Re: [gmx-users] Damping for pulled group

[Alex]

Code issues can be discussed on the gmx-developers mailing list.  
Feature requests can be made on redmine.gromacs.org.  The best case is 
to file the feature request, take it on yourself, and discuss any 
issues on gmx-developers :)



Thanks. Posted: http://redmine.gromacs.org/issues/2218
I have my own MD simulator, which features all of that stuff, but 
Gromacs runs many, many, MANY times faster. :)


Alex

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Re: [gmx-users] Damping for pulled group

[Justin Lemkul]

On 7/18/17 4:44 PM, Alex wrote:

Hi all,

This is more of a question about where I should make a suggestion for the
developers. It turns out that Gromacs pull code was designed nearly
perfectly to do simulated friction force microscopy (FFM), i.e. scanning a
surface with a tip. The only thing that's missing is that the equation of
motion for the pulled group's COM does not contain an artificial damping
term and the group is free to oscillate, which is a common occurrence in
underdamped situations even experimentally. For pulling in systems GMX was
designed for, the lack of additional damping makes perfect sense for things
that are immersed in solvents (which would readily provide any damping),
but most simulated FFM is in vacuum. Options other than umbrella are
physically flawed, unfortunately.

Would it had to add a damping term for the umbrella and where should I post
this request for the developers?



Code issues can be discussed on the gmx-developers mailing list.  Feature 
requests can be made on redmine.gromacs.org.  The best case is to file the 
feature request, take it on yourself, and discuss any issues on gmx-developers :)


-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] Ethanol energies with CHARMM ff

[Justin Lemkul]

On 7/18/17 1:28 PM, Sonia Milena Aguilera Segura wrote:

Dear GROMACS users,

I am running a 4 nm box of ethanol and once I finished the MD, I got the right T, P, density. However, I noticed that my energies are odd. After several trials with different parameters and box sizes I am getting a Total Energy between -1.2 to 0.6 KJ/mol (already normalizaed, Total energy/#molecules). I checked the potential energy at the end of minimization and this was around -65 kJ/mol. Then, I observed that during NVT equilibration my potential energy decreased to a value around -33 kJ/mol with a kinetic energy also around the same value (33 kJ/mol), and that's why my final total energies and, therefore, enthalpies are giving values around 0. I ran 


I don't understand how you're calculating your enthalpies.  The kinetic energy 
is irrelevant because it should cancel between the gas and liquid phases for a 
given temperature, so the dHvap value is /N +  + RT


also simulations with water, isopropanol, and acetonitrile and I am getting 
values of -52, -206, and-48, which seem reasonable to me. My paremeters have 
been already discussed in a previous mail (please see acetonitrile


Reasonable based on...?

-Justin

with CHARMM ff), and they seem to be right to be used with CHARMM ff. I am using 
version 2016.3 (I did the sa

  me in 5.1.2), sd integrator, Berendsen barostat for equilibration and P-R for 
MD production. Any ideas of what should I look for or what can I be doing wrong?

Thank you very much!!!,

Sonia Aguilera
PhD student
ENSCM



--
==

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
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Re: [gmx-users] Using nose-Hoover thermostat with berendsen barostat

[Justin Lemkul]

On 7/18/17 9:23 AM, jay patil wrote:

The reason for using berendsen is: I thought parrinello is sensitive, it's not 
wise to use it while equilibrating. So I was trying to use berendsen for 
equilibration and then production run with parrinello.
One more thought, my system is not well equilibrated, I know because it got 
disturbed when I pulled one water molecule from solvent region into the 
bilayer. Which disrupted the Bilayer a little bit. Then my system should blow 
up in initial stages only may be because of overlap. Why it is blowing up after 
few nano seconds of simulation.



Crashes can occur at any time; they're more frequent right at the outset but bad 
physics can manifest at any point.  If the system ran fine without any biasing 
potential, but then you turn on a bias and things become unstable, you should be 
troubleshooting whatever restraints you've added, not the barostat.  The 
pressure instability is a symptom, not a cause.


