Re: [gmx-users] Regarding creating the molecules...

[Dallas Warren]

Here is the link to the GROMACS page was referring to

http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation

On 14 Jun 2017 3:40 PM, "Dallas Warren"  wrote:

> Please keep discussion to the emailing list.
>
> 1/ and 2/ to construct the coordinate file for the molecules, I personally
> use Sybyl or the ATB website, but I'm sure there are many more options out
> there. GROMACS website may have links to some as well.
>
> 3/ not entirely sure what you are asking there.
>
> 4/ was answered in the link I provided in last reply. You do not mix
> forcefields, especially when you are someone with your experience.
>
> Learn to search, using literature databases and Google.
>
> And as stated in last email, read the literature, see what others have
> done, why they used particular forcefields, and decide whether that fits
> with your goals. Don't take the word of some random person on an emailing
> list for this, as it's your research and you have to justify it and ensure
> it is valid for what you want to do.
>
> The GROMACS website has a rough outline on how to perform a simulation, in
> general. Have a read of that, it has all this advice presented in it
> already.
>
>
> On 14 Jun 2017 2:43 PM, "Dilip H N"  wrote:
>
> Hello,
> 1] Can u kindly tell me how can i create molecules such as Methylamine(CH3
> NH2),Dimethylamine((CH3)2NH), Trimethylamine((CH3)3N),
> TrimethylamineNoxide ((CH3)3NO-).
> 2] are there any software's to create these molecules since i didn't find
> any pdb files for  the above said molecules...
> 3] and what are the changes tht i need to make in the residue names tht
> fit into the specific forcefield
> 4] how can i simulate the molecules if thy are in different forcefields..??
>
> Thank you..
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
>    Sent with Mailtrack
> 
>
>
>
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Re: [gmx-users] Regarding creating the molecules...

[Dallas Warren]

Please keep discussion to the emailing list.

1/ and 2/ to construct the coordinate file for the molecules, I personally
use Sybyl or the ATB website, but I'm sure there are many more options out
there. GROMACS website may have links to some as well.

3/ not entirely sure what you are asking there.

4/ was answered in the link I provided in last reply. You do not mix
forcefields, especially when you are someone with your experience.

Learn to search, using literature databases and Google.

And as stated in last email, read the literature, see what others have
done, why they used particular forcefields, and decide whether that fits
with your goals. Don't take the word of some random person on an emailing
list for this, as it's your research and you have to justify it and ensure
it is valid for what you want to do.

The GROMACS website has a rough outline on how to perform a simulation, in
general. Have a read of that, it has all this advice presented in it
already.


On 14 Jun 2017 2:43 PM, "Dilip H N"  wrote:

Hello,
1] Can u kindly tell me how can i create molecules such as Methylamine(CH3NH
2),Dimethylamine((CH3)2NH), Trimethylamine((CH3)3N), TrimethylamineNoxide
((CH3)3NO-).
2] are there any software's to create these molecules since i didn't find
any pdb files for  the above said molecules...
3] and what are the changes tht i need to make in the residue names tht fit
into the specific forcefield
4] how can i simulate the molecules if thy are in different forcefields..??

Thank you..
-- 
With Best Regards,

DILIP.H.N
Ph.D Student



   Sent with Mailtrack

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Re: [gmx-users] Ion flux/current

[Nikhil Maroli]

Hi,

It would be helpful for us (user's of Gromacs and people who do MD) to
get a predefined code for a particular reason. Kindly share it, or you
can provide it with your work so that we can cite your paper too.


Thanks
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[gmx-users] using groups in index for gmx select

[Sahithya S Iyer]

Hi gmx users,

Can anyone please tell me how to use a group in index file in gmx select.
For example -

*gmx select -n index.ndx -select 'name "OH2" and within 2 of com of name "P
and r 1-36"' -on P-water.ndx -s step7_production.tpr*

does not write out anything in the index (P-water.ndx) file. I have defined
this group in the index file. Can I use this in the -select command? If so,
how ?

 Basically I would like to select oxygen atoms of water molecules that are
2 nm around the phosphate groups of one monolayer.

Any help is much appreciated.
Thanks in advance.
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[gmx-users] Fatal error: Atom O01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.

[Rana Rehan Khalid]

Hi
I have read the chapter 5 of manual but i am confuse how can i add residue
into heme atom of .rtp ff
this is the coordinate due to which error come

HETATM 1529  O01 HEM   187   3.996  19.101  70.594  0.00
0.00   O

kindly guide me how i can make changes in the rtp file and .atp so that
this error remove
here is the heme rtp part of my selected ff where i can add O01 and also
tell me these 4 column and these values and tell me which value i add for
O01 like (FE FE 0.4 0 )
[ HEME ]
 [ atoms ]
   FEFE 0.4 0
   NANR-0.1 0
   NBNR-0.1 0
   NCNR-0.1 0
   NDNR-0.1 0
  CHA C-0.1 1
  HHAHC 0.1 1
  C1A C 0.0 2
  C2A C 0.0 2
  C3A C 0.0 2
  C4A C 0.0 2
  CMA   CH3 0.0 3
  CAA   CH2 0.0 4
  CBA   CH2 0.0 4
  CGA C 0.27000 5
  O1AOM-0.63500 5
  O2AOM-0.63500 5
  CHB C-0.1 6
  HHBHC 0.1 6
  C1B C 0.0 7
  C2B C 0.0 7
  C3B C 0.0 7
  C4B C 0.0 7
  CMB   CH3 0.0 8
  CAB   CR1 0.0 9
  CBB   CH2 0.0 9
  CHC C-0.110
  HHCHC 0.110
  C1C C 0.011
  C2C C 0.011
  C3C C 0.011
  C4C C 0.011
  CMC   CH3 0.012
  CAC   CR1 0.013
  CBC   CH2 0.013
  CHD C-0.114
  HHDHC 0.114
  C1D C 0.015
  C2D C 0.015
  C3D C 0.015
  C4D C 0.015
  CMD   CH3 0.016
  CAD   CH2 0.017
  CBD   CH2 0.017
  CGD C 0.2700018
  O1DOM-0.6350018
  O2DOM-0.6350018

thanks
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Re: [gmx-users] defining two interactions potentials for same pair of atoms

[Sahithya S Iyer]

Thanks for the reply Mark.

On Wed, Jun 14, 2017 at 4:34 AM, Mark Abraham 
wrote:

> Hi,
>
> On Tue, Jun 13, 2017 at 3:26 PM Sahithya S Iyer  wrote:
>
> > Hi gmx users,
> >
> > Can someone please tell me if it is possible to use two user defined
> > (non-bonded) potentials for the same pair of interaction sites.
> > For instance, if I have beads A and B, I can define non bonded
> interactions
> > as table_A_A.xvg, table_A_B.xvg, and table_B_B.xvgfor these two sites.
> But
> > what if I have divided the non-bonded interactions into say the repulsive
> > part and the attractive part and want to give them as separate input
> table
> > formats. Can this be done in gromacs ? If so, how ?
> >
>
> No, it can't. Make one table for the whole interaction between each pair of
> types, etc.
>
> If you decide later you want to observe some kind of decomposition of the
> energies of resulting configurations, use mdrun -rerun with tables that
> provide only one aspect of the interactions.
>
> Mark
>
>
> > Thanks is advance,
> > Sahithya.
> > --
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Re: [gmx-users] how to select index group in gmx hbond or any other command

[Justin Lemkul]

On 6/13/17 9:02 PM, Md. Imrul Reza Shishir wrote:

Dear all

I have to run gmx hbond command for several time. So i want to know is
there any command for gmx hbond like gmx distance (-select) to select
specific index group for analysis gmx hbond.

gmx hbond -f *.xtc -s *.tpr -n *.ndx -num *.xvg

for this command, I want to select different index group several time. I
want to make script file with all the command. Is it possible to add group
selection in the script file. Otherwise i have to select the group every
time in the terminal which is hilarious work for like 100 command.



http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts

-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] how to select index group in gmx hbond or any other command

[Md. Imrul Reza Shishir]

Dear all

I have to run gmx hbond command for several time. So i want to know is
there any command for gmx hbond like gmx distance (-select) to select
specific index group for analysis gmx hbond.

gmx hbond -f *.xtc -s *.tpr -n *.ndx -num *.xvg

for this command, I want to select different index group several time. I
want to make script file with all the command. Is it possible to add group
selection in the script file. Otherwise i have to select the group every
time in the terminal which is hilarious work for like 100 command.

