Re: [gmx-users] [EXTERNAL] Re: Lincs warning and Bond length not finite

[Smith, Micholas D.]

OPLS tends to be a common choice for graphene. That being said, if you really 
want to use gromos (for some reason), be sure (as Alex has stated) to make sure 
that the graphene edges match across the PBC otherwise do not use PBC (but then 
be sure to change your electrostatics appropriately and make sure the sheet is 
sufficiently large). 

-micholas

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of Alex
Sent: Sunday, May 3, 2020 9:04 PM
To: gmx-us...@gromacs.org
Subject: [EXTERNAL] Re: [gmx-users] Lincs warning and Bond length not finite

You have pressure scaling and LINCS convergence issues, suggesting that the 
starting configuration is far from equilibrium, as well as potentially other 
issues.

Gromos FF is not appropriate for graphene, and neither is turning C-C bonds 
into LINCS constraints, as set by your 'all-bonds' -- graphene is not a small 
organic molecule or a protein. Also, if your system is periodic in all 
directions, make sure the graphene edges are crystallographically commensurate 
with respect to PBC and the box size is appropriate. Finally, make sure that 
the small molecules you're depositing on graphene are properly pre-equilibrated.

Alex

On 5/3/2020 6:39 PM, Mohamed Abdelaal wrote:
> Hello everyone,
>
> I am simulating  the evaporation of non protein molecules on a 
> graphene sheet. I am using gromos force field and hence the lincs 
> constrain are set to all-bonds.  I have done the energy minimization 
> and NVT successfully without any warnings. During the NPT 
> equilibiration I got Lincs warning but the NPT equilibiration was 
> completed to the end. During the md production run, I received lincs 
> warning and Bond length not finite and sometimes I received " 
> nonbonded interaction between particles is larger than the table limit 2.437 
> nm".
>
> I have read that this means that my system is blowing up. Hence, I 
> have read the Blowing up and diagnosing unstable system  on gromacs 
> website, I can't recognize  any of the posted issues in my 
> files/simulation and hence,  I can't decide what exactly is the 
> problem or what should I change (it seems that my system is well 
> minimized and the temperature and pressure looks fine). I have added 
> in the below link, the NPT and md logs  and .mdp files and pictures 
> for the potential energy, Temperature, Pressure and Density.
>
> https://drive.google.com/drive/folders/1yyUJNg4yXnPfsxZ9gQ4LV5sqRKnJq9
> rF
>
> I have tried the simulation again with none as  lincs constrains and 
> it worked without any errors.
>
> I think the problem has something to do with the pressure since the 
> problem started during the NPT, but I don't know how exactly to find the 
> problem.
> Can anyone guide me please what should I change or how should I start ?
>
> Thanks,
> Mohamed
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Re: [gmx-users] [EXTERNAL] Lincs warning and Bond length not finite

[Smith, Micholas D.]

How did you set up your graphene sheet originally? Also are you treating the 
sheet as an infinite sheet (using with periodic molecules)? 

-Micholas

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of Mohamed 
Abdelaal
Sent: Sunday, May 3, 2020 8:40 PM
To: gmx-us...@gromacs.org; us...@maillist.sys.kth.se
Subject: [EXTERNAL] [gmx-users] Lincs warning and Bond length not finite

Hello everyone,

I am simulating  the evaporation of non protein molecules on a graphene sheet. 
I am using gromos force field and hence the lincs constrain are set to 
all-bonds.  I have done the energy minimization and NVT successfully without 
any warnings. During the NPT equilibiration I got Lincs warning but the NPT 
equilibiration was completed to the end. During the md production run, I 
received lincs warning and Bond length not finite and sometimes I received " 
nonbonded interaction between particles is larger than the table limit 2.437 
nm".

I have read that this means that my system is blowing up. Hence, I have read 
the Blowing up and diagnosing unstable system  on gromacs website, I can't 
recognize  any of the posted issues in my files/simulation and hence,  I can't 
decide what exactly is the problem or what should I change (it seems that my 
system is well minimized and the temperature and pressure looks fine). I have 
added in the below link, the NPT and md logs  and .mdp files and pictures for 
the potential energy, Temperature, Pressure and Density.

https://drive.google.com/drive/folders/1yyUJNg4yXnPfsxZ9gQ4LV5sqRKnJq9rF

I have tried the simulation again with none as  lincs constrains and it worked 
without any errors.

I think the problem has something to do with the pressure since the problem 
started during the NPT, but I don't know how exactly to find the problem.
Can anyone guide me please what should I change or how should I start ?

Thanks,
Mohamed
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Re: [gmx-users] [EXTERNAL] Re: Measuring bond distances, angles and dihedrals

[Smith, Micholas D.]

I had forgotten about gmx pairdist, thank you for the reminder Justin. 

Also a word of warning for the original suggestion of using VMD. Two words of 
caution: 1) Be sure you unwrap your trajectories carefully before using vmd for 
the analysis (otherwise you may get odd 'spikes' in your distances due to the 
PBC), 2) Since vmd doesn't have any topology information, all of the 
bonds/angles/dihedral information is inferred, so make sure you are using your 
selections very carefully. 

-Micholas

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of Justin Lemkul
Sent: Friday, April 17, 2020 9:23 AM
To: gmx-us...@gromacs.org
Subject: [EXTERNAL] Re: [gmx-users] Measuring bond distances, angles and 
dihedrals



On 4/17/20 9:19 AM, Smith, Micholas D. wrote:
> Gmx chi I believe gives the dihedral information. Distances can be 
> obtained from gmx mindist

More generally, gmx angle or gangle are for angles and dihedrals (and gangle 
can calculate angles between planes and/or vectors as may be required here), 
gmx distance or gmx pairdist for bond lengths.

-Justin

> -Micholas
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  On Behalf Of Yu Du
> Sent: Friday, April 17, 2020 5:32 AM
> To: gmx-us...@gromacs.org
> Subject: [EXTERNAL] Re: [gmx-users] Measuring bond distances, angles 
> and dihedrals
>
> Hi Robert,
>
> Yes, I always use VMD Tcl scripts to analyse trajectories after MD 
> simulation. The bond distances and angles between atom cluster centroids can 
> definitely be extracted by VMD.  But I don't know how to extract them using 
> GROMACS. If your project is not so urgent, VMD is your choice. It is fairly 
> flexible and can almost satisfy all your requirements.
>
> Cheers,
> Yu

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] Measuring bond distances, angles and dihedrals

[Smith, Micholas D.]

Gmx chi I believe gives the dihedral information. Distances can be obtained 
from gmx mindist

-Micholas

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of Yu Du
Sent: Friday, April 17, 2020 5:32 AM
To: gmx-us...@gromacs.org
Subject: [EXTERNAL] Re: [gmx-users] Measuring bond distances, angles and 
dihedrals

Hi Robert,

Yes, I always use VMD Tcl scripts to analyse trajectories after MD simulation. 
The bond distances and angles between atom cluster centroids can definitely be 
extracted by VMD.  But I don't know how to extract them using GROMACS. If your 
project is not so urgent, VMD is your choice. It is fairly flexible and can 
almost satisfy all your requirements.

Cheers,
Yu
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[gmx-users] Odd temperature spikes during T-REMD?

[Smith, Micholas D.]

Good morning,

I am experiencing a very bizarre problem during my T-REMD simulations of a 
(single-glycosylated residue) protein in water. During my T-REMD simulations, I 
find that my temperatures jumps from the expected range (my replicas are spaces 
between 310 to 350K) to 1000K or higher for 10 to 15 steps at a time and then 
fall back to the expected temperatures, and this occurs for all of the replicas.

The system contains ~25k atoms, so it isn't that large, and exchanges are 
occurring with -replex 500 (and I did test at -replex 1000 as well, same 
behavior).

I've tried using both Nose-Hoover and V-Rescale for the termostats, and I get 
the same behaviour. I ran additional relaxation simulations at each replicate 
independently without replex (where I don't see this spiking behavior) and 
tried again after the relaxations, and still no luck. Energy minimization of 
the original system looks fine, and simulating a similar sized system (almost 
the same protein actually) without the glycosylation didn't have this problem.

I am using gromacs2018.3 and my mdp options are the defaults you would obtain 
from CHARMM-GUI for a standard NPT simulation (with modified temperatures for 
the different replicas).

Any ideas? I am still trying to get to the bottom of why it is doing this, but 
was wondering if anyone else has had this happen them before.

===
Micholas Dean Smith, PhD. MRSC

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Re: [gmx-users] Normal mode analysis

[Smith, Micholas D.]

Where did you obtain your PDB? Is this a known crystal structure or other 
experimentally derived structure or is it a homology model? Sometimes the 
initial structures have minor artifacts that make energy minimization 
difficult. Perhaps a short-restrained MD simulation (10ps perhaps) with 
10kJ/mol position restraints could remove these artifacts and then you can 
re-minimize and run your normal mode calculation.