-Justin


Some insights will be helpful.

Thanks
Yogesh


On 18-Jul-2017, at 5:37 PM, Mark Abraham  wrote:

Hi,

The more Berendsen you use, the less physics you get ;-)

Mark


On Tue, 18 Jul 2017 13:44 jay patil  wrote:

Hi Experts,
Can we use nose-Hoover thermostat in combination with berendsen barostat.
When I use grompp command, it gives warning berendsen will not give true
ensemble, and with -maxwarn 1 option I am able to run the simulation.  My
doubt is: can we use this combination of thermostat and barostat. Or both
should be berendsen.
Any suggestion will be helpful.

Thanks

Yogesh
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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
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Re: [gmx-users] Regarding pdb2gmx and mdrun

[Justin Lemkul]

On 7/18/17 8:15 AM, S M Bargeen Turzo wrote:

Hey I have been trying to convert S100A8A9(has two chains) to .gro but
after energy minimization I am not getting an integer for the total charge
of the system.



What is the magnitude of this non-integer charge?  Did you do anything funny 
during pdb2gmx like using -missing?


-Justin


Secondly when I try to do molecular dynamics simulation using these
parameters:
;   0.5 ps NVT production with Langevin thermostat and GB implicit solvent
 INPUT

ld_seed = -1  ; Use random seed
# INTEGRATOR
##
define  = -DPOSRES
integrator  = sd; Langevin thermostat
dt  = 0.002 ; Timestep (ps)
nsteps  = 250   ; Simulation duration (timesteps)
nstcomm = 250   ; Center of mass motion removal interval
comm_mode   = angular; Center of mass motion removal mode
## ENSEMBLE
###
ref_t   = 300   ; System temperature (K)
tau_t   = 2.0   ; Thermostat time constant (ps)
tc_grps = system; Apply thermostat to complete system
## IMPLICIT SOLVENT
###
implicit_solvent = GBSA ; Generalized Born implicit solvent
gb_algorithm = HCT  ; Hawkins-Cramer-Truhlar radii calculation
nstgbradii  =  1
rgbradii = 0.0  ; Cutoff for Born radii calculation (A)
gb_epsilon_solvent  =  80
gb_saltconc   =  0
sa_algorithm =  Ace-approximation
sa_surface_tension  = 2.25936
### NONBONDED INTERACTIONS

cutoff_scheme = group   ; Method of managing neighbor lists
pbc   = no  ; Periodic boundary conditions disabled
coulombtype   = cut-off ; Calculate coulomb interactions using cutoff
rcoulomb  = 0.0 ; Coulomb cutoff of infinity
vdw_type  = cut-off ; Calculate van der Waals interactions using cutoff
rvdw  = 0.0 ; Van der Waals cutoff of infinity
rlist = 0.0 ; Neighbor list cutoff
nstlist   = 0   ; Do not update neighbor list
### OUTPUT

nstlog= 50  ; Log output interval (timesteps)
nstenergy = 50  ; Energy output interval (timesteps)
nstcalcenergy = 50  ; Energy calculation interval (timesteps)
nstxout   = 50  ; Trajectory output interval (timesteps)
nstvout   = 50  ; Velocity outout interval (timesteps)
nstfout = 50 ; Force output interval (timesteps)

I get segmentation fault(11). I don't know what this means. Can you please
help me out?



--
==

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
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Re: [gmx-users] nitrogen itp file with virtual site

[Justin Lemkul]

On 7/17/17 3:39 PM, Ali Ahmed wrote:

Dear Justin

Here is the topology file I wrote. I included all the parameters rather
than use a specific FF.

Thank you for your support

..

-

; virtual sites have zero mass which leads to zero Moment of inertia

;virual sites have charge only 0.482 e. to balance the nitrogen atom
negative charge -0.482 e.