-- 
*Md Imrul Reza Shishir*
Master Student
​​
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Re: [gmx-users] ATB topology: itp to top conversion

[Anna Lappala]

Thank you Mark and Justin! That makes sense, of course!!! Many thanks.

With best wishes 
Anna

> On Jun 13, 2017, at 17:22, Mark Abraham  wrote:
> 
> Hi,
> 
>> On Wed, Jun 14, 2017 at 1:07 AM Anna Lappala  wrote:
>> 
>> Dear all,
>> 
>> I am confused: I have my pdb file as well as the itp file produced by ATB.
>> I want to convert these into top and gro files but the molecule is not
>> recognised by the forcefield when I do the following:
>> 
>> pdb2gmx -f input.pdb -o output.gro -i topology.itp
>> 
> 
> pdb2gmx is mostly for matching stuff found in .rtp files to produce .itp
> files. You already have your .itp file.
> 
> 
>> I have looked through tutorials and on the mailing list, but mostly the
>> workaround is to #include the itp file into an existing top file - which i
>> do not have because i only have a heteromolecule, and no protein...
>> 
> 
> The .top files are intended to be edited and written, e.g.
> 
> #include "your.ff/forcefield.itp"
> #include "heteromolecule.itp"
> #include "your.ff/spc.itp"
> [system]
> whatever name you like
> [molecules]
> hetero 1
> SOL 10123
> 
> Mark
> 
> 
>> Many thanks for any suggestions.
>> Anna
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
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>> 
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Re: [gmx-users] Doubt about Free Energy control Minimization

[Justin Lemkul]

On 6/13/17 4:31 PM, Varvdekar Bhagyesh Rajendra wrote:

Dear Justin,

I aspire to derive energy-minimum structures when the interaction potential 
energy between the protein and the ligand are multiplied by 0.9, 0.8, 0.7,..., 
0.2, 0.1.

I presume the following Free Energy minimization code mentioned in gromacs 
tutorial may do the trick. I would appreciate if you could please verify if it 
produces my intended result.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/Files/em_steep.mdp



Possibly, but the outcomes may be unphysical.

-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] ATB topology: itp to top conversion

[Mark Abraham]

Hi,

On Wed, Jun 14, 2017 at 1:07 AM Anna Lappala  wrote:

> Dear all,
>
> I am confused: I have my pdb file as well as the itp file produced by ATB.
> I want to convert these into top and gro files but the molecule is not
> recognised by the forcefield when I do the following:
>
> pdb2gmx -f input.pdb -o output.gro -i topology.itp
>

pdb2gmx is mostly for matching stuff found in .rtp files to produce .itp
files. You already have your .itp file.


> I have looked through tutorials and on the mailing list, but mostly the
> workaround is to #include the itp file into an existing top file - which i
> do not have because i only have a heteromolecule, and no protein...
>

The .top files are intended to be edited and written, e.g.

#include "your.ff/forcefield.itp"
#include "heteromolecule.itp"
#include "your.ff/spc.itp"
[system]
whatever name you like
[molecules]
hetero 1
SOL 10123

Mark


> Many thanks for any suggestions.
> Anna
> --
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Re: [gmx-users] ATB topology: itp to top conversion

[Justin Lemkul]

On 6/13/17 7:06 PM, Anna Lappala wrote:

Dear all,

I am confused: I have my pdb file as well as the itp file produced by ATB. I 
want to convert these into top and gro files but the molecule is not recognised 
by the forcefield when I do the following:

pdb2gmx -f input.pdb -o output.gro -i topology.itp

I have looked through tutorials and on the mailing list, but mostly the 
workaround is to #include the itp file into an existing top file - which i do 
not have because i only have a heteromolecule, and no protein...



The purpose of pdb2gmx is to write a topology.  You already have that.  The .itp 
format (typically the topology of a single entity) is hardly different from that 
of a .top (which is a system topology).  A .top file:


1. #includes or otherwise has parameters from a parent force field
2. Has a [system] directive
3. Has a [molecules] directive

Your topology from ATB is based on a GROMOS force field parameter set, which is 
probably already in GROMACS and you can therefore start your .top with a 
suitable #include statement to that parent force field.  Then #include your 
.itp, add [system] and [molecules], and you have a functional .top file.


As for format conversion, use editconf, not pdb2gmx.  But you don't have to use 
.gro (a common misconception).


-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] Fwd: Using amber-ff14SB forcefield port to GROMACS - blowing up error

[Mark Abraham]

Hi,

On Mon, Jun 12, 2017 at 7:14 PM p.kartheek  wrote:

> Dear experts,
> Currently I am trying to model Protein-DNA complex systems, with updated
> Amber forcefield parameters. Parmbsc1 for DNA and *ff14SB* for protein,
> considering the unavailability of theses updated forcefield ports within
> gromacs, I have managed to generate the topologies through tleap module of
> ambertools. Latter these topologies were translated to gromacs format using
> "ParmED". However, I am not able to proceed beyond minimization step due to
> hydrogen atoms related blowing up error.


Make sure you get your topologies working on single-molecule systems before
you try to get the whole complex working.

I want to do equilibration by
> applying restraints on only heavy atoms of the systems excluding hydrogens.
> But don't know how to generate posre files for only heavy atoms as the
> make_ndx doesn't showing any option to exclude hydrogens in water and DNA.
>

Don't restrain the water molecules - nothing much would relax if you did
that.


> I can use grep to get all the indices of hydrogens from the gro file but is
> there anyway to supply file where the information of heavy atoms is saved
> instead of entering values manually. Any kind of the help will be highly
> appreciated.
>

gmx select is a good way to generate an arbitrary selection in an index
file. Use that with gmx genrestr to make your position-restraint file.

Mark


> Thanks in advance.
>
> --
> P. Kartheek,
> PhD Candidate, Computational Biophysical Chemistry,
> Center for Computational Natural Sciences and Bioinformatics,
> International Institute of Information Technology,
> Marimuthu Krishan Group,
> 9701577399,
> karthee...@research.iiit.ac.in,
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[gmx-users] ATB topology: itp to top conversion

[Anna Lappala]

Dear all,

I am confused: I have my pdb file as well as the itp file produced by ATB. I 
want to convert these into top and gro files but the molecule is not recognised 
by the forcefield when I do the following:

pdb2gmx -f input.pdb -o output.gro -i topology.itp 

I have looked through tutorials and on the mailing list, but mostly the 
workaround is to #include the itp file into an existing top file - which i do 
not have because i only have a heteromolecule, and no protein...

Many thanks for any suggestions.
Anna
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Re: [gmx-users] defining two interactions potentials for same pair of atoms

[Mark Abraham]

Hi,

On Tue, Jun 13, 2017 at 3:26 PM Sahithya S Iyer  wrote:

> Hi gmx users,
>
> Can someone please tell me if it is possible to use two user defined
> (non-bonded) potentials for the same pair of interaction sites.
> For instance, if I have beads A and B, I can define non bonded interactions
> as table_A_A.xvg, table_A_B.xvg, and table_B_B.xvgfor these two sites. But
> what if I have divided the non-bonded interactions into say the repulsive
> part and the attractive part and want to give them as separate input table
> formats. Can this be done in gromacs ? If so, how ?
>

No, it can't. Make one table for the whole interaction between each pair of
types, etc.