-Micholas


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

From: Katrien Clerx 
Sent: Wednesday, February 26, 2020 8:29 AM
To: Smith, Micholas D. ; gmx-us...@gromacs.org 

Subject: [EXTERNAL] RE: [gmx-users] Normal mode analysis


My structure does not contain any ions. Here are the commands that I used:



gmx_d pdb2gmx -f nm_*.pdb -o pdb2gmx.pdb -p topol.top -ff amber99sb -water 
tip3p -ignh



gmx_d editconf -f pdb2gmx.pdb -o editconf.pdb -bt dodecahedron -d 2.5



gmx_d grompp -f cg.mdp -c editconf.pdb -p topol.top -o cg.tpr

gmx_d mdrun -deffnm cg -v



gmx_d grompp -f bfgs.mdp -t cg.trr -c cg.tpr -p topol.top -o bfgs.tpr  -maxwarn 
1

gmx_d mdrun -deffnm bfgs -v



gmx_d grompp -f nm.mdp -t bfgs.trr -c bfgs.tpr -p topol.top -o nm.tpr





The used mdp files:

cg.mdp :

; Parameters describing what to do, when to stop and what to save

integrator = cg; Algorithm (cg= Conjugate Gradient 
minimization)

emtol= 0; Stop minimization when the maximum force < 
10.0 kJ/mol/nm

emstep  = 0.1  ; Energy step size

nsteps   = 50; Maximum number of

(minimization) steps to perform

nstcgsteep = 1000

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions

cutoff-scheme   = verlet

nstlist= 1  ; Frequency to update the 
neighbor list and long range forces

ns_type  = grid ; Method to determine 
neighbor list (simple, grid)

rlist= 1.4  ; Cut-off for making neighbor 
list (short range forces)

coulombtype   = PME

coulomb-modifier = Potential-shift

rcoulomb-switch = 1.0  ; Treatment of long range 
electrostatic interactions

rcoulomb  = 1.2  ; Short-range electrostatic cut-off

vdwtype = cutoff

vdw-modifier= force-switch

rvdw-switch = 1.0

rvdw  = 1.2; Short-range Van der Waals cut-off

fourierspacing  = 0.12

pme_order   = 4

ewald_rtol  =1e-09

epsilon_surface = 0

pbc = xyz  ; Periodic Boundary Conditions 
(yes/no)





bfgs.mdp:

;mdp for l-bfgs energy minimization

define   = -DFLEXIBLE

constraints  = none

integrator   = l-bfgs





; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions

cutoff-scheme   = verlet

nstlist= 10   ; Frequency to update the 
neighbor list and long range forces

ns_type  = grid ; Method to determine 
neighbor list (simple, grid)

rlist= 1.4  ; Cut-off for making neighbor 
list (short range forces)

coulombtype   = Reaction-Field

coulomb-modifier = potential-shift ; Treatment of long range 
electrostatic interactions

rcoulomb-switch = 1.0

rcoulomb  = 1.2  ; Short-range electrostatic cut-off

rvdw =  1.2

vdwtype = Cut-off

vdw-modifier = Force-switch

rvdw_switch = 1.0

fourierspacing  = 0.12

pme_order   = 4

epsilon_surface = 0

ewald_rtol   = 1e-9

pbc = xyz  ; Periodic Boundary Conditions 
(yes/no)





;

; Energy minimizing stuff

;

emtol= 0.0

emstep   = 0.0001

nstcgsteep= 1000

nbfgscorr  = 10

nsteps   = 50





nm.mdp:

;Parameters describing what to do, when to stop and what to save

define   = -DFLEXIBLE

integrator =nm  ;Algorithm(normal mode)



; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions

cutoff-scheme   = verlet

nstlist= 10   ; Frequency to update the 
neighbor list and long range forces

ns_type  = grid ; Method to determine 
neighbor list (simple, grid)

rlist= 1.4  ; Cut-off for making neighbor 
list (short range forces)

coulombtype   = Reaction-Field ; Treatment of long 
range electrostatic interactions

coulomb-modifier = potential-shift

rcoulomb-switch = 1.0

rcoulomb  = 1.2  ; Short-ra

Re: [gmx-users] Normal mode analysis

[Smith, Micholas D.]

Hmmm

How did you prepare the structure? Also, attachments are stripped from emails 
to the mailing list, can you please provide your mdp file as plain text in your 
reply.



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

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

Sent: Wednesday, February 26, 2020 7:52 AM
To: gmx-us...@gromacs.org 
Subject: [EXTERNAL] Re: [gmx-users] Normal mode analysis

Yes I used double precision for everything.



-Katrien







From: Smith, Micholas D.<mailto:smit...@ornl.gov>
Sent: woensdag 26 februari 2020 13:39
To: gmx-us...@gromacs.org<mailto:gmx-us...@gromacs.org>
Subject: Re: [gmx-users] Normal mode analysis



Is your build of GROMACS using double precision? NMA typically is performed 
with double precision, which is not the default gromacs build.

-Micholas

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

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

Sent: Wednesday, February 26, 2020 6:31 AM
To: gmx-us...@gromacs.org 
Subject: [EXTERNAL] [gmx-users] Normal mode analysis

?Hello,


Currently I am trying to perform a normal mode analysis on my pdb file using 
Gromacs 2019.3.

But during energy minimalisation I can't seem te get my energy low enough. it 
remains around 10^01-10^00.

I used the attached mdp-files.


Am I doing something wrong? If so, what am I doing wrong and how can I fix it?



Kind regards,


Katrien
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Re: [gmx-users] Normal mode analysis

[Smith, Micholas D.]

Is your build of GROMACS using double precision? NMA typically is performed 
with double precision, which is not the default gromacs build.

-Micholas

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

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

Sent: Wednesday, February 26, 2020 6:31 AM
To: gmx-us...@gromacs.org 
Subject: [EXTERNAL] [gmx-users] Normal mode analysis

?Hello,


Currently I am trying to perform a normal mode analysis on my pdb file using 
Gromacs 2019.3.

But during energy minimalisation I can't seem te get my energy low enough. it 
remains around 10^01-10^00.

I used the attached mdp-files.


Am I doing something wrong? If so, what am I doing wrong and how can I fix it?



Kind regards,


Katrien
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Re: [gmx-users] Slurm for GROMACS

[Smith, Micholas D.]

Unless you have multiple users and want to use SLURM as your scheduler/Manager 
for who gets to run when, you could just make a machines file and feed that to 
mpirun to use all of the computers (nodes) all of the time.



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

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Alexander 
Tzanov 
Sent: Wednesday, November 6, 2019 10:46 AM
To: gmx-us...@gromacs.org 
Subject: [EXTERNAL] Re: [gmx-users] Slurm for GROMACS

No you do not. If you are the only user.

On Nov 6, 2019 9:04 AM, "Shradheya R.R. Gupta"  wrote:
Thank you sir for your response.
For personal cluster of 6 computers  where I will be using all the nodes to
its fullest everytime still needed slurm?

Thank you

On Tue, 5 Nov, 2019, 7:32 PM Mark Abraham,  wrote:

> Hi,
>
> SLURM and OpenMPI do different things. SLURM is a resource manager, from
> which you might request multiple compute nodes. OpenMPI is a parallelism
> library that allows a program to run on those nodes. GROMACS is the
> program, and it doesn't care which MPI library is in use, or which resource
> manager sits above that. So SLURM + OpenMPI + GROMACS is fine.
>
> Mark
>
> On Tue, 5 Nov 2019 at 14:51, Shradheya R.R. Gupta <
> shradheyagu...@gmail.com>
> wrote:
>
> > Researchers,
> >  Is slrum required to run GROMACS on multiple computers or OpenMPI is
> fine?
> >
> > Thank you
> > Shradheya
> > DBT-BIF University of Rajasthan
> > --
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Re: [gmx-users] [EXTERNAL] Iterative Boltzman Inversion

[Smith, Micholas D.]

I am not sure if it is for martini or not but one that may be adapted (from 
what I can tell) is VOTCA .


-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of Maryam Sadeghi
Sent: Friday, November 1, 2019 7:32 PM
To: gmx-us...@gromacs.org
Subject: [EXTERNAL] [gmx-users] Iterative Boltzman Inversion

Dear All,

I was wondering if there are any codes in GROMACS for doing Iterative Boltzman 
Inversion to reproduce the target pair distribution functions for a MARTINI 
coarse grained structure given by atomistic simulations?

Best
Maryam
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Re: [gmx-users] [EXTERNAL] Ramachandran Plot for a Polymer

[Smith, Micholas D.]

gmx chi or gmx rama may work. I have used these for proteins, but it would be 
worth looking at the code to see if it would also work for polymers in general.