; the distance between two nitrogn atoms N--N is 0.11 nm

;the distance between two virtual sites is 0.15 nm

;the distance between nitrogen atom and virtual site is 0.02 nm. This makes
the virtual site attached to the nitrogen atom

;

[ atomtypes ]

; name  bond_typemasscharge   ptype  sigma  epsilon

N   N 0.000   0.000  A
0.332  0.3026

   MN   MN 0.000   0.000  A  0.000
0.000; MN is the virtual sites



This is incorrect; the virtual site should be particle type V, not A.




[ moleculetype ]

; name  nrexcl

N_2   2



[ atoms ]

;   nr   type  resnr residue  atom   cgnr charge   mass
typeBchargeB  massB

  1 N   1N_2 N1  1-0.482
14.0067

  2 N   1N_2 N2  1-0.482
14.0067

  3MN   1N_2 M11 0.482
0.

  4MN   1N_2 M2 1 0.4820.



[ constraints ]

; There are no bonds in this system

; Instead, we fix the distance between the mass centers such that

; the virtual sites can be reconstructed

 3   4   1   0.15



This is why your system is failing.  You're defining a constraint between the 
virtual sites and no bonded interaction at all between the N atoms.  If the N-N 
bond is to be constant at 0.11 nm, then set it as a constraint (between atoms 1 
and 2) and construct the virtual sites based on the real atoms in the system.


-Justin


[ system ]

CO2 in vacuo



[ molecules ]

N_2 30



On Mon, Jul 17, 2017 at 12:46 PM, Justin Lemkul  wrote:




On 7/17/17 12:31 PM, Ali Ahmed wrote:


Dear Justin
I have tried same what you have said. I followed the tutorial for CO2 but
didn't work, gave an error during the energy minimization . I'm not sure
what was the wrong, I noticed the N atoms (in the box) were separated from
the virtual site after the error.



If you have just N2 in a box in vacuo, then this would suggest a topology
problem.  Please post the exact text of your .itp file.  It should be quite
short and easy to spot any problems.

-Justin




On Mon, Jul 17, 2017 at 10:41 AM, Justin Lemkul  wrote:




On 7/17/17 11:38 AM, Ali Ahmed wrote:

Dear Justin

Thank you very much. As I saw in some literature (as in the link below)
that N atom has a negative charge and needs a massless positive charge.
I
tried with most of the FFs but could not produce nitrogen density above
critical point. I don'n know which FF is the best one and I'm new to MD
simulations and new GROMACS user.
Could you please tell me which FF should I use?



What you're citing is a custom model.  You can write the force field
files
very easily.  I see what you're trying to do now, but you should be clear
that N2 is not a negatively charged molecule simply because the N atoms
(in
this representation) have partial negative charges.  The virtual site
balances it out so that electrostatic properties are better represented.

The virtual site you need to create is a simple one, placed at the center
of the N-N bond, so this is virtual_sites2 with an "a" value of 0.5.

-Justin


Thank you very much I appreciate your support.



http://iopscience.iop.org/article/10.1088/0965-0393/24/4/045002/meta

On Mon, Jul 17, 2017 at 8:40 AM, Justin Lemkul  wrote:




On 7/16/17 9:20 PM, Ali Ahmed wrote:

Hello GROMACS users,


This is Ali, I'm new to Gromacs and doing MD simulation of nitrogen at
super critical point.The structure I use is different from regular
nitrogen
(N-N). As you know N atom has a negative charge which means the
nitrogen
molecule will be negatively charged, therefore I need to use massless
and


This is incorrect - N2 carries no formal charge.


charged virtual site to equilibrate the molecule. I have looked on the

tutorial about CO2 to produce the XXX.itp but didnot work with me.

Could
anyone have done it before tell me how to do it ?


You don't need virtual sites for a diatomic molecule.



-Justin

Here are the parameters:

N :mass =14.0067, epsilon =(0.3026 KJ/mol), sigma =(0.332 nm), Charge

=(-0.482 e).

XX (massless, charged particle ):mass =0, epsilon=0, sigma=0 Charge=
0.964
e.

Thank you very much.