If you decide later you want to observe some kind of decomposition of the
energies of resulting configurations, use mdrun -rerun with tables that
provide only one aspect of the interactions.

Mark


> Thanks is advance,
> Sahithya.
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Re: [gmx-users] WARNING: WARNING: Residue 1 named MET of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry

[Mark Abraham]

Hi,

On Tue, Jun 13, 2017 at 11:10 PM Rana Rehan Khalid 
wrote:

> dear sir
>
> I remove the hydrogen from my protein before creating the .top file rather
> then use ignore hydrogen command kindly tell me is it right to remove the
> hydrogen before simulation next gromacs steps
>

We can't decide that for you. Either way, pdb2gmx will build hydrogens back
in for you at standard conformations. Sometimes that is easier than dealing
with problematic atom naming or initial conformations.

Mark


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Re: [gmx-users] Fatal error: Atom N01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.

[Mark Abraham]

Hi,

Please do not use all capital letters in emails. People think it is like
shouting.

On Tue, Jun 13, 2017 at 11:25 PM Rana Rehan Khalid 
wrote:

> SIR
>
> I AM FACING ABOVE PROBLEM CAN YOU GUIDE ME HOW CAN I MAKE CHANGES IN .RTP
> FILE TO ADD THAT KIND OF INTERACTION BETWEEN FE AND NITRIC OXIDE NO
>

You should start by deciding what interactions you need to have - consult
the literature for what others have done, and reflect on that. If it is not
something others have done, then it is probably an unsuitable project for a
beginner. You will need to be well acquainted with the relevant parts of
chapter 5 of the reference manual. Good luck!

Mark


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Re: [gmx-users] Regarding the forcefield, topology..

[Dallas Warren]

1 and 2 are for you to research and decide.  Do a literature search
for simulation of those molecules, see what others have done etc.

Re 3) http://www.gromacs.org/Documentation/Terminology/Force_Fields#Usage
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 9 June 2017 at 15:12, Dilip H N  wrote:
> Hello,
> 1] I want to simulate molecules as 
> Methylamine(CH3NH2),Dimethylamine((CH3)2NH),
> Trimethylamine((CH3)3N), TrimethylamineN-oxide((CH3)3NO-).
> Can anybody suggest me the right forcefield in gromacs for these
> moleculesin which forcefield is this available along with its residues..
> 2] Are the forcefields for all these molecules available in the same
> forcefield..?
> 3] and thn i want to simulate an aminoacid with the above molecules...how
> can i simulate if the aminoacid and the above said molecules are in
> different forcefields..??
>
> Thank you
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
>    Sent with Mailtrack
> 
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[gmx-users] Ion flux/current

[Alex]

Hi all,

This isn't a question. My boss wrote a very nice utility that calculates
ionic fluxes (yes, my boss writes utilities for me). It is a neat perl
script that accepts a trajectory in pdb format and spits out ion fluxes for
all ion types selected by the user. We may add a few other useful features.

Would the developers like us to contribute this utility to the community?

Thanks,

Alex
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[gmx-users] Fatal error: Atom N01 in residue HEM 187 was not found in rtp entry HEME with 47 atoms while sorting atoms.

[Rana Rehan Khalid]

SIR

I AM FACING ABOVE PROBLEM CAN YOU GUIDE ME HOW CAN I MAKE CHANGES IN .RTP
FILE TO ADD THAT KIND OF INTERACTION BETWEEN FE AND NITRIC OXIDE NO
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Re: [gmx-users] WARNING: WARNING: Residue 1 named MET of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry

[Rana Rehan Khalid]

dear sir

I remove the hydrogen from my protein before creating the .top file rather
then use ignore hydrogen command kindly tell me is it right to remove the
hydrogen before simulation next gromacs steps
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[gmx-users] Doubt about Free Energy control Minimization

[Varvdekar Bhagyesh Rajendra]

Dear Justin,

I aspire to derive energy-minimum structures when the interaction potential 
energy between the protein and the ligand are multiplied by 0.9, 0.8, 0.7,..., 
0.2, 0.1.

I presume the following Free Energy minimization code mentioned in gromacs 
tutorial may do the trick. I would appreciate if you could please verify if it 
produces my intended result.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/Files/em_steep.mdp

Thanking in anticipation,

Best Regards,

Bhagyesh
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Re: [gmx-users] Pulling COM option

[Angela Marcela Murcia Rios]

I have already used enforced rotation to move gamma and yes it works good but 
now I want to just pull gamma a certain direction just by pulling it and see 
how the system reacts to this kind of force. I want to understand if it is 
possible to do this with the pulling COM option of GROMACS and how I would 
specify this with my system.



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: June 13, 2017 2:15:07 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Pulling COM option



On 6/13/17 1:58 PM, Angela Marcela Murcia Rios wrote:
> Hi Justin,
>
>
> I don't want two opposing forces acting on gamma and I don't want to apply it 
> to all of gamma only a specific region, which is what enforced rotation will 
> do. I only want to apply one directional force onto one side of gamma and see 
> how the whole system behaves. But the problem I'm facing is how do I specify 
> this in my mdp file.
>
>

Caveat: I have never used the enforced rotation feature.

But in reading the manual, the fixed axis option says it is applying a torque to
the specified atoms relative to an axis.  Isn't this exactly what you want?
It's not like attaching a spring between groups A and B, you're rotating group A
relative to an axis that you specify.

-Justin

>
> ---Angela
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  on behalf of Justin 
> Lemkul 
> Sent: June 13, 2017 1:50:35 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Pulling COM option
>
>
>
> On 6/13/17 1:48 PM, Angela Marcela Murcia Rios wrote:
>> Hi,
>>
>>
>> I'm not really intersected in the information that the Pulling COM option 
>> provides. I am really just interested in getting my protein move in a 
>> specific direction until it completes a full circle.
>>
>>
>> To be more specific my system is F1 ATPase and I just want to pull the gamma 
>> subunit until it it completes a full circle. I am completely aware that 
>> there is an "enforced rotation" option on GROMACS but this is a torque 
>> force, which I don't want to use.
>>
>
> Why not?  That's sort of the definition of torque, after all.
>
> -Justin
>
>>
>>
>> 
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>>  on behalf of Nikhil 
>> Maroli 
>> Sent: June 13, 2017 1:03:03 PM
>> To: gromacs.org_gmx-users@maillist.sys.kth.se
>> Subject: Re: [gmx-users] Pulling COM option
>>
>> Hi,
>> Out of curiosity, i wanted to ask you what information you will get by 
>> rotating
>> protein by 360 degrees.?
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at 
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
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>>
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>> mail to gmx-users-requ...@gromacs.org.
>>
>
> --
> ==
>
> 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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--
==

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] How to find the loading capacity of a nanostructure?

[faride badalkhani]

Dear all,

I have performed 50 ns of production MD simulation on a polymer that
contains several drug molecules. Now I need to find how many drugs (and
which ones) remain encapsulated into the polymer. I measured the COM
separation distance between polymer and each drug. However, the problem is
that the results obtained from MD trajectories to calculate the number of
complexed drugs are not in line with the COM distance plots.

Is that correct to consider drugs as part of a supramolecular complex if
they remain at distances shorter than or equal to Rg of the polymer
measured from the center of mass of the polymer along the simulation run.

I have used the following command
 gmx cluster -s md.tpr -f md_nopbc.xtc -n index.ndx -dist com_rmsd-dist.xvg
-o com_rmsd-clust.xpm -cutoff 1.4 -tu ns
but I do not know if it is correct.
I have chosen 1.4 nm as cutoff because the radius of gyration of polymer is
about 1.4 nm.

any help will be greatly appreciated.

Regards,
Farideh
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[gmx-users] How to find the loading capacity of a nanostructure?