-Micholas


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

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Shan 
Jayasinghe 
Sent: Wednesday, September 11, 2019 7:54 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: [EXTERNAL] [gmx-users] Ramachandran Plot for a Polymer

Dear Gromacs Users,

Can we get the Ramachandran plot for a polymer using Gromacs? If we can,
how do we do that? Appreciate your help.

Thank you.
--
Best Regards
Shan Jayasinghe
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Re: [gmx-users] Turning off electrostatic between molecules

[Smith, Micholas D.]

One idea, you could set the charges to zero and then build a tabulated 
potential to selectively mimic the electrostatic interactions between the gases 
and the crystal lattice. I am not sure I would call that particularly 
realistic, but it would be one way to selectively "turn-off" the electrostatics 
between different pairs.


-Micholas


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

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Tam, Benjamin 

Sent: Monday, August 12, 2019 7:38:51 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se 

Subject: [EXTERNAL] [gmx-users] Turning off electrostatic between molecules

Dear All,

I am thinking of a way to simulate a porous system where the gases are very 
diluted. I would like to add more molecules into the system in order to 
increase the statistic but would like to turn off molecules - molecules 
electrostatic interaction. I understand there are ways to turn off the Lennard 
Jones through [Non-bonded param] but how do you do it with charges? I still 
would like the gas molecules to interact with the surrounding crystal 
structure. Thank you very much.

Best regards,

Ben
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Re: [gmx-users] Density of ligand molecules around a particular residue

[Smith, Micholas D.]

gmx rdf should give you this. It will give you the radial distribution function 
of the ligand molecules about the specific residue.


-Micholas


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

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Pandya, Akash 

Sent: Friday, June 7, 2019 6:20:58 PM
To: gmx-us...@gromacs.org
Subject: [EXTERNAL] [gmx-users] Density of ligand molecules around a particular 
residue

Hi all,

I want to calculate the density of ligand molecules around a particular 
residue. Is there a gromacs tool that can achieve this? I've explored gmx 
spatial, gmx densmap but have had no luck. Any guidance will be much 
appreciated.

Akash
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Re: [gmx-users] Using grace in windows

[Smith, Micholas D.]

This is more of a linux subsystem question than a gromacs question; however, 
you may want to know that there is a native grace for windows: qtGrace (its on 
source-forge). Not exactly the same as grace, but works really well.


-Micholas


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

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of DEEPANSHU 
SINGLA 
Sent: Wednesday, May 8, 2019 9:44:36 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Using grace in windows

I am trying to plot graph from gromacs generated xvg files in windows 10 using 
Linux subsystem command line. I installed grace using the same command line. 
When I try to plot the graph using grce in the command line by using the 
following command : xmgrace filename.xvg

I get the following error:

Can't open display
Failed initializing GUI, exiting

Please, guide me help me in ploting the graph in windows.

Sent from Mail for Windows 10

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Re: [gmx-users] Force field error

[Smith, Micholas D.]

Hi Swapnil Bhujbal,


The parameters exist; however, the residue rtp file may not have entries for 
the phosphorylated residues. If you want to use pdb2gmx to you will need to add 
these residues into the rtp file associated with the force-field.


Hope that helps.


If you need to quickly perform the setup and do not want to mess around with 
the rtp file modifications, you may want to check out charmm-gui.org and use 
their input generator to get your topologies.


-Micholas


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

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Swapnil 
Bhujbal 
Sent: Monday, March 4, 2019 8:12:37 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Force field error

Dear Users,

I'm performing ligand-protein simulation. My protein has phosphothreonine
and phosphoserine residues. So I have cheched this forum and accordingly I
have downloaded Charm36 force field November 2018 (
http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs) and kept in my
installation directory (/usr/local/gromacs/share/gromacs/top). Upon hitting
pdb2gmx, I can see the downloaded force field for phosphorylated residues;
"Charm36" in the list, but after selecting this force field I got the
following error:


*Fatal error:Residue 'TPO' not found in residue topology database*

Please help me to solve this problem.

Thank you in advance.

Sincerely,
Mr. Swapnil Bhujbal
PhD Scholar,
School of Medicine,
Chosun University,
South Korea.
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Re: [gmx-users] gmx hbond

[Smith, Micholas D.]

You could use gmx select to create an index file containing water molecules 
obeying these criteria at each time-step, and then use gmx hbond for for each 
index (being sure to only look at the relevant frame only).


Something like this:


gmx select (your commands here to generate an index index file for each frame).


Then use a loop like so:

#where I assume index 0 is the amino acid you are interested in


for((i=1;i<$MAXFRAMES_SELECTION;i++)); do

echo "0 \r $i" | gmx hbonds -num -r 0.2 -b "$i" -e "$i"  -n 
index_file_containing_waters_at_2Ang_at_each_frame.ndx; sed -e '/\#/d' - 
'/\@/d' -e '/\&/d' hbnum.xvg >>hbnum_2Ang.dat; rm hbnum.xvg ;done


Make a new index file for the 0.2 to 0.4 Ang and repeat.


-Micholas


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

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

Sent: Sunday, January 6, 2019 12:41:41 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gmx hbond

Use VMD/extensions/hydrogen bonds

> On Jan 6, 2019, at 11:01 AM, rose rahmani  wrote:
>
> hi,
>
> I want to know the number of hydrogen bonds of amino acid with water in
> different distances above surface. for example in first 0.2nm, in second
> 0.2 nm(0.2-0.4 nm) above surface. how can i do it by gmx hbond? I couldn't
> find any proper option for that.
>
> best
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Re: [gmx-users] Response required

[Smith, Micholas D.]

Your using more atoms than LigParGen allows. Try generating a topology for a 
trimer, tetramer, and pentamer (if you can) and then use the resulting output 
topologies as a template for building 3 types of PEO residues: 1 with a linkage 
to the beginning of the chain, 1 with a linkage to the end of the chain, and 
one between two central monomers, in the gromacs rtp file.



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

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of 
molashahimar...@aut.ac.ir 
Sent: Friday, December 28, 2018 9:50:05 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Response required


Hi everyone

When I submit  a PEO chain consists of 23 monomers to LigParGen
web-based service to make a topology file, there is no problem. But when I 
submit a PEO chain consists of 100 monomers I give an error:
 * Found residue ligand OXY
 * Unknown error. Please, check the input file. If you are not able to find the 
error, we suggests to use the SMILE code.
 * How should I do?
 *
Regards

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This email was Anti Virus checked by  Security Gateway.
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Re: [gmx-users] best force field for small proteins

[Smith, Micholas D.]

There isn't really a good answer to that question without more information. 

If you want all-atom then the standard choices are:

OPLS-AA (variants exist)
CHARMM (variants exist)
AMBER (variants exist)

If your protein has a lot of disorder, traditionally, some flavor of AMBER or 
OPLS would be good choice, if it is a nice folded structure then CHARMM is also 
a fine choice.

Since you have a ligand you will need to consider which force-field will also 
have parameters that will be reliable for the ligand. CHARMM has cgenff for 
ligands (I would suggest using the CHARMM-GUI to get these parameters since it 
has a nice interface), Amber has gaff (not my area of expertise for ligands), 
and OPLS is pretty much tinker-toys, so you can generate ligand parameters 
directly from a nice little webserver provided by the jorgensen group 
(LigParGen). 

Hope that helps. There are some papers comparing the force-fields for a number 
of proteins/peptides floating around also (I would suggest checking JCIM and 
JCTC as they these comparisons typically show up in these journals)

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


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

Sent: Thursday, October 18, 2018 8:54 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] best force field for small proteins

Hello everyone. I wanna to use MD for a protein with about 50 Amino acid
and without ligand. what are the best force fields for this purpose?
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Re: [gmx-users] Aggregation Analysis

[Smith, Micholas D.]

You may be able to use gmx clustsize to do this, but it may require some 
careful atom-selections.

-Micholas

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


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

Sent: Friday, September 21, 2018 9:02 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] Aggregation Analysis

Dear Gromacs users,


I want to classify some peptide aggregates in my simulation box,
I'd like to know which are the atoms belonging to each 'aggregate' to
study the aggregate shapes.


Is there any gromacs tool suitable for this purpose?
the best will be to select the atoms according to some kind of
distance cut-off and then to print an index file containing the list
of the atomic number for each of the aggregate.


Thank you in advance,
Aishwarya
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Re: [gmx-users] Documentation on gmx densorder?

[Smith, Micholas D.]

Thanks you for directing me to the paper. Before I switch to off-line 
questions, do you recall what his inputs needed to be? I keep getting the error:

" Program: gmx densorder, version 2016.3
Source file: src/gromacs/gmxana/gmx_densorder.cpp (line 808)

Fatal error:
No or not correct number (2) of output-file-series: 1

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
"

When I add the flag -Spect or -or after it finishes reading my trr file.