--


==

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility 

Re: [gmx-users] Equilibration of Lipid Bilayers created through charmm-gui

[Justin Lemkul]

On 7/17/17 2:14 PM, Nidhin Thomas wrote:

Hello  everyone,

I have created an 'alpha-helix protein embedded in a lipid bilayer’ system 
using charmm-gui.

I used the mdp files provided by charmm-gui directly without changing the 
number of steps or constraints for equilibration. I ran final simulation for 
200 ns without any constraints and obtained a system in which there was no 
water penetration into the bilayer.



I'm assuming you mean restraints?  You certainly should be using constraints.


I compared my results against a research paper and I see water penetration into 
the bilayer for that system. They didn’t use charm-gui for modeling and they 
had frozen the protein during the initial equilibration compared to my system.



Freezing is a very severe and artificial perturbation.  It's entirely possible 
that water leaked in as an artifact of having an immobile protein.



Should we always freeze the protein during the initial equilibration time and 
let lipids settle before starting the equilibration with constraints to protein?



Not necessarily.  I rarely find freezing necessary or appropriate.


When I used the mdp files obtained from charmm-gui directly, I checked the RMSD 
values of the protein and it’s within 3 Angstrom which I think is within the 
acceptable range. Also average protein tilt within the lipids is also constant. 
Could you please tell me what else I can check to confirm if my system is fully 
equilibrated ?



Check convergence by looking at the time-dependence of any relevant property.

-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] Regarding calculation of coordination number

[Dallas Warren]

2) to calculate it yourself you integrate the area under the g(r)
curve between the two minima and multiple that by the atomic density.
Easy to do, even can do in a spreadsheet such as Excel.

https://en.wikibooks.org/wiki/Molecular_Simulation/Radial_Distribution_Functions#Coordination_Numbers

Try searching the emailing list too, many times what you are asking
has been asked many times before
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 19 July 2017 at 02:13, Dilip H N  wrote:
> Hello,
> i have calculated the radial distribution function through the commands as:-
> gmx rdf -f ab.ttr -s ab.tpr -n ab.ndx -o rdf_ab.xvg -ref x -sel y -cn
> cn_ab.xvg
>
> 1] my doubt is tht whether -cn option is calculating the co-ordination
> number ie., running coordination number [N(r)] or just the coordination
> number [CN]..??
> Because when i compare the 1st minima of rdf value to the corresponding
> coordination number tht i have got by -cn flag is not matching.. i am
> getting very less coordination number even with the corresponding
> second/third minima value of rdf also..
> can anybody help??
> 2] And if want to calculate coordination number by the formula, how can i
> do tht.?? should i manually integrate and calculate the values till 1st
> minima or do i need to write a small code for tht.?? how could i solve this
> issue..??
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
>  Sent with Mailtrack
> 
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Re: [gmx-users] Best Force Field For Gases at High pressure

[Dallas Warren]

Check the literature .

https://scholar.google.com.au/scholar?q=molecular+dynamics+simulation+of+gases+at+high+pressure
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 19 July 2017 at 01:22, Sam Dav  wrote:
> Hello GROMACS users
> Does anyone have an idea about the suitable force field for gases (Methane,
> Oxygen, and  Nitrogen) at high pressure (above 300 bar)?. I have tried with
> most of the force fields in GROMACS but the physical properties were far
> from the experimental values.
> Thank you in advance
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[gmx-users] Fwd: gmx select querry

[shivangi nangia]

Date: Mon, Jul 17, 2017 at 11:26 AM
Subject: gmx select querry
To: Discussion list for GROMACS users 


Hello All,


I have a question regarding the usage of gmx select.


I want to select water molecules in a particular subset in z-direction
(example z > 5 and z < 10) for each frame of my trajectory and then carry
out analysis using g_mindist on each frame of the trajectory (with
selections)

For example: system consists of peptide 1 and peptide2, membrane, water and
ions.

using g_mindist, I want to calculate the number of contacts peptide1 is
making with water vs. peptide2 in z >5 and z < 10 over the whole trajectory.