[faride badalkhani]

Dear all,

I have performed 50 ns of production MD simulation on a polymer that
contains several drug molecules. Now I need to find how many drugs (and
which ones) remain encapsulated into the polymer. I measured the COM
separation distance between polymer and each drug. However, the problem is
that the results obtained from MD trajectories to calculate the number of
complexed drugs are not in line with the COM distance plots.

Is that correct to consider drugs as part of a supramolecular complex if
they remain at distances shorter than or equal to Rg of the polymer
measured from the center of mass of the polymer along the simulation run.

I have used the following command
 gmx cluster -s md.tpr -f md_nopbc.xtc -n index.ndx -dist com_rmsd-dist.xvg
-o com_rmsd-clust.xpm -cutoff 1.4 -tu ns
but I do not know if it is correct.
I have chosen 1.4 nm as cutoff because the radius of gyration of polymer is
about 1.4 nm.

any help will be greatly appreciated.

Regards,
Farideh
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Re: [gmx-users] Pulling COM option

[Justin Lemkul]

On 6/13/17 1:58 PM, Angela Marcela Murcia Rios wrote:

Hi Justin,


I don't want two opposing forces acting on gamma and I don't want to apply it 
to all of gamma only a specific region, which is what enforced rotation will 
do. I only want to apply one directional force onto one side of gamma and see 
how the whole system behaves. But the problem I'm facing is how do I specify 
this in my mdp file.




Caveat: I have never used the enforced rotation feature.

But in reading the manual, the fixed axis option says it is applying a torque to 
the specified atoms relative to an axis.  Isn't this exactly what you want? 
It's not like attaching a spring between groups A and B, you're rotating group A 
relative to an axis that you specify.


-Justin



---Angela


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: June 13, 2017 1:50:35 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Pulling COM option



On 6/13/17 1:48 PM, Angela Marcela Murcia Rios wrote:

Hi,


I'm not really intersected in the information that the Pulling COM option 
provides. I am really just interested in getting my protein move in a specific 
direction until it completes a full circle.


To be more specific my system is F1 ATPase and I just want to pull the gamma subunit 
until it it completes a full circle. I am completely aware that there is an 
"enforced rotation" option on GROMACS but this is a torque force, which I don't 
want to use.



Why not?  That's sort of the definition of torque, after all.

-Justin





From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Nikhil Maroli 

Sent: June 13, 2017 1:03:03 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Pulling COM option

Hi,
Out of curiosity, i wanted to ask you what information you will get by rotating
protein by 360 degrees.?
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--
==

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

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

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

==
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--
==

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] Pulling COM option

[Angela Marcela Murcia Rios]

Hi Justin,


I don't want two opposing forces acting on gamma and I don't want to apply it 
to all of gamma only a specific region, which is what enforced rotation will 
do. I only want to apply one directional force onto one side of gamma and see 
how the whole system behaves. But the problem I'm facing is how do I specify 
this in my mdp file.



---Angela


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: June 13, 2017 1:50:35 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Pulling COM option



On 6/13/17 1:48 PM, Angela Marcela Murcia Rios wrote:
> Hi,
>
>
> I'm not really intersected in the information that the Pulling COM option 
> provides. I am really just interested in getting my protein move in a 
> specific direction until it completes a full circle.
>
>
> To be more specific my system is F1 ATPase and I just want to pull the gamma 
> subunit until it it completes a full circle. I am completely aware that there 
> is an "enforced rotation" option on GROMACS but this is a torque force, which 
> I don't want to use.
>

Why not?  That's sort of the definition of torque, after all.

-Justin

>
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  on behalf of Nikhil 
> Maroli 
> Sent: June 13, 2017 1:03:03 PM
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] Pulling COM option
>
> Hi,
> Out of curiosity, i wanted to ask you what information you will get by 
> rotating
> protein by 360 degrees.?
> --
> 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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> mail to gmx-users-requ...@gromacs.org.
>

--
==

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] Doubt about g_lie

[Justin Lemkul]

On 6/13/17 9:02 AM, Varvdekar Bhagyesh Rajendra wrote:

Dear Justin,

I have used PME in the production runs of my systems for finding Delta 
G_Binding using g_lie. But many threads on Gromacs forum warn against it and 
advise to rerun the whole trajectory using Reaction field Zero, but the cutoff 
for this rerun is not clearly given. Some threads say a cutoff with large 
cutoff using RF-0 is necessary. Can you please uggest as to what 
cutoff(Relative to the system) should be given while re-running the trajectory 
and what all changes have to be done in the original mdp file(which uses PME). 
Also, a brief explanation for the whole process for the need of the re-run 
would be beneficial. Following are the changes I made after studying the past 
threads:



You'll have to use much larger cutoffs such that the interaction energies 
converge (or at least close to it), which may or may not be possible.  I'm not 
sure if there's a real "rule" here and I have never relied on a LIE estimate for 
a free energy.


-Justin



;; With PME  ;;; | ;; Re-Run without PME ;;
-
  ; Neighborsearching |  ; Neighborsearching
   ns_type = grid  ; search neighboring grid  |  ns_type = grid 
 ; search neighboring grid cells
   nstlist = 5 ; 10 fs|  nstlist = 5
 ; 10 fs
   rlist   = 0.9   ; short-range neighborlist |  rlist   = 1.2  
 ; short-range neighborlist cutoff (nm)
   rcoulomb= 0.9   ; short-range electrostatic|  rcoulomb= 0.9  
 ; short-range electrostatic cutoff (in nm)
   rvdw= 1.4   ; short-range van der Waals|  rvdw= 1.4  
 ; short-range van der Waals cutoff (in nm)
  |
; Electrostatics | ; Electrostatics
coulombtype = PME| coulombtype  =  
Reaction-Field-zero
  | epsilon_rf  =  0
---

Best Regards,

Bhagyesh



--
==

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] How to interpret gmx H_bond analysis?

[Justin Lemkul]

On 6/13/17 11:25 AM, Adarsh V. K. wrote:

Dear gmx users,

How to interpret gmx H_bond analysis?

I have done 20 ns simulation of a protein-ligand complex
(Enzyme-inhibitor). The H-bond analysis shows absence of H-bonds (zero) in
several frames during the first 2ns of simulation. But from 2 ns onwards
consistent (at least one) H bonds are seen till the end of simulation (Is
this due to restraining of ligand?)

How can we interpret this protein-ligand simulation.

Whether the ligand will 'fall off' from the protein during the first 2 ns
of simulation since there are many zero H bonds till reaching 2 ns?
Why consistent H bonds after 2ns seen ?



I answered this a couple of days ago:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2017-June/113678.html

-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] Pulling COM option

[Justin Lemkul]

On 6/13/17 1:48 PM, Angela Marcela Murcia Rios wrote:

Hi,


I'm not really intersected in the information that the Pulling COM option 
provides. I am really just interested in getting my protein move in a specific 
direction until it completes a full circle.


To be more specific my system is F1 ATPase and I just want to pull the gamma subunit 
until it it completes a full circle. I am completely aware that there is an 
"enforced rotation" option on GROMACS but this is a torque force, which I don't 
want to use.



Why not?  That's sort of the definition of torque, after all.

-Justin





From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Nikhil Maroli 

Sent: June 13, 2017 1:03:03 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Pulling COM option

Hi,
Out of curiosity, i wanted to ask you what information you will get by rotating
protein by 360 degrees.?
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--
==

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

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

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

==
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Re: [gmx-users] Pulling COM option

[Angela Marcela Murcia Rios]

Hi,


I'm not really intersected in the information that the Pulling COM option 
provides. I am really just interested in getting my protein move in a specific 
direction until it completes a full circle.


To be more specific my system is F1 ATPase and I just want to pull the gamma 
subunit until it it completes a full circle. I am completely aware that there 
is an "enforced rotation" option on GROMACS but this is a torque force, which I 
don't want to use.