Thank you,

Micholas



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


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of David van der 
Spoel 
Sent: Friday, August 31, 2018 5:46 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Documentation on gmx densorder?

Den 2018-08-30 kl. 15:34, skrev Smith, Micholas D.:
> Dear GMX users,
>
>
> I was wondering if anyone has used the gmx densorder (originally g_densorder) 
> in the past utility in the past. I have system with an interface and the idea 
> of "
>
> gmx densorder reduces a two-phase density distribution along an axis, computed
> over a MD trajectory, to 2D surfaces fluctuating in time, by a fit to a
> functional profile for interfacial densities" seems rather interesting. 
> However, I haven't found any more documentation on this tool (i.e. what the 
> binary format of its output is actually used for).
>
>
> If anyone has used it and has some pointers on what the output should be read 
> with, or remembers the paper(s) it originated from it would be quite useful.

Guilty as charged:
https://pubs.acs.org/doi/abs/10.1021/ct500459x
It was the student who implemented the code and used it however, but
feel free to contact me off line if you have more questions.
>
>
> Thanks,
>
>
> Micholas
>
>
> ===
> Micholas Dean Smith, PhD. MRSC
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>


--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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[gmx-users] Documentation on gmx densorder?

[Smith, Micholas D.]

Dear GMX users,


I was wondering if anyone has used the gmx densorder (originally g_densorder) 
in the past utility in the past. I have system with an interface and the idea 
of "

gmx densorder reduces a two-phase density distribution along an axis, computed
over a MD trajectory, to 2D surfaces fluctuating in time, by a fit to a
functional profile for interfacial densities" seems rather interesting. 
However, I haven't found any more documentation on this tool (i.e. what the 
binary format of its output is actually used for).


If anyone has used it and has some pointers on what the output should be read 
with, or remembers the paper(s) it originated from it would be quite useful.


Thanks,


Micholas


===
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
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[gmx-users] Heterogeneous GPU cluster question?

[Smith, Micholas D.]

Dear users (and developers),

My sys. admin. is exploring purchasing some more GPU nodes for our cluster and 
was curious if we could get away with running GROMACS on a cluster that has two 
different types of GPUs, i.e. 70% of the nodes have 2 p100 gpus while 30% have 
volta (both have 2 gpu's per node).? 

I've been looking through the mailing list, but haven't bumped into this 
situation before. 

My inclination was to just purchase the "older" p100 since that is what all of 
the nodes are currently sporting, but thought I would ask to see if anyone has 
tried this kind of set-up before.

Thanks,

-Micholas

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


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

Sent: Tuesday, August 28, 2018 10:08 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] rerun doesn't calculate Coulomb & LJ interactions 
between groups

On 8/28/18 10:04 AM, Irem Altan wrote:
> Hi,
>
> I ran some umbrella sampling simulations on GPUs. I want to get the Coulomb 
> and LJ energy between certain groups (chain A - chain B, chain A - solvent, 
> etc.) , so I ran rerun:
> gmx mdrun -rerun umbrella1.xtc -nb cpu -v -deffnm umbrella1
> However, when I run gmx energy on the output .edr file:
> gmx energy -f umbrella1.edr -o umbrella1_ener.xvg
> I only get 50 terms listed, as opposed to ~90 that contains things like 
> "LJ-SR:SOL-Chain_A". What am I missing?
> The executable is created with the following command:
> gmx grompp -f umbrella.mdp -c conf1.gro -p topol.top -n index.ndx -maxwarn 1 
> -o umbrella1.tpr
> where chain A, chain B, and SOL are defined in index.ndx.

The contents of index.ndx are irrelevant unless you've actually specific
which energygrps you want to define (in the .mdp file). Also, why are
you using -maxwarn 1? This should almost never be done.

-Justin

--
==

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

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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] energy minimization

[Smith, Micholas D.]

LigParGen generates new atom types for each ligand topology it generates. The 
output files from LigParGen should contain terms for opls800-925 (if necessary) 
in the generated topology file. These need to be included in the force-field 
file you use for use in your simulations. 

A warning should be made about LigParGen: each atom is given a unique atomtype. 
For instance if you have a 25 atom ligand, you will have atomtypes opls 800 
through opls824. Some of these may be repeats. This means that if you want to 
run with a different ligand you have to change these atomtype definitions each 
time.

Hope that helps.


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


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

Sent: Wednesday, July 25, 2018 8:17 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] energy minimization

On 7/24/18 7:24 AM, farial tavakoli wrote:
> Dear Justin
>
> I used LigParGen server to generate ligand topology but I dont know what 
> changes I have to do in .itp file.
>   when I issued this command:
> gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tor
>
> faced this error:ERROR 1 [file LIG.itp, line 11]:
>Atomtype opls_800 not found
> I checked the aminoacids.rtp file  of  
> /usr/local/gromacs/share/gromacs/top/oplsaa.ff and found there is not 
> atomtype opls_800 and 801 and ... in this file. while the LIG.itp which 
> generated by LigParGen server has atomtype opls_800 , 801 and ... .
> I have to modify all of these atomtype opls_ in order to correspond to with 
> aminoacid.rtp file?
> I would be thankfull if you help me.
> bestFraial

It looks like your topology introduces new atom types. Check the
LigParGen documentation to see if it requires a different version of the
force field or if the parameters are provided somewhere.

-Justin

--
==

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

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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] REMD Showing Zero Exchange Probability

[Smith, Micholas D.]

How frequently are you trying to exchange?

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


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

Sent: Friday, July 20, 2018 4:39 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] REMD Showing Zero Exchange Probability

Dear all,
I have performed REMD for a system containing Protein, Reline, Urea and
Water in the temperature range 290 to 450 K consist of 16 replicas out of
47 replicas generated by REMD temperature generator. But after the MD
simulation the exchange probability is zero. I have used position
restraints for reline, urea and protein. Is there any chance that position
restraints  cause the exchange probability to be zero?  I have one more
query that, the REMD temperature generator produced around 45 to 54
replicas for my system in the required temperature range. But I have only
80 processors to do the job, So is it necessary to choose the consecutive
temperature replicas given by the REMD temperature generator or I can skip
some temperatures in between?

If I am using the equation *Ti = T0 exp (k* i)*, what determines the value
of 'k'  how it affects the exchange probability? How can I choose the value
of 'k' for an arbitrary system?

Thanks in advance...
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Re: [gmx-users] Deuterium atoms

[Smith, Micholas D.]

Typically, deuterium is treated with the same parameters as H, but with double 
the mass. Most papers don't even bother with the re-parameterization, using the 
argument that the bond-lengths will not change substantially. Instead the 
authors focus on how the dynamics are slowed. 

If you really want to use deuterium properly you should consider 
re-parameterizing, but it really boils down to what phenomena you are most 
interested in looking at? Which begs the question, why are you using D instead 
of H? Are you trying to match an experiment that had deuterurated samples?

As an aside, If this is extremely low-temp or related to proton tunneling then 
you may also need to consider not doing traditional MD, but instead 
Ring-Polymer MD (i.e. Path Integral Molecular Dynamics), because the BO 
approximation may not applicable. But then you can't use gromacs for that...

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


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

Sent: Thursday, June 21, 2018 9:09 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Deuterium atoms

On 6/21/18 9:05 AM, Hermann, Johannes wrote:
> Hello Justin,
>
> okay that is beyond my expertise. Do you know / think if there will be
> a force field in the future where deuterium is present?
>

There are tons of published studies that have done MD with deuterium. I
suggest you start there.

-Justin

> All the best
>
> Johannes
>
>
> On 21.06.2018 15:01, Justin Lemkul wrote:
>>
>>
>> On 6/21/18 8:53 AM, Hermann, Johannes wrote:
>>> Hello Justin,
>>>
>>> thank you for your answer. So the only way to simulate with
>>> deuterium atoms would be a parametrization of the force field, in
>>> particular the bonded force constant?
>>>
>>
>> At minimum. All parameters are connected, so angles and dihedrals may
>> be affected by different vibrational frequencies.
>>
>> -Justin
>>
>>> Thank you in advance!
>>>
>>> All the best
>>>
>>> Johannes
>>>
>>>
>>> On 21.06.2018 14:16, Justin Lemkul wrote:


 On 6/21/18 3:47 AM, Hermann, Johannes wrote:
> Thanks Vytautas, might solve it! And additionally change the mass
> in the force field.
>
>

 Increasing the mass will also change the vibrational frequency of
 any bonds involved, requiring a reparametrization of the bonded
 force constant. If you're using constraints, this does not matter,
 but then I sort of wonder why you're bothering to replace H with D
 and expect to see any kind of difference.