When I try to make selection using:
The option pdbatoms selected only lists the selected atoms.
The option pdbatoms all lists everything.

The -on options gives me the index file of only selected atoms:

gmx_mpi select -f 432000g1.gro -s ../../3run_npt_noposre.tpr -select
'(resname TIP3 and name OH2) and z  > -10 and z < 20'  -oi -pdbatoms
selected -on insel.ndx
I am a little confused how to incoporate the slections in odere to carry
out the analysis I am interested in.

Kindly suggest.

Thanks for your time in advance.

Regards,
sn
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Re: [gmx-users] Damping for pulled group

[Alex]

I mean would it be hard to add a damping term. Sorry, half asleep. :)

Alex

On Tue, Jul 18, 2017 at 2:44 PM, Alex  wrote:

> Hi all,
>
> This is more of a question about where I should make a suggestion for the
> developers. It turns out that Gromacs pull code was designed nearly
> perfectly to do simulated friction force microscopy (FFM), i.e. scanning a
> surface with a tip. The only thing that's missing is that the equation of
> motion for the pulled group's COM does not contain an artificial damping
> term and the group is free to oscillate, which is a common occurrence in
> underdamped situations even experimentally. For pulling in systems GMX was
> designed for, the lack of additional damping makes perfect sense for things
> that are immersed in solvents (which would readily provide any damping),
> but most simulated FFM is in vacuum. Options other than umbrella are
> physically flawed, unfortunately.
>
> Would it had to add a damping term for the umbrella and where should I
> post this request for the developers?
>
> Thank you,
>
> Alex
>
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[gmx-users] Damping for pulled group

[Alex]

Hi all,

This is more of a question about where I should make a suggestion for the
developers. It turns out that Gromacs pull code was designed nearly
perfectly to do simulated friction force microscopy (FFM), i.e. scanning a
surface with a tip. The only thing that's missing is that the equation of
motion for the pulled group's COM does not contain an artificial damping
term and the group is free to oscillate, which is a common occurrence in
underdamped situations even experimentally. For pulling in systems GMX was
designed for, the lack of additional damping makes perfect sense for things
that are immersed in solvents (which would readily provide any damping),
but most simulated FFM is in vacuum. Options other than umbrella are
physically flawed, unfortunately.

Would it had to add a damping term for the umbrella and where should I post
this request for the developers?

Thank you,

Alex
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[gmx-users] Ethanol energies with CHARMM ff

[Sonia Milena Aguilera Segura]

Dear GROMACS users, 

I am running a 4 nm box of ethanol and once I finished the MD, I got the right 
T, P, density. However, I noticed that my energies are odd. After several 
trials with different parameters and box sizes I am getting a Total Energy 
between -1.2 to 0.6 KJ/mol (already normalizaed, Total energy/#molecules). I 
checked the potential energy at the end of minimization and this was around -65 
kJ/mol. Then, I observed that during NVT equilibration my potential energy 
decreased to a value around -33 kJ/mol with a kinetic energy also around the 
same value (33 kJ/mol), and that's why my final total energies and, therefore, 
enthalpies are giving values around 0. I ran also simulations with water, 
isopropanol, and acetonitrile and I am getting values of -52, -206, and-48, 
which seem reasonable to me. My paremeters have been already discussed in a 
previous mail (please see acetonitrile with CHARMM ff), and they seem to be 
right to be used with CHARMM ff. I am using version 2016.3 (I did the sa
 me in 5.1.2), sd integrator, Berendsen barostat for equilibration and P-R for 
MD production. Any ideas of what should I look for or what can I be doing 
wrong? 