From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Nikhil Maroli 

Sent: June 13, 2017 1:03:03 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Pulling COM option

Hi,
Out of curiosity, i wanted to ask you what information you will get by rotating
protein by 360 degrees.?
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Re: [gmx-users] Pulling COM option

[Nikhil Maroli]

Hi,
Out of curiosity, i wanted to ask you what information you will get by rotating
protein by 360 degrees.?
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[gmx-users] How to interpret gmx H_bond analysis?

[Adarsh V. K.]

Dear gmx users,

How to interpret gmx H_bond analysis?

I have done 20 ns simulation of a protein-ligand complex
(Enzyme-inhibitor). The H-bond analysis shows absence of H-bonds (zero) in
several frames during the first 2ns of simulation. But from 2 ns onwards
consistent (at least one) H bonds are seen till the end of simulation

How can we interpret this protein-ligand simulation.

Whether the ligand will 'fall off' from the protein during the first 2 ns
of simulation since there are many zero H bonds till reaching 2 ns?
Why consistent H bonds after 2ns seen ?

Regards,

Adarsh V. K.
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[gmx-users] How to interpret gmx H_bond analysis?

[Adarsh V. K.]

Dear gmx users,

How to interpret gmx H_bond analysis?

I have done 20 ns simulation of a protein-ligand complex
(Enzyme-inhibitor). The H-bond analysis shows absence of H-bonds (zero) in
several frames during the first 2ns of simulation. But from 2 ns onwards
consistent (at least one) H bonds are seen till the end of simulation (Is
this due to restraining of ligand?)

How can we interpret this protein-ligand simulation.

Whether the ligand will 'fall off' from the protein during the first 2 ns
of simulation since there are many zero H bonds till reaching 2 ns?
Why consistent H bonds after 2ns seen ?

Regards,

Adarsh V. K.
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[gmx-users] defining two interactions potentials for same pair of atoms

[Sahithya S Iyer]

Hi gmx users,

Can someone please tell me if it is possible to use two user defined
(non-bonded) potentials for the same pair of interaction sites.
For instance, if I have beads A and B, I can define non bonded interactions
as table_A_A.xvg, table_A_B.xvg, and table_B_B.xvgfor these two sites. But
what if I have divided the non-bonded interactions into say the repulsive
part and the attractive part and want to give them as separate input table
formats. Can this be done in gromacs ? If so, how ?

Thanks is advance,
Sahithya.
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[gmx-users] Doubt about g_lie

[Varvdekar Bhagyesh Rajendra]

Dear Justin,

I have used PME in the production runs of my systems for finding Delta 
G_Binding using g_lie. But many threads on Gromacs forum warn against it and 
advise to rerun the whole trajectory using Reaction field Zero, but the cutoff 
for this rerun is not clearly given. Some threads say a cutoff with large 
cutoff using RF-0 is necessary. Can you please uggest as to what 
cutoff(Relative to the system) should be given while re-running the trajectory 
and what all changes have to be done in the original mdp file(which uses PME). 
Also, a brief explanation for the whole process for the need of the re-run 
would be beneficial. Following are the changes I made after studying the past 
threads:

;; With PME  ;;; | ;; Re-Run without PME ;;
-
 ; Neighborsearching |  ; Neighborsearching
  ns_type = grid  ; search neighboring grid  |  ns_type = grid  
; search neighboring grid cells
  nstlist = 5 ; 10 fs|  nstlist = 5 
; 10 fs
  rlist   = 0.9   ; short-range neighborlist |  rlist   = 1.2   
; short-range neighborlist cutoff (nm)  
  
  rcoulomb= 0.9   ; short-range electrostatic|  rcoulomb= 0.9   
; short-range electrostatic cutoff (in nm)
  rvdw= 1.4   ; short-range van der Waals|  rvdw= 1.4   
; short-range van der Waals cutoff (in nm)
 |
; Electrostatics | ; Electrostatics
coulombtype = PME| coulombtype  =  
Reaction-Field-zero 
 | epsilon_rf  =  0
---

Best Regards,

Bhagyesh
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Re: [gmx-users] error in running md

[Justin Lemkul]

On 6/13/17 8:51 AM, VARSHA RANI wrote:

Thanks for reply.
As suggested by Mark Abraham, I ran same calculation  for energy
minimization for pentacene single molecule.
minim.mdp is same and screen output is

writing lowest energy coordinates.

Steepest Descents converged to Fmax < 10 in 78 steps
Potential Energy  =  1.0244328e+02
Maximum force =  9.6825466e+00 on atom 10
Norm of force =  5.3154244e+00



This is entirely normal.  You have a single molecule and no solvent, so in a 
case like this, the energy is dominated by internal (bonded) terms, which are 
strictly positive.  There is no solvent, e.g. water, which is normally dominated 
by favorable electrostatic interactions.


-Justin


and the pdb for one molecule of pentacene is as

petacene-pdb

ATOM  1  C1   PE 1   1.247  -0.647  -0.108  1.00  2.95   1PE
ATOM  2  C2   PE 1   0.775  -0.326   1.167  1.00  2.95   1PE
ATOM  3  C3   PE 1   1.477  -0.610   2.344  1.00  2.95   1PE
ATOM  4  C4   PE 1   0.973  -0.271   3.594  1.00  2.95   1PE
ATOM  5  C5   PE 1   1.723  -0.555   4.797  1.00  2.95   1PE
ATOM  6  C6   PE 1   1.242  -0.219   6.006  1.00  2.95   1PE
ATOM  7  C7   PE 1  -0.042   0.431   6.128  1.00  2.95   1PE
ATOM  8  C8   PE 1  -0.769   0.717   5.013  1.00  2.95   1PE
ATOM  9  C9   PE 1  -0.297   0.392   3.691  1.00  2.95   1PE
ATOM 10  C10  PE 1  -1.004   0.678   2.556  1.00  2.95   1PE
ATOM 11  C11  PE 1  -0.516   0.340   1.278  1.00  2.95   1PE
ATOM 12  H1   PE 1   2.068  -1.076  -0.188  1.00  2.95   1PE
ATOM 13  H2   PE 1   2.301  -1.037   2.287  1.00  2.95   1PE
ATOM 14  H3   PE 1   2.549  -0.976   4.732  1.00  2.95   1PE
ATOM 15  H4   PE 1   1.740  -0.406   6.768  1.00  2.95   1PE
ATOM 16  H5   PE 1  -0.373   0.653   6.968  1.00  2.95   1PE
ATOM 17  H6   PE 1  -1.594   1.135   5.108  1.00  2.95   1PE
ATOM 18  H7   PE 1  -1.826   1.106   2.630  1.00  2.95   1PE
ATOM 19  C12  PE 1  -1.247   0.647   0.108  1.00  2.95   1PE
ATOM 20  C13  PE 1  -0.775   0.326  -1.167  1.00  2.95   1PE
ATOM 21  C14  PE 1  -1.477   0.610  -2.344  1.00  2.95   1PE
ATOM 22  C15  PE 1  -0.973   0.271  -3.594  1.00  2.95   1PE
ATOM 23  C16  PE 1  -1.723   0.555  -4.797  1.00  2.95   1PE
ATOM 24  C17  PE 1  -1.242   0.219  -6.006  1.00  2.95   1PE
ATOM 25  C18  PE 1   0.042  -0.431  -6.128  1.00  2.95   1PE
ATOM 26  C19  PE 1   0.769  -0.717  -5.013  1.00  2.95   1PE
ATOM 27  C20  PE 1   0.297  -0.392  -3.691  1.00  2.95   1PE
ATOM 28  C21  PE 1   1.004  -0.678  -2.556  1.00  2.95   1PE
ATOM 29  C22  PE 1   0.516  -0.340  -1.278  1.00  2.95   1PE
ATOM 30  H8   PE 1  -2.068   1.076   0.188  1.00  2.95   1PE
ATOM 31  H9   PE 1  -2.301   1.037  -2.287  1.00  2.95   1PE
ATOM 32  H10  PE 1  -2.549   0.976  -4.732  1.00  2.95   1PE
ATOM 33  H11  PE 1  -1.740   0.406  -6.768  1.00  2.95   1PE
ATOM 34  H12  PE 1   0.373  -0.653  -6.968  1.00  2.95   1PE
ATOM 35  H13  PE 1   1.594  -1.135  -5.108  1.00  2.95   1PE
ATOM 36  H14  PE 1   1.826  -1.106  -2.630  1.00  2.95   1PE
TER