 -Justin

> On 21.06.2018 09:24, Vytautas Rakeviius wrote:
>> Just change all D to H in structure file IMHO.
>>
>>  On Wednesday, June 20, 2018, 5:39:18 PM GMT+3, Hermann,
>> Johannes  wrote:
>> Dear all,
>>
>> is there any force field in gromacs (or elsewhere) which can handle
>> deuterium atoms?
>>
>> All the best
>>
>> Johannes
>>
>

>>>
>>
>

--
==

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

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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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[gmx-users] Gromacs do oscillatory shear/box deformation?

[Smith, Micholas D.]

Greetings gromacs community


I've be thinking at looking at some viscoelastic properties and was hoping to 
avoid the slow convergence of the green-kubo method and use NEMD methods; 
however, from the manual I can't tell if the deformation options in for the mdp 
file are oscillatory or constant. So put simply: Does gromacs support 
oscillatory shear/deformations or do I need to use something else?


Thanks,


-Micholas



===
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
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Re: [gmx-users] md simulation of oil hydrocarbon / L-OPLS

[Smith, Micholas D.]

Hydrocarbons with less than 200 atoms can be generate from the server I 
mentioned. For larger hydrocarbons, it would be best to develop smaller 
residues ( say C8 through C16 ) and stitch them together to form the larger 
hydrocarbons and then validate the models/tune the parameters as necessary. 
This in itself is a fairly massive undertaking since you would essentially be 
making a new force-field (similar to how protein force-fields were developed). 
That being said, it would be immensely useful.

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


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Atila 
Petrosian 
Sent: Tuesday, May 29, 2018 9:29 PM
To: gmx-users
Subject: [gmx-users] md simulation of oil hydrocarbon / L-OPLS

Dear Micholas,

I have many hydrocarbons (small to large) for study,  C8 - C50, .
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Re: [gmx-users] md simulation of oil hydrocarbon / L-OPLS

[Smith, Micholas D.]

Since octane is not huge hydrocarbon, you could use LigParGen ( 
http://zarbi.chem.yale.edu/ligpargen/gmx_tutorial.html ) from Jorgensen's lab 
to generate an itp file for octane, which you could use as your guide to build 
an rtp.

-Micholas

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


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

Sent: Tuesday, May 29, 2018 3:10 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] md simulation of oil hydrocarbon / L-OPLS

On 5/29/18 3:08 PM, Atila Petrosian wrote:
> I know your mean. But there is not octane residue type in rtp file.

Then you'll have to make one, using the existing molecules as a guide.
The OPLS atom types for such a species should be straightforward to assign.

-Justin

--
==

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

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

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] Simulating protein-lipid interactions

[Smith, Micholas D.]

Mixing force-fields is generally considered a bad idea. Though there are some 
papers where people do mix the force-fields,  these are limited cases and 
typically require substantial validation against experimental data and 
additional tuning of the resulting mixed force-field.

-Micholas


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


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Gonzalez 
Fernandez, Cristina 
Sent: Wednesday, May 23, 2018 10:42 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Simulating protein-lipid interactions

Dear Gromacs users,



I want to simulate the interaction of a protein and a lipid. For the protein 
simulation I have chosen the CHARMM27 force field, because is the one I had 
selected for the lipid simulation. Does the force field have to be the same for 
both molecules? How I select the best force field for the protein? Where can I 
find information about force fields?





Any help will highly been appreciated.



Best,

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Re: [gmx-users] pause a run?

[Smith, Micholas D.]

Try the explicit command:

gmx mdrun -s md.tpr -cpi md.cpt -c (your configuration_outfile_here) -o (your 
trajectory file here) -e (your energy file here) -cpo md.cpt -v -g (your log 
file here)



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


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

Sent: Friday, March 23, 2018 11:16 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] pause a run?

So I killed one of my runs, then I used the "-cpi" command and tried this
" gmx mdrun -deffnm md.tpr -cpi md.cpt". But it was asking for file
"topol.tpr", which I don't have.. any help?
Thanks,
MD

On Fri, Mar 23, 2018 at 10:41 AM, MD  wrote:

> ​You mean I could use the md.cpt to re-run it?​
>
> On Fri, Mar 23, 2018 at 10:35 AM, Smith, Micholas D. 
> wrote:
>
>> If you are writing state files, you can just kill the jobs and use them
>> to restart.
>>
>> ===
>> Micholas Dean Smith, PhD. MRSC
>> Post-doctoral Research Associate
>> University of Tennessee/Oak Ridge National Laboratory
>> Center for Molecular Biophysics
>>
>> 
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of MD <
>> refm...@gmail.com>
>> Sent: Friday, March 23, 2018 10:33 AM
>> To: gmx-us...@gromacs.org
>> Subject: [gmx-users] pause a run?
>>
>> Hi Gromacs Folks,
>>
>> I was running 6 md runs at the same time (not super fast computer, so it
>> could take 3 months to complete based on rough estimation). However, I
>> need
>> to prioritize two runs now but I don't want to just kill the other 4 since
>> it has been several weeks since I started the runs.
>>
>> I wonder if there is a way I could "pause" the other 4 runs at this point?
>>
>> Thanks a bunch,
>>
>> MD
>> --
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>> send a mail to gmx-users-requ...@gromacs.org.
>>
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>>
>
>
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Re: [gmx-users] pause a run?

[Smith, Micholas D.]

If you are writing state files, you can just kill the jobs and use them to 
restart.  

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


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

Sent: Friday, March 23, 2018 10:33 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] pause a run?

Hi Gromacs Folks,

I was running 6 md runs at the same time (not super fast computer, so it
could take 3 months to complete based on rough estimation). However, I need
to prioritize two runs now but I don't want to just kill the other 4 since
it has been several weeks since I started the runs.

I wonder if there is a way I could "pause" the other 4 runs at this point?

Thanks a bunch,

MD
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Re: [gmx-users] Fw: asking guidance

[Smith, Micholas D.]

Add the -sep flag that will split the writting into multiple files instead of 1 
large pdb. Alternatively you could script up a spliting program with something 
like awk 

awk 'BEGIN{filename="MyFile_"i".pdb"}{print $0>filename; if $0~/ENDMDL/; 
i++;filename="MyFile_"i".pdb"}}' 

-Micholas

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


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Mansoureh 
Shahbazi 
Sent: Friday, March 09, 2018 11:13 AM
To: gmx-us...@gromacs.org
Cc: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Fw: asking guidance

Dear director,I am using Gromacs package to perform MD simulations and I have a 
100 ns long MD simulation. For the further assays, I must split this 100 ns 
trajectory into 100 pdb files (to get one pdf file from each 1000 ps or 1 ns of 
simulation).

I have found two commands:
gmx trjconv -s topol.tpr -f md_0_1.xtc -dt 1000 -o trj.pdb
gmx trjconv –f md.xtc –s md.tpr –b 1 –e 1000 –o md.pdb (and -b 1001 -e 2000 and 
so on )

I tried both of them. But for the first one, I got only one pdb file and for 
the second command, I have to repeat the command 100 times to get them and 
furthermore I am not sure it gives the correct results.  Can you please tell me 
is there any command to split the 100 ns trajectory with the time intervals of 
1000 ps and get 100 pdb files at one time?  If no, please make me aware that is 
the second command gives the true result?  I am looking forward to your answer, 
Thanks in advance for your guidance,Sincerely yours,Mansoureh


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

[Smith, Micholas D.]

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

Regards,

Micholas

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


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

Thank You Micholas


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

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

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

Any suggestions ?


Thank You


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

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

[Smith, Micholas D.]

Alternatively, if the visualization is the only place you don't see the bond 
(but if you check the topology file and it does show a bond between the metal 
and the linker is defined) it could be a visualization issue. In that case look 
at the trjconv command options to center the system and account for the pbc's.

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

____
From: Smith, Micholas D.
Sent: Tuesday, March 06, 2018 10:52 AM
To: gmx-us...@gromacs.org
Subject: Re: Geometry Optimization for Metal organic Frame works

Its the topology generation. It didn't capture that a bond should be where you 
expected it to be. Bonds will not break in gromacs, so if you are seeing less 
bonds than you expected its in the topology.


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


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Nagasree 
Garapati 
Sent: Tuesday, March 06, 2018 10:49 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] Geometry Optimization for Metal organic Frame works

Hi All


I am new user for GROMACS and I am trying model Metal Organic Frame works (MOFs)

I have crystal structure (CIF) file downloaded from Cambridge Crystallographic 
Data Center (CCDC) and used OBGMX tool to develop force field parameters and 
used following minim.mdp file for optimization. But after optimization, when I 
visualize the output .gro file I see that all the bonds between the Metal atom 
and the linker is broken and no.of bonds is less than the original bonds.

Can this be due to the topology file created or am I missing something in mdp 
file. If anyone has experience with modeling MOFs using GROMACS, I really 
appreciate your help.


