Re: [gmx-users] Normal-mode analysis in Gromacs

[David van der Spoel]

Den 2018-03-08 kl. 00:53, skrev Kevin C Chan:

Dear Users,

I have encountered several questions when I try to perform NMA on a protein
structure from an equilibrated MD simulation. I were basically referred to
the gromacs manual (
http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis) and some
threads in the mailing list.

First, Gromacs (and in some literature) suggest to have L-BFGS energy
minimization (sometimes after steep and cg calculations) of the structure
before NMA and L-BFGS generally requires shifted/switched interactions.
However, for vdW the option should have been changed by introducing the
vdw-modifier and l-bfgs seems to still recognize it as cutoff.

Second, for electrostatics, the option has been improved by
Reaction-field-zero but is it still suitable for NMA calculation?

Third, I have achieved a maximum force of 9.78750e-01 using cg and still
got the warning: "The force is probably not small enough to ensure that you
are at a minimum." Usually how stable do we have to achieve in order to
avoid the warning?

Thanks in advance for any experience shared.

You need to compile gromacs in double precision to get to low forces.



Kevin
OSU Pharmacy




--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
--
Gromacs Users mailing list

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

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

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

[gmx-users] Hamiltonian replica exchange in gromacs 4.6.7

[Carlo Martinotti]

Hello everybody,

So i am trying to set up a replica exchange with solute tempering simulation 
for my membrane-drug systems. We modified the gromacs source code in a way that 
allows the modification of the hamiltonian of singular pairs of interactions 
(eg solute-water, solute-solute, ion-solute etc). Until now I tested this part 
on single simulations and it's now working as intended. Now though i have to 
switch on the replica exchange part and allow them to exchange.
Right now i tried to set up a test system with 2 replicas at the same 
temperatures, but with different scaling.
Again, remember this is an in house modification of the code, not the classical 
REST methodology.
I launch the classical mdrun -multidir -replex and the system is complaining 
that there is nothing to exchange cause the systems are the same. I assume that 
this is because the temperature of two systems are actually the same and he is 
using equation 3.141 from manual 4.6.7 part 3.13.

So here is my question:

From my understanding of manual 4.6.7 part 3.13, to allow the exchange as per 
equation 3.142 i MUST use the lambda routine. My idea is then to try to trick 
the program inserting the same values of lambdas in both of the replicas so to 
force gromacs tu use the equation 3.142 for the evaluation of the probability 
of exchange.
I am pretty sure that the program is going to complain about that, but in the 
case i can eliminate the check for identical lambdas in the source code.

Do you think this would suffice? Or do you see things that i am missing out ?

Of course i know that without knowing what exact tweaks of the code we did you 
can't answer accurately, but assume that when a single tempered simulation is 
run the functions to compute the forces and the vdw terms are changed in the 
beginning of the simulations and they stay changed for the whole of the 
simulation, so that when gromacs will compute the cross terms in ((U1(x2) − 
U1(x1)) + (U2(x1) − U2(x2)) it should be assumed to use the right hamiltonian.

Thanks in advance for the time and effort!

-- 
Gromacs Users mailing list

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

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

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

[gmx-users] OPLS-AA parameters for dimethylsiloxane

[Alex]

Hi all,

Before I start possibly reinventing the wheel, does anyone here have a
decent OPLS-AA topology for dimethylsiloxane? LipParGen produces a
topology, but for a different FF, and the otherwise excellent OPLS-AA
topology builder from ERG fails outright. Not exactly a Gromacs question, I
know.

There is of course this work: https://pubs.acs.org/doi/abs/10.1021/jp047434r
but I thought I'd ask before I start hammering it into something
OPLS-compatible...
Thank you,

Alex
-- 
Gromacs Users mailing list

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

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

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

[gmx-users] viscosity calculation using Green-Kubo

[Jo]

Hello,

I would like to calculate viscosity using the Green-Kubo method.  I
understand that the viscosity calculation using g_energy uses the msd
method.  Is there any built in command in gromacs for green-kubo? Or would
I need to do that by hand?

Thanks,

Jo
-- 
Gromacs Users mailing list

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

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

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

[gmx-users] viscosity calculation using g_energy

[Jo]

Hello,

I would like to calculate viscosity of a box of water using g_energy.  I
used the line g_energy -f production.edr -vis viscosity.xvg, where the
viscosity.xvg generated shows bulk and shear viscosity (cP) by time (ps).
However, the value are several orders of magnitude above the correct value
for viscosity.  For SPCE water, the viscosity is ~0.7 cP, where the gromacs
output shows 100+ cP.

I have my system equilibrated and I know that other properties such as
energy and density are calculated correctly.

I believe I am having the same issues as in the person in this previous
post.
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2009-March/040458.html

Can you please direct on what I might be doing wrong?