As there is no amino acid in this molecule, I have created a residue
named 'PE'. for this I have edited some files in the 'top' directory
of gromacs. The files are..'residues.types.dat', 'residues.xml',
'refi_aa.dat' and besides that for oplsaa force field, I edited
'aminoacids.rtp' file also.



regards


On Tue, Jun 13, 2017 at 4:57 PM, Mark Abraham 
wrote:


Hi,

Technically this is energy minimization, not md. But likely the energy
should be negative. It's hard to help because you haven't told us what is
in the system, but if it's multiple organic molecules, start with one, to
see if your topology works appropriately.

Mark

On Tue, 13 Jun 2017 12:45 VARSHA RANI  wrote:


Hi,

I ran minim.mdp for my system with 3456 atoms.  But lowest energy after
minimization is positive.

*here is th screen output*

Step= 4509, Dmax= 4.5e-05 nm, Epot=  4.06554e+02 Fmax= 9.86206e+00, atom=
3521

writing lowest energy coordinates.

Back Off! I just backed up em.gro to ./#em.gro.1#

Steepest Descents converged to Fmax < 10 in 4510 steps
Potential Energy  =  4.0655389e+02
Maximum force =  9.8620596e+00 on atom 352
Norm of force =  3.3500545e+00

NOTE: 16 % of the run time was spent in pair search,
   you might want to increase nstlist (this has no effect on accuracy)


*Below is txt of minim.mdp file *

; minim.mdp - used as input into grompp to generate em.tpr
integrator= 

Re: [gmx-users] error in running md

[VARSHA RANI]

Thanks for reply.
As suggested by Mark Abraham, I ran same calculation  for energy
minimization for pentacene single molecule.
minim.mdp is same and screen output is

writing lowest energy coordinates.

Steepest Descents converged to Fmax < 10 in 78 steps
Potential Energy  =  1.0244328e+02
Maximum force =  9.6825466e+00 on atom 10
Norm of force =  5.3154244e+00

and the pdb for one molecule of pentacene is as

petacene-pdb

ATOM  1  C1   PE 1   1.247  -0.647  -0.108  1.00  2.95   1PE
ATOM  2  C2   PE 1   0.775  -0.326   1.167  1.00  2.95   1PE
ATOM  3  C3   PE 1   1.477  -0.610   2.344  1.00  2.95   1PE
ATOM  4  C4   PE 1   0.973  -0.271   3.594  1.00  2.95   1PE
ATOM  5  C5   PE 1   1.723  -0.555   4.797  1.00  2.95   1PE
ATOM  6  C6   PE 1   1.242  -0.219   6.006  1.00  2.95   1PE
ATOM  7  C7   PE 1  -0.042   0.431   6.128  1.00  2.95   1PE
ATOM  8  C8   PE 1  -0.769   0.717   5.013  1.00  2.95   1PE
ATOM  9  C9   PE 1  -0.297   0.392   3.691  1.00  2.95   1PE
ATOM 10  C10  PE 1  -1.004   0.678   2.556  1.00  2.95   1PE
ATOM 11  C11  PE 1  -0.516   0.340   1.278  1.00  2.95   1PE
ATOM 12  H1   PE 1   2.068  -1.076  -0.188  1.00  2.95   1PE
ATOM 13  H2   PE 1   2.301  -1.037   2.287  1.00  2.95   1PE
ATOM 14  H3   PE 1   2.549  -0.976   4.732  1.00  2.95   1PE
ATOM 15  H4   PE 1   1.740  -0.406   6.768  1.00  2.95   1PE
ATOM 16  H5   PE 1  -0.373   0.653   6.968  1.00  2.95   1PE
ATOM 17  H6   PE 1  -1.594   1.135   5.108  1.00  2.95   1PE
ATOM 18  H7   PE 1  -1.826   1.106   2.630  1.00  2.95   1PE
ATOM 19  C12  PE 1  -1.247   0.647   0.108  1.00  2.95   1PE
ATOM 20  C13  PE 1  -0.775   0.326  -1.167  1.00  2.95   1PE
ATOM 21  C14  PE 1  -1.477   0.610  -2.344  1.00  2.95   1PE
ATOM 22  C15  PE 1  -0.973   0.271  -3.594  1.00  2.95   1PE
ATOM 23  C16  PE 1  -1.723   0.555  -4.797  1.00  2.95   1PE
ATOM 24  C17  PE 1  -1.242   0.219  -6.006  1.00  2.95   1PE
ATOM 25  C18  PE 1   0.042  -0.431  -6.128  1.00  2.95   1PE
ATOM 26  C19  PE 1   0.769  -0.717  -5.013  1.00  2.95   1PE
ATOM 27  C20  PE 1   0.297  -0.392  -3.691  1.00  2.95   1PE
ATOM 28  C21  PE 1   1.004  -0.678  -2.556  1.00  2.95   1PE
ATOM 29  C22  PE 1   0.516  -0.340  -1.278  1.00  2.95   1PE
ATOM 30  H8   PE 1  -2.068   1.076   0.188  1.00  2.95   1PE
ATOM 31  H9   PE 1  -2.301   1.037  -2.287  1.00  2.95   1PE
ATOM 32  H10  PE 1  -2.549   0.976  -4.732  1.00  2.95   1PE
ATOM 33  H11  PE 1  -1.740   0.406  -6.768  1.00  2.95   1PE
ATOM 34  H12  PE 1   0.373  -0.653  -6.968  1.00  2.95   1PE
ATOM 35  H13  PE 1   1.594  -1.135  -5.108  1.00  2.95   1PE
ATOM 36  H14  PE 1   1.826  -1.106  -2.630  1.00  2.95   1PE
TER


As there is no amino acid in this molecule, I have created a residue
named 'PE'. for this I have edited some files in the 'top' directory
of gromacs. The files are..'residues.types.dat', 'residues.xml',
'refi_aa.dat' and besides that for oplsaa force field, I edited
'aminoacids.rtp' file also.



regards


On Tue, Jun 13, 2017 at 4:57 PM, Mark Abraham 
wrote:

> Hi,
>
> Technically this is energy minimization, not md. But likely the energy
> should be negative. It's hard to help because you haven't told us what is
> in the system, but if it's multiple organic molecules, start with one, to
> see if your topology works appropriately.
>
> Mark
>
> On Tue, 13 Jun 2017 12:45 VARSHA RANI  wrote:
>
> > Hi,
> >
> > I ran minim.mdp for my system with 3456 atoms.  But lowest energy after
> > minimization is positive.
> >
> > *here is th screen output*
> >
> > Step= 4509, Dmax= 4.5e-05 nm, Epot=  4.06554e+02 Fmax= 9.86206e+00, atom=
> > 3521
> >
> > writing lowest energy coordinates.
> >
> > Back Off! I just backed up em.gro to ./#em.gro.1#
> >
> > Steepest Descents converged to Fmax < 10 in 4510 steps
> > Potential Energy  =  4.0655389e+02
> > Maximum force =  9.8620596e+00 on atom 352
> > Norm of force =  3.3500545e+00
> >
> > NOTE: 16 % of the run time was spent in pair search,
> >   you might want to increase nstlist (this has no effect on accuracy)
> >
> >
> > *Below is txt of minim.mdp file *
> >
> > ; minim.mdp - used as input into grompp to generate em.tpr
> > integrator= steep; Algorithm (steep = steepest descent
> > minimization)
> > emstep  = 0.01 ; Energy step size
> > ;emtol= 1000.0  ; Stop minimization when the maximum force <
> > 1000.0 kJ/mol/nm
> > 

Re: [gmx-users] Regarding hydrogen bond dynamics

[Justin Lemkul]

On 6/13/17 2:44 AM, Dilip H N wrote:

Hello,
I want to study the hydrogen bond dynamics (continuous and intermittent) of
my system of amino acid with solvent mixture.
I have tried gmx hbond..but i am unable to figure it out
Is there any other means to study the hydrogen bonding of the above
system



The purpose of gmx hbond is to compute hydrogen bonds, so no, there's no other 
tool in GROMACS to do this.  But if you want useful help, you have to actually 
describe what you're doing, what you tried, and why it didn't work to your 
expectations.