Thank you very much!!!, 

Sonia Aguilera 
PhD student 
ENSCM 
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[gmx-users] Regarding calculation of coordination number

[Dilip H N]

Hello,
i have calculated the radial distribution function through the commands as:-
gmx rdf -f ab.ttr -s ab.tpr -n ab.ndx -o rdf_ab.xvg -ref x -sel y -cn
cn_ab.xvg

1] my doubt is tht whether -cn option is calculating the co-ordination
number ie., running coordination number [N(r)] or just the coordination
number [CN]..??
Because when i compare the 1st minima of rdf value to the corresponding
coordination number tht i have got by -cn flag is not matching.. i am
getting very less coordination number even with the corresponding
second/third minima value of rdf also..
can anybody help??
2] And if want to calculate coordination number by the formula, how can i
do tht.?? should i manually integrate and calculate the values till 1st
minima or do i need to write a small code for tht.?? how could i solve this
issue..??
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With Best Regards,

DILIP.H.N
Ph.D Student



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[gmx-users] Best Force Field For Gases at High pressure

[Sam Dav]

Hello GROMACS users
Does anyone have an idea about the suitable force field for gases (Methane,
Oxygen, and  Nitrogen) at high pressure (above 300 bar)?. I have tried with
most of the force fields in GROMACS but the physical properties were far
from the experimental values.
Thank you in advance
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Re: [gmx-users] Using nose-Hoover thermostat with berendsen barostat

[jay patil]

The reason for using berendsen is: I thought parrinello is sensitive, it's not 
wise to use it while equilibrating. So I was trying to use berendsen for 
equilibration and then production run with parrinello. 
One more thought, my system is not well equilibrated, I know because it got 
disturbed when I pulled one water molecule from solvent region into the 
bilayer. Which disrupted the Bilayer a little bit. Then my system should blow 
up in initial stages only may be because of overlap. Why it is blowing up after 
few nano seconds of simulation.

Some insights will be helpful.

Thanks
Yogesh

> On 18-Jul-2017, at 5:37 PM, Mark Abraham  wrote:
> 
> Hi,
> 
> The more Berendsen you use, the less physics you get ;-)
> 
> Mark
> 
>> On Tue, 18 Jul 2017 13:44 jay patil  wrote:
>> 
>> Hi Experts,
>> Can we use nose-Hoover thermostat in combination with berendsen barostat.
>> When I use grompp command, it gives warning berendsen will not give true
>> ensemble, and with -maxwarn 1 option I am able to run the simulation.  My
>> doubt is: can we use this combination of thermostat and barostat. Or both
>> should be berendsen.
>> Any suggestion will be helpful.
>> 
>> Thanks
>> 
>> Yogesh
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Re: [gmx-users] Using nose-Hoover thermostat with berendsen barostat

[jay patil]

Hi Mark,
Currently I am struggling with equilibrating the system. I am constraining a 
water molecule in a Bilayer at a fixed distance from the COM of the Bilayer. I 
tried many things like changing pressure coupling, temp coupling, varying time 
constants, rlist, varying step size, increasing warnangle, relaxing Lincs 
constrain, etc. But my system is blowing up after few nano seconds of 
simulation. Error is pressure coupling more than 1%. Volume was steady 
initially till few nano seconds and then suddenly it started oscillating and 
then system blows up. I checked every parameter one by one, varying in feasible 
range but no success. :(
The Bilayer I am using is simulated for 500ns. Bilayer properties are well 
estimated compared to experimental value. I am unable to get what I am doing 
wrong. 
Any suggestion will be helpful.


Thanks
Yogesh

> On 18-Jul-2017, at 5:37 PM, Mark Abraham  wrote:
> 
> Hi,
> 
> The more Berendsen you use, the less physics you get ;-)
> 
> Mark
> 
>> On Tue, 18 Jul 2017 13:44 jay patil  wrote:
>> 
>> Hi Experts,
>> Can we use nose-Hoover thermostat in combination with berendsen barostat.
>> When I use grompp command, it gives warning berendsen will not give true
>> ensemble, and with -maxwarn 1 option I am able to run the simulation.  My
>> doubt is: can we use this combination of thermostat and barostat. Or both
>> should be berendsen.
>> Any suggestion will be helpful.
>> 
>> Thanks
>> 
>> Yogesh
>> --
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>> 
>> * Please search the archive at
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>> posting!
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>> 
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[gmx-users] Regarding pdb2gmx and mdrun

[S M Bargeen Turzo]

Hey I have been trying to convert S100A8A9(has two chains) to .gro but
after energy minimization I am not getting an integer for the total charge
of the system.