Thank You


; minim.mdp - used as input into grompp to generate em.tpr
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 75.0  ; Stop minimization when the maximum force < 100.0 kJ/mol/nm
emstep  = 0.1  ; Energy step size
nsteps = 1000   ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range 
forces
cutoff-scheme   = Verlet
ns_type = grid ; Method to determine neighbor list (simple, grid)
coulombtype = Cut-off ; Treatment of long range electrostatic interactions
rcoulomb = 2.0 ; Short-range electrostatic cut-off
rvdw = 2.0 ; Short-range Van der Waals cut-off
rlist = 2.0 ; Short-range neighbor cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)


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

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

[Smith, Micholas D.]

Its the topology generation. It didn't capture that a bond should be where you 
expected it to be. Bonds will not break in gromacs, so if you are seeing less 
bonds than you expected its in the topology.


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


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Nagasree 
Garapati 
Sent: Tuesday, March 06, 2018 10:49 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] Geometry Optimization for Metal organic Frame works

Hi All


I am new user for GROMACS and I am trying model Metal Organic Frame works (MOFs)

I have crystal structure (CIF) file downloaded from Cambridge Crystallographic 
Data Center (CCDC) and used OBGMX tool to develop force field parameters and 
used following minim.mdp file for optimization. But after optimization, when I 
visualize the output .gro file I see that all the bonds between the Metal atom 
and the linker is broken and no.of bonds is less than the original bonds.

Can this be due to the topology file created or am I missing something in mdp 
file. If anyone has experience with modeling MOFs using GROMACS, I really 
appreciate your help.


Thank You


; minim.mdp - used as input into grompp to generate em.tpr
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 75.0  ; Stop minimization when the maximum force < 100.0 kJ/mol/nm
emstep  = 0.1  ; Energy step size
nsteps = 1000   ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range 
forces
cutoff-scheme   = Verlet
ns_type = grid ; Method to determine neighbor list (simple, grid)
coulombtype = Cut-off ; Treatment of long range electrostatic interactions
rcoulomb = 2.0 ; Short-range electrostatic cut-off
rvdw = 2.0 ; Short-range Van der Waals cut-off
rlist = 2.0 ; Short-range neighbor cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)


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

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Re: [gmx-users] Creating Forcefield without ffbonded.itp

[Smith, Micholas D.]

You could do something similar in a Top file. Or make unique names for the 
parameters to correspond directly the the specific molecule you are interested 
in.

-Micholas

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


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

Sent: Thursday, March 01, 2018 10:40 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] Creating Forcefield without ffbonded.itp

Hello,

is it possible to include all needed bonded parameters (bond lenght,
bond angle,...) in the .rtp file and ignore the ffbonded.itp completely?
Such case would be if a molecules structure has specified parameters
which only fit said structure. According to the manual bond length and
angle should be possible but the force constants are not mentioned.

Greets,
Momin

--
Momin Ahmad

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

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Re: [gmx-users] g_sans calculation

[Smith, Micholas D.]

>From what I understand very few people use the g_sans tool. One alternative is 
>to use CRYSON (if you are looking at biopolymers such as 
>proteins/dna/polysaccarides). Alternatively, SASSENA is also an option but it 
>has a lot of dependences. 

CRYSON: https://www.embl-hamburg.de/biosaxs/manuals/cryson.html

SASSENA: www.sassena.org (accessible through the internet-wayback machine at:   
https://web.archive.org/web/20170724080028/http://www.sassena.org/  )

nMoldyn: 
http://dirac.cnrs-orleans.fr/plone/software/nmoldyn/nmoldyn_user_guide.pdf/view

Hope this helps


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


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

Sent: Friday, February 23, 2018 3:14 PM
To: gmx-us...@gromacs.org
Subject: [gmx-users] g_sans calculation

 Dear Gromacs Users,

I am calculating the g_sans in the simulation but I am not able to find how
it is calculated. The help content is minimal. I am just wondering if
anyone has looked into how it is calculated (any reference to algorithm?).

Regards,
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Re: [gmx-users] ZNO-HSA (Human Serum albumin) Interaction

[Smith, Micholas D.]

Hard to tell from your descriptions. Things to consider:

1) Is the force-field for the ZnO particle realistic (have you validated it or 
have evidence that it is accurate)
2) If the ZnO particle has a net charge and you are running PME you are going 
to need to neutralize the system such that it accounts for both the protein and 
the ZnO nanoparticle
3) Why do you think it is wrong? What experimental evidence can you compare to 
benchmark if your results are reasonable?

We can't tell you if your results are "right or wrong," that's your 
responsibility to know this and justify it before submitting to review, but the 
questions above may help drive your thinking a bit on this.

Hope that helps. 

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


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Hassan 
Aaryapour 
Sent: Wednesday, February 21, 2018 3:47 AM
To: gromacs.org_gmx-users; gmx-us...@gromacs.org
Subject: [gmx-users] ZNO-HSA (Human Serum albumin) Interaction

Dear Gromacs Users;

I am studying the toxicity effect of ZnO nanoparticle (with a partial
charges of +1.026 and -1.026 for Zinc and Oxygen atoms, respectively) on
the Albumin structure by Gromacs. For MD simulation the nanoparticle was
placed at a distance of 1nm of protein, after running pdb2gmx, the
simulation box was solvated by TIP3P waters. The net charge of protein in
physiological condition is -14 that was neutralized by adding sodium and
chloride ions to box. Then, energy minimization, NVT and NPT were done.
>From the beginning of md simulation, the protein structure began to be
unfolded slowly before binding nanoparticle to it and after binding, the
protein structure changed dramatically. I cannot consider the charge of ZnO
as zero like silver or gold nanoparticles. So, I am confused that whether
the study method is correct or wrong for this interaction? Do the results
seem logical?

Thanks
Hassan Aryapour
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Re: [gmx-users] Usage of GROMACS

[Smith, Micholas D.]

Hi Momin,

Unfortunately, crystalline structures are, as you have experienced, not the 
easiest thing to simulate using gromac's system building tools. Typically, 
people working on MOFs, clays, general polymers, and other non-biological 
systems use something like LAMMPS (or DL_Poly like you have already noted). 
That being said, it isn't impossible to use gromacs for these types of systems, 
it just takes a bit of time. 

One tool that can be useful for these types of systems with gromacs, however, 
is the x2top tool. It is far from perfect, but it can get you started in the 
right direction.

-Micholas

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


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

Sent: Monday, December 04, 2017 8:27 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] Usage of GROMACS

Hello,

is GROMACS meant to be used for simulations of crystaline structures
(Metal Organic Frameworks, porous materials, minerals, ...)? Almost
every paper working on MD simulations with said structures use DL_Poly
or other software. So my question would be is there a community that
uses GROMACS to simulate crystaline structures? Porting .cif files to
pdb and then trying to run pdb2gmx with writing a .rtp file is very time
consuming.

Cheers
Momin

--
Momin Ahmad

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

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Re: [gmx-users] how to output intramolecular pair interaction parameters

[Smith, Micholas D.]

You could use an energy group exclusion and then perform gmx mdrun -rerun where 
all of the pairs you aren't interested in are excluded from the energy 
calculation.

>From the manual:


energygrp-excl:
Pairs of energy groups for which all non-bonded interactions are excluded. 
An example: if you have two energy groups Protein and SOL, specifying
energygrp-excl = Protein Protein  SOL SOL
would give only the non-bonded interactions between the protein and the 
solvent. This is especially useful for speeding up energy calculations with 
mdrun -rerun and for excluding interactions within frozen groups. 

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


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Srinivasa 
Ramisetti 
Sent: Thursday, November 16, 2017 12:48 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] how to output intramolecular pair interaction parameters

Hi all,


I would like to know if there is any way to output intramolecular pair 
interaction parameters that are generated by gromacs.


Thank you,

Srinivasa
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Re: [gmx-users] convergence of PMF

[Smith, Micholas D.]

One way to get some degree of confidence is to use the bootstrapping/error 
analysis options provided in gmx wham. But Justin is right you are looking for 
time invariance. So: use the first portion of your trajectory (say first 60%) 
and compute the PMF, then use the first 65% of your trajectory and see if it 
has changed (and by how much), then 70%, and 80% and so on. If you have 
converged (within reason), you should see that at some point, as you add more 
time to the analysis the PMF doesn't change (in any statistically significant 
way), when that occurs you have "converged". 


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


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

Sent: Thursday, November 16, 2017 8:04 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] convergence of PMF

On 11/16/17 3:34 AM, abhisek Mondal wrote:
> Hi,
>
>  I have derived a PMF (protein-ligand) using umbrella sampling method.
> But how can I comment if the obtained PMF has converged well ? What are the
> ways to check the convergence of a PMF ?