Thank you,

Jo
-- 
Gromacs Users mailing list

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

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

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

[gmx-users] X2top error, Could only find a forcefield type for 0 out of 66 atoms

[John Adams]

Dear Gromacs users,
I am trying to transform my PDP file for AL2O3 surface to a top file using
x2top. I have defined my forcefield.itp and .n2t file. However, I keep
recieving an error telling me that "Could only find a forcefield type for 0
out of 66 atoms"

my PDB file looks like
COMPNDUNNAMED
AUTHORGENERATED BY OPEN BABEL 2.3.2
CRYST14.7598.243   17.151  90.00  90.00  90.00 P1  1
HETATM1  O   LIG 1   3.201   0.667   3.490  1.00  0.00
  O
HETATM2  O   LIG 1   0.822   4.789   3.490  1.00  0.00
  O
HETATM3  O   LIG 1   0.822   2.041   7.821  1.00  0.00
  O
HETATM4  O   LIG 1   3.201   6.163   7.821  1.00  0.00
  O
HETATM5  B   LIG 1   3.201   3.415  12.151  1.00  0.00
  B
HETATM6  B   LIG 2   0.822   7.536  12.151  1.00  0.00
  B
HETATM7  O   LIG 1   1.017   1.928   3.490  1.00  0.00
  O
HETATM8  O   LIG 1   3.397   6.050   3.490  1.00  0.00
  O
HETATM9  O   LIG 1   3.397   3.302   7.821  1.00  0.00
  O
HETATM   10  O   LIG 1   1.017   7.424   7.821  1.00  0.00
  O


my itp file looks like
 #define _ff_clayff
 [ defaults ]
   ; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
   1   2   yes 0.5 0.5

[ atomtypes ]

; name   mass  chargeptype  sigma  eps
 ho   1  1.00800 0.4250A0.0e-01  0.0e-01
;clayFF_hydroxylhydrogen
 oh   8 15.99800-0.9500A3.16557e-01  6.50209e-01
;ClayFF_hydroxyloxygen
 ob   8 15.99800-1.0500A3.16557e-01  6.50209e-01
;ClayFF_bridgingoxyge
 ao  13 26.98200 1.5750A4.27128e-01  6.0e-06
;ClayFF_octahedalaluminium

[ bondtypes ]
; ij  func   b0  kb
   oh ho   10.1000 554134.9

 [ angletypes ]
 ;  ijk  func   th0   cth
   ao   ohho1109.47125.52


my .n2t file looks like

B   oh   -0.950015.998  1H   0.100  ;hydroxyl oxygen
O   ob   -1.299615.998  0   ;bridging oxygen
with double substitution
H   ho   -1.080815.998  1B   0.100  ;hydroxyl hydrogen
with substitution
AL  ao1.575026.982  0   ;octahedral
aluminium


Your help is really appreciated
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

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

Re: [gmx-users] thermostat and barostat

[Mark Abraham]

Hi,

The pressure coupling algorithms operate globally (but possibly
anisotropically)

Mark

On Wed, Mar 7, 2018, 17:43 Faezeh Pousaneh  wrote:

> Hi,
>
> I simulate a system which is very sensitive to chosen thermostat and
> barostat. I see information in
> Gromacs webpage (*
> http://www.gromacs.org/Documentation/Terminology/Thermostats
> *) that some
> thermostat are not good for systems with very few degrees of freedom (as my
> system).
> Is it the same with barostats? if so, which barostat I should choose (for
> no-interacting system)?
>
> Best 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
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

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

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

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

[gmx-users] thermostat and barostat

[Faezeh Pousaneh]

Hi,

I simulate a system which is very sensitive to chosen thermostat and
barostat. I see information in
Gromacs webpage (*http://www.gromacs.org/Documentation/Terminology/Thermostats
*) that some
thermostat are not good for systems with very few degrees of freedom (as my
system).
Is it the same with barostats? if so, which barostat I should choose (for
no-interacting system)?

Best 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

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

Re: [gmx-users] Fw: Geometry Optimization for Metal organic Frame works

[Momin Ahmad]

Hi,

i am also simulating MOFs with gromacs and can say that OBGMX is not the 
best way to generate the topology file. It has many flaws but shows some 
ideas. I am currently creating my own forcefield using the UFF4MOF by M. 
Addicoat. You can have a look at it:


https://pubs.acs.org/doi/abs/10.1021/ct400952t

Greets,
Momin


Am 07.03.2018 um 14:25 schrieb Nagasree Garapati:

Thank You Micholas


I have created the topology files using initial input file in OBGMX and it 
shows that there are 20 unique bond terms, out of which there are 3 bonds 
between the metal ion and the N2 in linker.

However, when I tried to create topolgies using the optimized final output 
(final.gro) file in OBGMX, nothing is created I have empty files for both .top 
and .itp files.

I believe there is something wrong with the topology files, but I am not able 
to figure out where is the mistake.

Any suggestions ?


