structure blowing up after increased the temperature

[Sameer Edirisinghe]

Thank you for the help Dr. Jsutin

On 3/21/17 12:39 PM, Sameer Edirisinghe wrote:
> Dear users,
>
> I'm trying to find the melting point and Tg of my polymer system using
> Density vs temperature curve. I'm using all oplsaa forcefield and  I'm
going
> for NVT and followed by NPT equilibration ( Both at 523K) of 400ps each.
> then after the production run (at 523K for 5ns) the system is blowing up
> and can be observed broken molecules of the trajectory from VMD. But no
> blowing up occurring at 300K temperature (200ns).
>

"Broken" molecules are a consequence of PBC, not instability.

*I used -pbc nojump flag in trajconv command but still molecules seems to
be broken*

> But if I only did the production run (at 523K) up to 200ps it seems no
> blowing up occurring until 200ps.
>

Systems simulated at higher temperature will naturally diffuse faster,
therefore
cross periodic boundaries more frequently or more quickly.

> Note. used .mdp files has attached with the mail
>

The mailing list does not accept attachments.

> 1) I'm not sure if the .mdp files caused the blowing up or the topology
> caused the blow up of the system.
>
> 2) Can use same .mdp files by only changing coupling temperature for any
> temperature?
>

High-temperature simulations often require shorter time steps and perhaps a
bit
tighter regulation of temperature and pressure to be stable, but as of yet
we
have no evidence that your simulation was actually unstable.

*Here i used 0.001ps as time step. Do i need to reduce it more ?*

*Pressure and temperature have fluctuations after the equilibration while
pressure seems to have higher fluctuations.*

*see my temperature and pressure coupling options below. I used them for
both equilibrium and production run.*

*tcoupl = Nose-Hoover*
*tc-grps = MD ; *
*tau_t = 8; *
*ref_t = 523  ;*

*; Pressure coupling is on*
*pcoupl= Parrinello-Rahman *
*pcoupltype= isotropic; uniform scaling of box vectors*
*tau_p= 5.0; time constant, in ps*
*ref_p= 1.0; reference pressure, in bar*
*compressibility = 4.46e-5; *

Thanks
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[gmx-users] Topology CHarmm

[RAHUL SURESH]

Dear Gromacs users

How to execute the file cgenff_charm2gmx.py file?

I tried

*chmod +x cgenff_charm2gmx.py

No result

** python cgenff_charm2gmx.py

Usage: DRUG drug.mol2 drug.str charmm36.ff

I didnt get any output files
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Re: [gmx-users] Topology for charmm

[Justin Lemkul]

On 3/21/17 4:54 AM, RAHUL SURESH wrote:

how to generate charmm topology file for gromacs using charmm2gmx python
script?

I have generated the stream file using cgenff.parachem server.?

I wish to have a comprehensive answer



Use the CGenFF conversion script here:

http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs

and read the header of the script.  The syntax is quite simple.

-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

==
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Re: [gmx-users] query about structural consistency

[Hannes Loeffler]

On Tue, 21 Mar 2017 13:09:46 +0530
abhisek Mondal  wrote:

> Hi,
> 
> I just have a basic query.
> 
> I'm working with a protein-ligand system with a goal of performing
> Umbrella sampling in gromacs. So first, after I build the complex, I'm
> going for NVT and followed by NPT equilibration of 20ns each. After
> equilibration, is it mandatory that my equilibrated protein-ligand
> complex matches exactly with the crystal structure used for
> equlibration (I mean before and after) ?
> 
> Please be comprehensive. I just need to understand something.

It's easy to ask for a "comprehensive" answer on a mailing list but
what you need to realise is that you are really asking about is the
basics of molecular simulation.  There is no quick answer to this and
whole text books have been written on the topic.

The way "equilibration" is typically used is to really mean to reach a
nearby local minimum and expect to see a convergent behaviour with
respect to a chosen target property.  This paper,
dx.doi.org/10.1021/acs.jctc.5b00784 may be an interesting starting
point.

You may also want to abandon words like "exact" or "correct" in this
context.