How would you check convergence of any quantity? You have to determine
if the result is changing over time, and if it is invariant (within the
context of available statistics), then the quantity is converged.

-Justin

--
==

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

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

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

==

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Re: [gmx-users] gmx solvate problem

[Smith, Micholas D.]

You may want to consider using something a little more powerful than gmx 
solvate for this, such as packmol 
(http://www.ime.unicamp.br/~martinez/packmol/home.shtml).

Alternatively, you could construct a layer of water in a separate file and 
concatenate them together (generate the layer of water in a box with an off-set 
in coordinates to avoid clashes with where your ice will be).

-Micholas

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


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Alexandr 
Nasedkin 
Sent: Wednesday, November 08, 2017 9:40 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] gmx solvate problem

Hi Golnaz,


Try to increase default VdW radius scaling: option -scale in gmx solvate.

If there are large cavities in ICE you may have problem at water
interface though.


Best regards,

Alexandr



On 08/11/2017 15:04, G R wrote:
> Hi All,
>
> I’m simulating a box of tip4p ice. when I use the gmx solvate to fill the
> top and below part of the ice surface with solvent (the solvent is tip4p
> water), some of water molecules go to inside of the ice layers. I did not
> receive any errors, but the coordinate files became messy after salvation.
> I don't know how can I insert water molecules on the top and bellow of the
> surface correctly.
>
> Thank you in advance for any help,
> Golnaz

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Re: [gmx-users] non-neutral system

[Smith, Micholas D.]

A requirement of PME is that the net charge is zero. Adding counter-ions would 
be considered standard-fare. Check out the paper:  
https://www.unc.edu/~perera/PAPERS/JChemPhys_1995_103_8577.pdf for details (A 
smooth particle mesh Ewald method).

Best of luck

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


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Faezeh 
Pousaneh 
Sent: Monday, November 06, 2017 5:50 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] non-neutral system

Hi,

I  have a system containing similar charged atoms. So the total charge is
not zero.

Simulation results with cut-off coulomb seems reasonable,  but using PME
they are wrong (total columb potential is negative value which must be
positive). Any idea why?

If I use counter-ions to neutralize the system, I am afraid the properties
I am looking for (viscosity) will be influenced.

Best regards
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Re: [gmx-users] pdb (CTAB) into .GRO

[Smith, Micholas D.]

Justin is right, x2top is not "smart" but it can get you in the point you in a 
helpful direction.

-Micholas

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


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

Sent: Sunday, November 05, 2017 12:13 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] pdb (CTAB) into .GRO

On 11/3/17 10:38 AM, Smith, Micholas D. wrote:
> One thing to try is to build the CTAB molecule with gmx x2top. You'll need to 
> be careful about what it produces, but it can be helpful.

The only word of caution here is that you have to still tell x2top what
everything's charges and connectivities are, meaning you have to
pre-parametrize those interactions. x2top isn't smart enough to actually
do the hardest work for you, it just spits out a topology with a quality
equal to what you tell it :)

-Justin

--
==

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

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

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

==

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Re: [gmx-users] pdb (CTAB) into .GRO

[Smith, Micholas D.]

One thing to try is to build the CTAB molecule with gmx x2top. You'll need to 
be careful about what it produces, but it can be helpful.


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


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

Sent: Friday, November 03, 2017 6:35 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] pdb (CTAB) into .GRO

Force field in gromacs reads only standard amino acids/DNA/RNA residue. In
your pdb file residue name XXX is not defined in gromos ff. If your system
is other than protein then use ATB to generate topolgy.


Virus-free.
www.avast.com

<#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

On Fri, Nov 3, 2017 at 2:19 PM, Adriano Santana Sanchez <
adriano.santanasanc...@kaust.edu.sa> wrote:

>  Dear all,
>
>  I am a beginner with gromacs and I have already done some online
> tutorials.
>  I am now trying to create from a PDB coordinate file (a CTAB molecule) the
>  corresponding .GRO and .TOP files to run MD simulations.
>
>  gmx pdb2gmx -f ctab.pdb -o ctab_processed.gro -water spce
>
>  then choose FF gromos96 53a6 but get error message:
>
>  Residue 'XXX' not found in topology database
>
> I am sure this FF has been used for this molecule before and I cannot
>
> find this CTAB on the residue database. What can I do?
>
> Thanks,
> Adriano
>
> --
>
> --
> This message and its contents, including attachments are intended solely
> for the original recipient. If you are not the intended recipient or have
> received this message in error, please notify me immediately and delete
> this message from your computer system. Any unauthorized use or
> distribution is prohibited. Please consider the environment before printing
> this email.
> --
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Re: [gmx-users] CHARMM ff cutoffs

[Smith, Micholas D.]

Fair enough. 

Consider this then: of the systems tested in the CHARMM36m publication; which 
one is closest to yours (sequence similarity, structure)? That would be one way 
to decide which cut-off would be appropriate. 

Alternatively, you could just run the simulation multiple times with multiple 
cut-offs and see which one corresponds closest with experimental knowledge 
(though this would be challenge for IDPs, unless there is a known set of 
metastable structures that get sampled).

-Micholas

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


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

Sent: Thursday, October 19, 2017 10:46 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] CHARMM ff cutoffs

Dear Micholas,

First of all, thank you for your input. I understand the whole cutoff
problematic and it is my desire to stick to the standard. However (and
maybe I didn't explain this part properly), the CHARMM36m publication
reports different cutoffs (if you check the SI) depending on which protein
is simulated. This publication *IS* the standard, right? I am well aware
that other CHARMM implementations use 1.2 nm, but if you go further back in
time, the cutoffs have taken other values. But I digress, the main question
here is, how can I justify my choice when the official publication reports
these two values and does not provide an explanation for it? I am well
aware that the 1.2 nm value is the *de facto* value, but that is not an
acceptable justification in the eyes of a journal referee, as we all can
understand.

Thanks!
J



On Thu, Oct 19, 2017 at 4:33 PM, Smith, Micholas D. 
wrote:

> João,
>
> If you use the CHARMM-GUI (charmm-gui.org) to build your systems, they
> set their "standard" cut-offs to be 1.2nm, unless there is a membrane, then
> they set it to 1.4nm (at least that's what it use to do).
>
> Changing cut-offs is kind of a mess. A lot of people will argue that the
> cut-offs are explicitly part of the force-field, and so whatever cut-offs
> were used for the parameterization are what you absolutely must use. But
> then you'll find papers (lake you did) that uses 0.95nm cut-offs and get
> reasonable results.
>
> I would stick to the standard unless you have a really good reason (not
> performance) for toying with the cut-offs.
>
> -Micholas
>
> ===
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of João
> Henriques 
> Sent: Thursday, October 19, 2017 10:03 AM
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] CHARMM ff cutoffs
>
> Dear all,
>
> Is there any piece of literature that explicitly states what is the *de
> facto* cutoff for CHARMM FFs, i.e., for the LJ and electrostatic
> interactions? The old gromacs site states it's 1.2 nm:
>
> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM
>
> However, I've read Robert Best's C36 and Huang's C36m papers, along with
> older CHARMM ff publications by MacKerell and Co., and I'm rather confused
> at this point. E.g., on the C36m paper, the RS peptide is simulated with
> 0.95 nm cutoffs and other proteins with 1.2 nm. Robert is consistent and
> uses 1.2 nm all the way. Older publications use even shorter cutoffs.
>
> I know the cutoffs can probably be toyed with to a certain extent (Stefano
> Piana and Kresten Lindorff-Larsen showed that on their 2012 paper), but a
> recent paper by Davide Mercadante on JCTC seems to show that it is not so
> simple for IDPs, and shortening the cutoffs is a no-no (even though he did
> it for his KBFF and AMBER FFs, not CHARMM).
>
> In my work I use CHARMM36m with 1.2 nm, but, looking at the literature,
> there's no way I can justify my choice when the original C36m does not
> stick to a single cutoff selection...
>
> I know Justin is/was affiliated with the MacKerell lab, so maybe he can
> shed some light on this subject. Anyone else is encouraged to give their
> input as well.
>
> Thank you in advance,
> Best regards,
> João
> --
> Gromacs Users mailing list
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> * Please search the archive at http://www.gromacs.org/
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>
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Re: [gmx-users] CHARMM ff cutoffs

[Smith, Micholas D.]

João,

If you use the CHARMM-GUI (charmm-gui.org) to build your systems, they set 
their "standard" cut-offs to be 1.2nm, unless there is a membrane, then they 
set it to 1.4nm (at least that's what it use to do).

Changing cut-offs is kind of a mess. A lot of people will argue that the 
cut-offs are explicitly part of the force-field, and so whatever cut-offs were 
used for the parameterization are what you absolutely must use. But then you'll 
find papers (lake you did) that uses 0.95nm cut-offs and get reasonable results.