Thank You


With Regards
Nagasree Garapati
Research Assistant Professor
Dept of Chemical and Biomedical Engineering
West Virginia University
PO Box 6102
Morgantown, WV 26506-6102
304 293-5028(O)
304 276-3674(M)



--
Momin Ahmad

Karlsruhe Institute of Technology (KIT)
Steinbuch Centre for Computing (SCC)
Hermann-von-Helmholtz-Platz 1
76344 Eggenstein-Leopoldshafen
Phone: +49 721 608-24286
E-Mail: momin.ah...@kit.edu

--
Gromacs Users mailing list

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

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

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

Re: [gmx-users] Gromacs Tutorial by Justin

[Faezeh Pousaneh]

Thank you.


Best regards


On Wed, Mar 7, 2018 at 1:38 PM, Justin Lemkul  wrote:

>
>
> On 3/7/18 6:24 AM, Faezeh Pousaneh wrote:
>
>> Dear Justin,
>>
>> I have 2 questions regarding your tutorial on Carbon Dioxide in this link:
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx
>> -tutorials/vsites/index.html
>>
>> 1- I see that in your simple simulation you use no boundary conditions,
>> pbc=no, should it be always so for this model?
>>
>> 2- You use
>>   comm-mode = angular,
>> is that necessary?
>>
>
> The simulation is a simple gas-phase system, which does not use PBC and
> hence requires angular COM motion removal.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

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

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

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

Re: [gmx-users] Geometry Optimization for Metal organic Frame works

[Smith, Micholas D.]

I would contact the OBGMX folks concerning this, as it sound like a software 
issue. If it works to produce a topology file for your initial coordinate 
system but not your optimized coordinates (presuming the same system 
composition, just modified geometry) than something seems amiss with their 
webserver.

Regards,

Micholas

===
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Nagasree 
Garapati 
Sent: Wednesday, March 07, 2018 8:25 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] Fw: Geometry Optimization for Metal organic Frame works

Thank You Micholas


I have created the topology files using initial input file in OBGMX and it 
shows that there are 20 unique bond terms, out of which there are 3 bonds 
between the metal ion and the N2 in linker.

However, when I tried to create topolgies using the optimized final output 
(final.gro) file in OBGMX, nothing is created I have empty files for both .top 
and .itp files.

I believe there is something wrong with the topology files, but I am not able 
to figure out where is the mistake.

Any suggestions ?


Thank You


With Regards
Nagasree Garapati
Research Assistant Professor
Dept of Chemical and Biomedical Engineering
West Virginia University
PO Box 6102
Morgantown, WV 26506-6102
304 293-5028(O)
304 276-3674(M)

--
Gromacs Users mailing list

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

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

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

-- 
Gromacs Users mailing list

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

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

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

[gmx-users] Fw: Geometry Optimization for Metal organic Frame works

[Nagasree Garapati]

Thank You Micholas


I have created the topology files using initial input file in OBGMX and it 
shows that there are 20 unique bond terms, out of which there are 3 bonds 
between the metal ion and the N2 in linker.

However, when I tried to create topolgies using the optimized final output 
(final.gro) file in OBGMX, nothing is created I have empty files for both .top 
and .itp files.

I believe there is something wrong with the topology files, but I am not able 
to figure out where is the mistake.

Any suggestions ?


Thank You


With Regards
Nagasree Garapati
Research Assistant Professor
Dept of Chemical and Biomedical Engineering
West Virginia University
PO Box 6102
Morgantown, WV 26506-6102
304 293-5028(O)
304 276-3674(M)

-- 
Gromacs Users mailing list

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

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

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

Re: [gmx-users] segmentation fault

[Justin Lemkul]

On 3/7/18 6:11 AM, sp...@iacs.res.in wrote:

Hii all
I am trying to simulate biomolecule in Guanidinium chloride in
AMBER99sb-ildn force field. I have prepared the topology of GdmCl taking
the parameters from ffbonded.itp and ffnonbonded.itp. It goes well in
energy minimization step but in NVT step files are generated and shows
segmentation fault(core dumped). How to solve this problem?
I have verified the topology of GdmCl by matching the density with the
experimental density. My another question is that should I proceed 
with the

topology by matching density only? Looking for some suggestions.



http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

-Justin

--
==

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

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

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

==

--
Gromacs Users mailing list

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

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

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

Re: [gmx-users] Gromacs Tutorial by Justin

[Justin Lemkul]

On 3/7/18 6:24 AM, Faezeh Pousaneh wrote:

Dear Justin,

I have 2 questions regarding your tutorial on Carbon Dioxide in this link:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/index.html

1- I see that in your simple simulation you use no boundary conditions,
pbc=no, should it be always so for this model?

2- You use
  comm-mode = angular,
is that necessary?


The simulation is a simple gas-phase system, which does not use PBC and 
hence requires angular COM motion removal.


-Justin

--
==

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

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

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

==

--
Gromacs Users mailing list

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

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

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

[gmx-users] Gromacs Tutorial by Justin

[Faezeh Pousaneh]

Dear Justin,

I have 2 questions regarding your tutorial on Carbon Dioxide in this link:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/index.html

1- I see that in your simple simulation you use no boundary conditions,
pbc=no, should it be always so for this model?

2- You use
 comm-mode = angular,
is that necessary?

thanks for answer.

Best 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

* 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.