Cheers,
Hannes.
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[gmx-users] Fwd: CNT Water and DNA protein, Not working

[Abhishek Agrawal]

-- Forwarded message --
From: Abhishek Agrawal 
Date: Tue, Mar 21, 2017 at 2:25 PM
Subject: CNT Water and DNA protein, Not working
To: gmx-us...@gromacs.org


Hare Krishna Everyone!

OBJECITVE:
See I am aiming to make a system having
CNT
Water
DNA
to study the interaction of DNA with the CNT, when CNT has some charged
molecule attached to it or any one C be have some charge.

SPECIFICATIONS:
GROMACS 5.0.7
fftw
Python
VMD
i3 5005 2.0 GHz 4GB Ubuntu 16.04 LTS

PROBLEM:
Going through many tutorials, gromacs mailing list and Andre tutorial for
CNT on Gromacs site, I found that whatever I do, by making custom
forcefield or going by default forcefield with the GROMACS nothing is
working for me.
It gives error that residue "UNL" or whatever the PDB has, is not found in
the topolgy database,, this is for the default forcefield.
I make custom one, then CNT is accepted but then on solvating the Water is
not. Going forward DNA shall also be not accepted as it is not available in
the custom forcefield.

SUMMARY:
What to do to make a system having:
CNT Water and DNA, the FORCEFIELD is the major issue.
Please guide.

Regards,
Abhishek Agrawal
AMITY UNIVERSITY
Research Associate @ NIT Patna
NOIDA, INDIA
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Re: [gmx-users] query about structural consistency

[abhisek Mondal]

I really appreciate your thoughts. I know about the words like "exact" or
"correct" does not stand in such scenario. I just needed an expert opinion
regarding the quality assurance of the equilibrated structure. People often
tend to ask question like how can you say that your model is properly
equilibrated to perform a production MD, we are all more or less familier
with that.

Thanks again for the comment.

Best regards,
Abhisek

On Tue, Mar 21, 2017 at 5:26 PM, Hannes Loeffler  wrote:

> On Tue, 21 Mar 2017 13:09:46 +0530
> abhisek Mondal  wrote:
>
> > Hi,
> >
> > I just have a basic query.
> >
> > I'm working with a protein-ligand system with a goal of performing
> > Umbrella sampling in gromacs. So first, after I build the complex, I'm
> > going for NVT and followed by NPT equilibration of 20ns each. After
> > equilibration, is it mandatory that my equilibrated protein-ligand
> > complex matches exactly with the crystal structure used for
> > equlibration (I mean before and after) ?
> >
> > Please be comprehensive. I just need to understand something.
>
> It's easy to ask for a "comprehensive" answer on a mailing list but
> what you need to realise is that you are really asking about is the
> basics of molecular simulation.  There is no quick answer to this and
> whole text books have been written on the topic.
>
> The way "equilibration" is typically used is to really mean to reach a
> nearby local minimum and expect to see a convergent behaviour with
> respect to a chosen target property.  This paper,
> dx.doi.org/10.1021/acs.jctc.5b00784 may be an interesting starting
> point.
>
> You may also want to abandon words like "exact" or "correct" in this
> context.
>
>
> Cheers,
> Hannes.
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> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*
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Re: [gmx-users] NORMAL MODES analysis to compute specific heats

[Justin Lemkul]

On 3/20/17 9:34 AM, Juan José Galano Frutos wrote:

Hi there:

I've been googled a bit about this issue (
http://thread.gmane.org/gmane.science.biology.gromacs.user/49139,
http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis,
https://groups.google.com/forum/#!topic/archive-gmx-users/5C5Q8m9X21g), but
I've not found answers to my doubts yet.

My situation is that I want to obtain specific heats (Cp) of my systems
(protein solvated and neutralized) but, of course, at the Temperature and
Pressure of my experiments. So, my idea here is carry out a Normal Modes
analysis to extract the Hessian matrix but at least after the equilibration
step of my system. I'm interested in doing it so because Cp values only
make sense in relation with Temperature.
My doubts come up, however, when I read through the posted discussion and I
find that NM analyses apparently should be performed after minimization
steps (Conjugate gradient and/or L-BFGS). Then, I would like to ask you if
that is really so or if it is possible carry out this calculation after,
for instance, an equilibration or a productive step in which, of course,
some previous minimizations have already been performed as usual?