-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] Periodic Cell of Cyclohexane--LINCS Warnings

[Justin Lemkul]

On 6/13/17 12:13 AM, Billy Williams-Noonan wrote:

"Side issue, not related to your problem - use gmx grompp -t state.cpt to
get the full-precision coordinates and box."

I used gmx energy to plot the box coordinates over time.  Using P-R with a
2 fs timestep and tau_p of 2 ps, the box shrinks to a certain point, and
then the system "blows up".  This can also be visualised in VMD.  There is
no such problem when increasing tau_p to 6 ps.  Thanks, I think I know what
the problem is.

"At minimum, your use of rvdw = 1.0 is incorrect.  It should be 1.4.  This
could be related to instability of systems dominated by vdW interactions."

Thank you, will set rvdw to 1.4 nm.  I initially assumed 1.0 nm would be
fine, as that is how I read the mdp settings page for Gromacs*:*

rvdw (1) 



Do not conflate a default setting required for a syntactically correct input 
file with a scientifically valid setting.



When I found out that my rvdw was wrong, I noticed that many people seem to
be using the wrong value for the cut-offs and still getting published.  I
understand that the varying force-fields were optimised under different
conditions.  My system appears to be stable now with the current
parameters, but I will fix to make the long-term energetics more correct
anyway.



It's not a matter of "making things more accurate/correct" - the cutoffs are 
part of the force field, and if you get them wrong, it's likely that your 
simulation is invalid based on an imbalance of forces because you're violating 
the assumptions in the force field, most of which rely on a cancellation of 
errors.  And indeed, people publish wrong things all the time.  It's up to the 
researcher to do his/her homework about the force field, how it should be 
employed, and what it's caveats are, in designing the experiment.  Too often MD 
simulations are done via "cut and paste" from tutorials, unrelated work, etc. 
The literature is rife with junk, unfortunately.  Be skeptical!


-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] Technqiues for Applying Assymmetric Ion Concentrations?

[Justin Lemkul]

On 6/12/17 10:47 PM, petar.zuvela wrote:

Isn't it just easier to compute the number of ions ?
It is basic chem and quite simple.
N (atoms) = n / mol * Na / mol -1
n / mol = c / mol dm-3 * V / dm3

Here V is volume of the box, and c is concentration of either of the ions.
After computing the number of ions, just add them to the box.

No need for complicated things like making two water boxes.



It is if you wish to model ion asymmetry across the membrane.

To preserve that asymmetry, one would need semipermeable walls (e.g. flat-bottom 
restraints) that work on the ions but not the water.  That confines the ions to 
their given compartments.  But then, too, the two layers still interact via PBC 
even if ions don't cross the boundary itself.


-Justin


All the best,
Petar Zuvela



Sent from my Samsung Galaxy smartphone.

 Original message 
From: Dallas Warren 
Date: 6/13/17 10:23 AM (GMT+08:00)
To: GROMACS users 
Subject: Re: [gmx-users] Technqiues for Applying Assymmetric Ion Concentrations?

I'd just make two separate water boxes that are the appropriate size
to go either side of the bilayer, add required ions to each one, then
simply join the two coordinate files together with the bilayer by
simply copy/paste them together. May require adjusting of the
coordinates by translations before joining.

BTW, make sure you consider what happens at the other side of the
water slabs to the bilayer. Are they joined via the PBC?
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 8 June 2017 at 11:09, Sanim Rahman  wrote:

Hello Users,

I am planning to do a bilayer simulation with asymmetric ion concentrations
using slab boundaries. I am trying to modify the concentration of each
ionic species on each side of the bilayer, however, I am struggling to find
a technique that will allow me to effectively manipulate the concentrations
of each side of the bilayer. Are there any suggestions on how to do this? I
would imagine splitting the system in half at the hydrophobic core and then
using the genion command for each half would do the trick but I am unaware
of any commands that will allow me to split the system as such.

The membrane system that I am using is from CHARMM-GUI.

I will truly appreciate your input.

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

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

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

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Re: [gmx-users] Doubt about Free Energy Calculations using g_bar

[Justin Lemkul]

On 6/12/17 5:44 PM, Varvdekar Bhagyesh Rajendra wrote:

Dear Justin,

So if I am interpreting it correct, it is reasonable if sc-coul = no even when 
partial coulomb interpolation takes place during transition from couple-lambda0 
= none to couple-lambda1 = vdw-q , right?



Yes.  But again I must emphasize that your approach to treating a peptide is 
going to fraught with problems.  This is not an effective way to get a binding 
free energy.


-Justin


Thank you for the reply,

-
Bhagyesh

- Original Message -
From: "Justin Lemkul" 
To: gmx-us...@gromacs.org
Sent: Tuesday, June 13, 2017 2:18:30 AM
Subject: Re: [gmx-users] Doubt about Free Energy Calculations using g_bar

On 6/12/17 11:47 AM, Varvdekar Bhagyesh Rajendra wrote:

Dear Justin,

I have compiled the following free energy code for use in the g_bar program for 
finding Binding affinity of a Protein-ligand complex, with ligand being a 
peptide. I would appreciate if you could please verify it's correctness and 
perhaps suggest any valuable improvements, if deemed necessary.

I am not sure about the input in the parameters for: *sc-coul* and 
*couple-intramol* though.

Since couple-lambda0 = none and couple-lambda1 = vdw-q, I assume coulomb 
interpolation must be taking place, and sc-coul should be *yes*.



Not necessarily.  Scaling Coulombic interactions linearly is what is more
commonly done.


Also, as my ligand is a peptide, I presume couple-intramol should also be *yes*.



If you're dealing with a peptide, you shouldn't be doing an alchemical
transformation.  It will probably never converge.  PMF or MM/PBSA are much
better approaches for determining binding free energies for these types of 
systems.

-Justin



; Free energy control

free_energy  = yes
init_lambda_state= 0
delta_lambda = 0
calc_lambda_neighbors= 1; only immediate neighboring windows
; Vectors of lambda specified here
; Each combination is an index that is retrieved from init_lambda_state for 
each simulation

; init_lambda_state012345678910 
  11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26 
  27   28   29   30   31   32   33   34   35   36   37   38   39   40
vdw_lambdas  = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 
0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 1.00 1.00 1.00 1.00 1.00 
1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.05 0.10 0.15 0.20 0.25 
0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00
; We are not transforming any bonded or restrained interactions
bonded_lambdas   = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
restraint_lambdas= 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
temperature_lambdas  = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00

; Options for the decoupling
sc-alpha = 0.5
sc-coul  = ??   ; As linear interpolation of Coulomb takes 
place, I suppose it should be *yes*
sc-power = 1.0
sc-sigma = 0.3
couple-moltype   = Protein_chain_B  ; name of moleculetype to 
decouple
couple-lambda0   = none ; interactions are turned off in the 
beginning
couple-lambda1   = vdw-q; all interactions are on in the end
couple-intramol  = ??   ; since my ligand is a peptide, I suppose 
the intramol interactions should be *yes*
nstdhdl  = 10


Thanking in anticipation,

Best Regards,

Bhagyesh


- Original Message -
From: "Justin Lemkul" 
To: gmx-us...@gromacs.org
Sent: Sunday, June 11, 2017 7:01:26 AM
Subject: Re: [gmx-users] Doubt about Free Energy Calculations using g_bar

On 6/10/17 6:15 AM, Varvdekar Bhagyesh Rajendra wrote:

Dear Justin,

Just so we are on the same page, this means that if I don't touch the topology 
file and use the following mdp snippet, charges *are present* in the topology 
file for the ligand group and they are automatically set to zero while turning 
on vdW interactions (from 0 to 1) right ? 