Secondly when I try to do molecular dynamics simulation using these
parameters:
;   0.5 ps NVT production with Langevin thermostat and GB implicit solvent
 INPUT

ld_seed = -1  ; Use random seed
# INTEGRATOR
##
define  = -DPOSRES
integrator  = sd; Langevin thermostat
dt  = 0.002 ; Timestep (ps)
nsteps  = 250   ; Simulation duration (timesteps)
nstcomm = 250   ; Center of mass motion removal interval
comm_mode   = angular; Center of mass motion removal mode
## ENSEMBLE
###
ref_t   = 300   ; System temperature (K)
tau_t   = 2.0   ; Thermostat time constant (ps)
tc_grps = system; Apply thermostat to complete system
## IMPLICIT SOLVENT
###
implicit_solvent = GBSA ; Generalized Born implicit solvent
gb_algorithm = HCT  ; Hawkins-Cramer-Truhlar radii calculation
nstgbradii  =  1
rgbradii = 0.0  ; Cutoff for Born radii calculation (A)
gb_epsilon_solvent  =  80
gb_saltconc   =  0
sa_algorithm =  Ace-approximation
sa_surface_tension  = 2.25936
### NONBONDED INTERACTIONS

cutoff_scheme = group   ; Method of managing neighbor lists
pbc   = no  ; Periodic boundary conditions disabled
coulombtype   = cut-off ; Calculate coulomb interactions using cutoff
rcoulomb  = 0.0 ; Coulomb cutoff of infinity
vdw_type  = cut-off ; Calculate van der Waals interactions using cutoff
rvdw  = 0.0 ; Van der Waals cutoff of infinity
rlist = 0.0 ; Neighbor list cutoff
nstlist   = 0   ; Do not update neighbor list
### OUTPUT

nstlog= 50  ; Log output interval (timesteps)
nstenergy = 50  ; Energy output interval (timesteps)
nstcalcenergy = 50  ; Energy calculation interval (timesteps)
nstxout   = 50  ; Trajectory output interval (timesteps)
nstvout   = 50  ; Velocity outout interval (timesteps)
nstfout = 50 ; Force output interval (timesteps)

I get segmentation fault(11). I don't know what this means. Can you please
help me out?
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Re: [gmx-users] CHARMM force file error in gromacs

[Mark Abraham]

Hi,

The list cannot accept attachments. What did you to try to understand why
the pair of files that you think match do not match for the program?

Mark

On Tue, 18 Jul 2017 09:19 Vikram Dalal  wrote:

> Hi everyone,
>
>
> I have to do molecular dynamics simulation of a zinc containing protein.
>
> I have kept the Zn molecule along with the protein and generate the
> topology file by using CHARMM36 force field in Gromacs5.1.4.
>
> I have downloaded the CHARMM36 force field from this link:-
>
>  http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs
>
>
>
>
> I have converted the ligand PDB file into mol2 by discovery studio
> visualizer. I have submitted this mol2 on CGenFF and get the str file.
>
> But I got the -2.0 charge on my ligand in str file.
>
> Then I kept this str file, mol2 file, cgenff_charmm2gmx.py
> and charmm36-jul2017.ff in same directory.
>
> I ran the "python cgenff_charmm2gmx.py" PDC pdc.mol2 pdc.str charmm36-ff
> from the terminal of same directory.
>
> I got this message:-
>
>
>
>
> NOTE1: Code tested with python 2.7.3. Your version: 2.7.12 (default, Nov
> 19 2016, 06:48:10)
>
> [GCC 5.4.0 20160609]
>
>
>
>
> NOTE2: Please be sure to use the same version of CGenFF in your
> simulations that was used during parameter generation:
>
> --Version of CGenFF detected in pdc.str : 4.0
>
> --Version of CGenFF detected in charmm36.ff//forcefield.doc : 4.0
>
>
>
>
> NOTE3: In order to avoid duplicated parameters, do NOT select the 'Include
> parameters that are already in CGenFF' option when uploading a molecule
> into CGenFF.
>
> Error in atomgroup.py: read_mol2_coor_only: no. of atoms in mol2 (17) and
> top (15) are unequal
>
> Usually this means the specified residue name does not match between str
> and mol2 files
>
>
>
>
>
>
>
> I have attached here my mol2, str, cgenff_charmm2gmx.py
> and charmm36-jul2017.ff.tgz.
>
>
>
>
> Thank you in advance.
>
>
>
> --
> Thanks & Regards,
> VIKRAM DALAL
> Research Scholar
> Department of Biotechnology
> Indian Institute of Technology, Roorkee
> INDIA
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Re: [gmx-users] Using nose-Hoover thermostat with berendsen barostat