I've not understood also the suggestion made in one of the above referenced
discussions in which David Van der Spoel recommended set all cut-offs to
zero (=infinite), see below:


You can use the g96 coordinate format instead of using the trr file
from the conjugate gradients energy minimization.
Set all cut-offs to zero (= infinite).


What's the reason for that?
Where one should set to zero the cut-offs...? Just in the NM step or
that is for the minimization steps?



NMA requires that you be in an energy minimum (and hence the requirement for 
exhaustive energy minimization, well below what is normally considered adequate 
for a standard MD simulation), is typically done in vacuo (hence "infinite" 
cutoffs/no PBC) and is only valid if the fundamental modes of motion are 
harmonic.  At elevated temperature (anything non-0 K) you have anharmonicity in 
many motions and the harmonic approximation fails.


-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

==
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Re: [gmx-users] Index is larger than the number of atoms in the trajectory file

[Justin Lemkul]

On 3/20/17 4:24 PM, Mahboobeh Eslami wrote:

Hi all GMX usersI hope you are wellI have simulated a protein-ligand complex. 
My protein has two calcium ions. I want to use GMXPBSA approach for free energy 
calculation.
If I remove calcium ions,  I will get following error in the first step of 
MMPBSA calculation:Fatal error:
Index[1673] 1676 is larger than the number of atoms in the
trajectory file (1675). There is a mismatch in the contents
of your -f, -s and/or -n files.How can I solve this problem. please guide me


You probably only saved a subset of the system when writing the trajectory, 
which is now out of sync with an index file that was presumably constructed from 
the whole system.  Re-create the index file or save corresponding groups when 
writing the trajectory.


-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

==
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Re: [gmx-users] DSSP

[Justin Lemkul]

On 3/21/17 5:13 AM, Aishwarya Dhar wrote:

Following procedure I have used
1. Downloaded  http://swift.cmbi.ru.nl/gv/dssp/
dssp-2.0.4-linux-i386 and renamed it dssp

2.made dssp  executable  and moved it to usr/local/bin

3.Then ran the command from the current location where the tpr and trr
files are present do_dssp -s  md.tpr -f md.trr -o ss.xpm  -ver 2.0

4.There are 91 residues in your selected group dssp cmd='/usr/local/bin/dssp
-i ddixopnV -o dd4YitS9 > /dev/null 2> /dev/null'
trn version: GMX_trn_file (single precision)
Reading frame   0 time0.000
Back Off! I just backed up ddixopnV to ./#ddixopnV.1#

It seems that the run is going on for two weeks and dssp analysis couldnt
be done



How many frames did you save?  do_dssp is a very slow program (it's just a 
wrapper to call dssp) and if you have tons of frames, it will take a long time. 
You can always list the files in the directory in which do_dssp is operating and 
you should see temporary files prefixed with "dd" being created and over-written.


You can always test whether or not do_dssp is working by passing it a single 
frame to -f, rather than waiting for a very expensive .trr file to be processed 
in full.


-Justin

















Thanks




Sincerely

Aishwarya Dhar



--
==

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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[gmx-users] g_mmpbsa

[Kulkarni R]

 Hi gromacs users,

How to install mmpbsa using cgywin?

I am using gromacs through cgywin.

Thanks,
Kulkarni.R
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[gmx-users] Structure blowing up after increased the temperature

[Sameer Edirisinghe]

Dear users,

I'm trying to find the melting point and Tg of my polymer system using
Density vs temperature curve. I'm using all oplsaa forcefield and  I'm going
for NVT and followed by NPT equilibration ( Both at 523K) of 400ps each.
then after the production run (at 523K for 5ns) the system is blowing up
and can be observed broken molecules of the trajectory from VMD. But no
blowing up occurring at 300K temperature (200ns).

But if I only did the production run (at 523K) up to 200ps it seems no
blowing up occurring until 200ps.

Note. used .mdp files has attached with the mail

1) I'm not sure if the .mdp files caused the blowing up or the topology
caused the blow up of the system.

2) Can use same .mdp files by only changing coupling temperature for any
temperature?

Any suggestion would precious.

Regards
Bhagya Karunarathna
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