Re: [gmx-users] GPCR insertion in POPC_Cholesterol bilayer

[Archana Sonawani-Jagtap]

Thanks for the reply. I have built the bilayer using CHARMM- gui.

On Jun 13, 2017 2:20 AM, "Justin Lemkul"  wrote:



On 6/12/17 4:12 PM, Archana Sonawani-Jagtap wrote:

> Hi all,
>
> I am trying to insert GPCR in POPC with 30 mol% cholesterol bilayer. I am
> using Inflategro method for insertion but I found that the script does not
> recognize the cholesterol molecules and they are not inflated during the
> inflation step.
>
>
If you have more than one lipid type, you have to modify the script to
account for this fact.


Can anyone please let me know which method to use or I have missed any step?
>
>
Build it online with CHARMM-GUI.

-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] error in running md

[Mark Abraham]

Hi,

Technically this is energy minimization, not md. But likely the energy
should be negative. It's hard to help because you haven't told us what is
in the system, but if it's multiple organic molecules, start with one, to
see if your topology works appropriately.

Mark

On Tue, 13 Jun 2017 12:45 VARSHA RANI  wrote:

> Hi,
>
> I ran minim.mdp for my system with 3456 atoms.  But lowest energy after
> minimization is positive.
>
> *here is th screen output*
>
> Step= 4509, Dmax= 4.5e-05 nm, Epot=  4.06554e+02 Fmax= 9.86206e+00, atom=
> 3521
>
> writing lowest energy coordinates.
>
> Back Off! I just backed up em.gro to ./#em.gro.1#
>
> Steepest Descents converged to Fmax < 10 in 4510 steps
> Potential Energy  =  4.0655389e+02
> Maximum force =  9.8620596e+00 on atom 352
> Norm of force =  3.3500545e+00
>
> NOTE: 16 % of the run time was spent in pair search,
>   you might want to increase nstlist (this has no effect on accuracy)
>
>
> *Below is txt of minim.mdp file *
>
> ; minim.mdp - used as input into grompp to generate em.tpr
> integrator= steep; Algorithm (steep = steepest descent
> minimization)
> emstep  = 0.01 ; Energy step size
> ;emtol= 1000.0  ; Stop minimization when the maximum force <
> 1000.0 kJ/mol/nm
> nsteps= 50 ; Maximum number of (minimization) steps to
> perform
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist= 10  ; Frequency to update the neighbor
> list and long range forces
> rlist= 2 ; cut-off for making neighbour list (short
> range forces)
> cutoff-scheme   = Verlet
> ns_type= grid; Method to determine neighbor list
> (simple, grid)
> coulombtype= PME; Treatment of long range electrostatic
> interactions
> rcoulomb= 0.9 ; Short-range electrostatic cut-off
> rvdw= 0.9; Short-range Van der Waals cut-off
> pbc= xyz ; Periodic Boundary Conditions (yes/no)
>
>
>
> regards
> --
> Gromacs Users mailing list
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> posting!
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Re: [gmx-users] error in running md

[Vytautas Rakeviius]

Check structure, mainly atom numbers given in messages. Bad contacts or 
something.
 

On Tuesday, June 13, 2017 1:45 PM, VARSHA RANI  
wrote:
 

 Hi,

I ran minim.mdp for my system with 3456 atoms.  But lowest energy after
minimization is positive.

*here is th screen output*

Step= 4509, Dmax= 4.5e-05 nm, Epot=  4.06554e+02 Fmax= 9.86206e+00, atom=
3521

writing lowest energy coordinates.

Back Off! I just backed up em.gro to ./#em.gro.1#

Steepest Descents converged to Fmax < 10 in 4510 steps
Potential Energy  =  4.0655389e+02
Maximum force    =  9.8620596e+00 on atom 352
Norm of force    =  3.3500545e+00

NOTE: 16 % of the run time was spent in pair search,
      you might want to increase nstlist (this has no effect on accuracy)


*Below is txt of minim.mdp file *

; minim.mdp - used as input into grompp to generate em.tpr
integrator    = steep        ; Algorithm (steep = steepest descent
minimization)
emstep          = 0.01        ; Energy step size
;emtol        = 1000.0      ; Stop minimization when the maximum force <
1000.0 kJ/mol/nm
nsteps        = 50    ; Maximum number of (minimization) steps to
perform
; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist            = 10              ; Frequency to update the neighbor
list and long range forces
rlist            = 2        ; cut-off for making neighbour list (short
range forces)
cutoff-scheme      = Verlet
ns_type            = grid        ; Method to determine neighbor list
(simple, grid)
coulombtype        = PME        ; Treatment of long range electrostatic
interactions
rcoulomb        = 0.9        ; Short-range electrostatic cut-off
rvdw            = 0.9        ; Short-range Van der Waals cut-off
pbc            = xyz        ; Periodic Boundary Conditions (yes/no)



regards
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[gmx-users] error in running md

[VARSHA RANI]

Hi,

I ran minim.mdp for my system with 3456 atoms.  But lowest energy after
minimization is positive.

*here is th screen output*

Step= 4509, Dmax= 4.5e-05 nm, Epot=  4.06554e+02 Fmax= 9.86206e+00, atom=
3521

writing lowest energy coordinates.

Back Off! I just backed up em.gro to ./#em.gro.1#

Steepest Descents converged to Fmax < 10 in 4510 steps
Potential Energy  =  4.0655389e+02
Maximum force =  9.8620596e+00 on atom 352
Norm of force =  3.3500545e+00

NOTE: 16 % of the run time was spent in pair search,
  you might want to increase nstlist (this has no effect on accuracy)


*Below is txt of minim.mdp file *

; minim.mdp - used as input into grompp to generate em.tpr
integrator= steep; Algorithm (steep = steepest descent
minimization)
emstep  = 0.01 ; Energy step size
;emtol= 1000.0  ; Stop minimization when the maximum force <
1000.0 kJ/mol/nm
nsteps= 50 ; Maximum number of (minimization) steps to
perform
; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist= 10  ; Frequency to update the neighbor
list and long range forces
rlist= 2 ; cut-off for making neighbour list (short
range forces)
cutoff-scheme   = Verlet
ns_type= grid; Method to determine neighbor list
(simple, grid)
coulombtype= PME; Treatment of long range electrostatic
interactions
rcoulomb= 0.9 ; Short-range electrostatic cut-off
rvdw= 0.9; Short-range Van der Waals cut-off
pbc= xyz ; Periodic Boundary Conditions (yes/no)



regards
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[gmx-users] Regarding hydrogen bond dynamics

[Dilip H N]

Hello,
I want to study the hydrogen bond dynamics (continuous and intermittent) of
my system of amino acid with solvent mixture.
I have tried gmx hbond..but i am unable to figure it out
Is there any other means to study the hydrogen bonding of the above
system

Thank you.

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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[gmx-users] Regarding hydrogen bond dynamics

[Dilip H N]

Hello,
I want to study the hydrogen bond dynamics (continuous and intermittent) of
my system of amino acid with solvent mixture.
I have tried gmx hbond..but i am unable to figure it out
Is there any other means to study the hydrogen bonding of the above
system

Thank you.

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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