[Mark Abraham]

Hi,

The more Berendsen you use, the less physics you get ;-)

Mark

On Tue, 18 Jul 2017 13:44 jay patil  wrote:

> Hi Experts,
> Can we use nose-Hoover thermostat in combination with berendsen barostat.
> When I use grompp command, it gives warning berendsen will not give true
> ensemble, and with -maxwarn 1 option I am able to run the simulation.  My
> doubt is: can we use this combination of thermostat and barostat. Or both
> should be berendsen.
> Any suggestion will be helpful.
>
> Thanks
>
> Yogesh
> --
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[gmx-users] Using nose-Hoover thermostat with berendsen barostat

[jay patil]

Hi Experts,
Can we use nose-Hoover thermostat in combination with berendsen barostat. When 
I use grompp command, it gives warning berendsen will not give true ensemble, 
and with -maxwarn 1 option I am able to run the simulation.  My doubt is: can 
we use this combination of thermostat and barostat. Or both should be 
berendsen. 
Any suggestion will be helpful.

Thanks

Yogesh
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[gmx-users] CHARMM force file error in gromacs

[Vikram Dalal]

Hi everyone,


I have to do molecular dynamics simulation of a zinc containing protein. 
 
I have kept the Zn molecule along with the protein and generate the topology 
file by using CHARMM36 force field in Gromacs5.1.4.

I have downloaded the CHARMM36 force field from this link:- 

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



 
I have converted the ligand PDB file into mol2 by discovery studio visualizer. 
I have submitted this mol2 on CGenFF and get the str file.
 
But I got the -2.0 charge on my ligand in str file.
 
Then I kept this str file, mol2 file, cgenff_charmm2gmx.py and 
charmm36-jul2017.ff in same directory. 
 
I ran the "python cgenff_charmm2gmx.py" PDC pdc.mol2 pdc.str charmm36-ff from 
the terminal of same directory.
 
I got this message:-
 



NOTE1: Code tested with python 2.7.3. Your version: 2.7.12 (default, Nov 19 
2016, 06:48:10) 

[GCC 5.4.0 20160609]




NOTE2: Please be sure to use the same version of CGenFF in your simulations 
that was used during parameter generation:

--Version of CGenFF detected in pdc.str : 4.0

--Version of CGenFF detected in charmm36.ff//forcefield.doc : 4.0




NOTE3: In order to avoid duplicated parameters, do NOT select the 'Include 
parameters that are already in CGenFF' option when uploading a molecule into 
CGenFF.

Error in atomgroup.py: read_mol2_coor_only: no. of atoms in mol2 (17) and top 
(15) are unequal

Usually this means the specified residue name does not match between str and 
mol2 files







I have attached here my mol2, str, cgenff_charmm2gmx.py and 
charmm36-jul2017.ff.tgz.
 



Thank you in advance. 



--
Thanks & Regards,
VIKRAM DALAL
Research Scholar
Department of Biotechnology
Indian Institute of Technology, Roorkee
INDIA
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