I would stick to the standard unless you have a really good reason (not 
performance) for toying with the cut-offs.

-Micholas

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


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

Sent: Thursday, October 19, 2017 10:03 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] CHARMM ff cutoffs

Dear all,

Is there any piece of literature that explicitly states what is the *de
facto* cutoff for CHARMM FFs, i.e., for the LJ and electrostatic
interactions? The old gromacs site states it's 1.2 nm:

http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM

However, I've read Robert Best's C36 and Huang's C36m papers, along with
older CHARMM ff publications by MacKerell and Co., and I'm rather confused
at this point. E.g., on the C36m paper, the RS peptide is simulated with
0.95 nm cutoffs and other proteins with 1.2 nm. Robert is consistent and
uses 1.2 nm all the way. Older publications use even shorter cutoffs.

I know the cutoffs can probably be toyed with to a certain extent (Stefano
Piana and Kresten Lindorff-Larsen showed that on their 2012 paper), but a
recent paper by Davide Mercadante on JCTC seems to show that it is not so
simple for IDPs, and shortening the cutoffs is a no-no (even though he did
it for his KBFF and AMBER FFs, not CHARMM).

In my work I use CHARMM36m with 1.2 nm, but, looking at the literature,
there's no way I can justify my choice when the original C36m does not
stick to a single cutoff selection...

I know Justin is/was affiliated with the MacKerell lab, so maybe he can
shed some light on this subject. Anyone else is encouraged to give their
input as well.

Thank you in advance,
Best regards,
João
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Re: [gmx-users] CLASS II force fields

[Smith, Micholas D.]

Do you have a particular one in mind?

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


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of 
dimitris.g.mintis 
Sent: Friday, October 06, 2017 12:15 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] CLASS II force fields

Does anyone knows how to incorporate class 2 potential in GROMACS?



Thanks

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Re: [gmx-users] linux or windows

[Smith, Micholas D.]

Gromacs is an easier install on Linux. Also its utilities were designed (as far 
as I know) for the linux environment. 

If you need windows, I would suggest a duel-boot or virtual instance of windows 
within linux.

-Micholas

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


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

Sent: Tuesday, September 26, 2017 1:00 PM
To: gmx-us...@gromacs.org
Subject: [gmx-users] linux or windows

Dear all users,
I want to install gromacs on my PC, but I don't know which operating system is 
better: linux or windows and it is important that doesn't loose capabilities of 
the software? In any case, which version of operating system is better for 
installation?
Thanks in advance,Negar
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Re: [gmx-users] Secondary structure content

[Smith, Micholas D.]

If i remember correctly the DSSP plot should be something like residue # on 
y-axis, and time on the x-axis, then it is normally a color plot of what 
secondary structure each residue is in at that time point. Secondary structure 
content (%) vs time sounds more like a single plot of the fraction of residues 
(%) of residues at each time point that are not in a 'coil' state. 

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


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

Sent: Saturday, September 09, 2017 5:48 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Secondary structure content

Dear all,
I am confused with 'dssp' output graph i.e "number of residues vs time". Is
it also called "secondary structure content(%) vs time" ?? Or it is
different term?

please, anyone help me to solve this confusion  or send me any link
contained proper definition of these two.

Thanks in advance
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Re: [gmx-users] Result analysis of protein water

[Smith, Micholas D.]

First: Welcome to the wonderful world of MD. 

Second, 10ns for a 164 residue protein is nowhere near enough simulation time. 
If you are looking for just small modifications, you could do an alignment of 
the backbones of the proteins in each trajectory and compare all frames to 
all-frames using the rmsd (you'd end up with a matrix of rmsd values comparing 
trajectory 1 to trajectory 2). 

Other things to consider are: salt-bridges, hydrogen-bond networks, and 
secondary-structure measurements (STRIDE or DSSP).

Good Luck.

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


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

Sent: Friday, September 08, 2017 12:30 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se; gmx-us...@gromacs.org
Subject: Re: [gmx-users] Result analysis of protein water

Hello All,

I have performed MD on a protein water for 10ns, protein with total 164
residues in two chains. I have got the result graphs of radius of gyration
and rmsd for both wild and mutant. Wanted to attach the graphs but could
not due to bytes limit. There is one residue mutation (M -> T) in the
protein. I am new to MD analysis. Could you please let me know how to know
if the mutation is causing any conformational change. I can look at the
trajectories obtained of wild and mutant type, but to make accurate
analysis I would need more information. Also, please do share with me how
can i do more analysis to see the effect of mutations. Please let me know
if I need to provide more information.

Thanks & Regards.
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Re: [gmx-users] Memory issues using -ac option of gmx hbond

[Smith, Micholas D.]

I had a similar problem. Using gromacs 2016.3's hbond tool fixed this. 


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


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Jared 
Sagendorf 
Sent: Monday, August 07, 2017 5:46 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Memory issues using -ac option of gmx hbond

I'm trying to analyzing hydrogen bonds between a DNA and protein complex.
When using the -ac option of gmx hbond, I'm getting segmentation faults
which look like an out-of-memory problem.

However, I'm giving the process 64gb of memory, and an additional 64gb of
virtual memory. How memory intenstive is this program??

Note I am using version 5.1.13. A snippet of the output is below

Calculating hydrogen bonds between DNA_interface (919 atoms) and
Protein_interface (1026 atoms)
Found 138 donors and 458 acceptors
Making hbmap structure...done.
...
Found 117 different hydrogen bonds in trajectory
Found 156 different atom-pairs within hydrogen bonding distance
Merging hbonds with Acceptor and Donor swapped
- Reduced number of hbonds from 117 to 116
- Reduced number of distances from 156 to 156
Average number of hbonds per timeframe 16.544 out of 31602 possible

 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
D. van der Spoel, P. J. van Maaren, P. Larsson and N. Timneanu
Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media
J. Phys. Chem. B 110 (2006) pp. 4393-4398
  --- Thank You ---  

Doing autocorrelation according to the theory of Luzar and Chandler.
[hpc3338:34436] *** Process received signal ***
[hpc3338:34436] Signal: Segmentation fault (11)
[hpc3338:34436] Signal code: Address not mapped (1)
[hpc3338:34436] Failing at address: 0xfde7c370
[hpc3338:34436] [ 0] /lib64/libpthread.so.0(+0xf370)[0x7ff5c3810370]
[hpc3338:34436] [ 1]
/usr/usc/gromacs/5.1.3/cpu/lib64/libgromacs_mpi.so.1(+0x464449)[0x7ff5c4a7b449]
[hpc3338:34436] [ 2]
/usr/usc/gromacs/5.1.3/cpu/lib64/libgromacs_mpi.so.1(cross_corr+0x39)[0x7ff5c4a7b019]
[hpc3338:34436] [ 3]
/usr/usc/gromacs/5.1.3/cpu/lib64/libgromacs_mpi.so.1(+0x339bb2)[0x7ff5c4950bb2]
[hpc3338:34436] [ 4]
/usr/usc/gromacs/5.1.3/cpu/lib64/libgromacs_mpi.so.1(gmx_hbond+0x312e)[0x7ff5c4947aae]
[hpc3338:34436] [ 5]
/usr/usc/gromacs/5.1.3/cpu/lib64/libgromacs_mpi.so.1(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x267)[0x7ff5c47b4637]
[hpc3338:34436] [ 6] gmx_mpi(main+0xba)[0x40bfea]
[hpc3338:34436] [ 7]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7ff5c2c01b35]
[hpc3338:34436] [ 8] gmx_mpi[0x40be69]
[hpc3338:34436] *** End of error message ***


Am I doing something wrong here?
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Re: [gmx-users] adding new ion within the oplsaa force field

[Smith, Micholas D.]

If you want the ion to be recognized as an individual residue, you need to 
stick it in the *.rtp file. 

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


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Jose 
Borreguero 
Sent: Friday, June 23, 2017 3:50 PM
To: gromacs
Subject: [gmx-users] adding new ion within the oplsaa force field

Dear Gromacs users,

I'm trying to add a new type of atom as an ion. Looking at already existing
ions, such as sodium (NA), I see there's an entry both in files ions.itp
and aminoacids.rtp. My question is, what is the rationale of declaring ions
both as ions and as residues? Is this always required?

Best,
Jose Borreguero
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Re: [gmx-users] Error running GMX 5.14

[Smith, Micholas D.]

What does your *.mdp file look like? Its hard to judge what the next step 
should be from what you've given so far.

-Micholas

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


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Sergio 
Manzetti 
Sent: Tuesday, June 20, 2017 7:48 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] Error running GMX 5.14

Hi, I have a system with DNA and water, and given the charge of the DNA of -20, 
genion was used to add +20 charge to the gro file. The energy minimization step 
gives then a warning:

WARNING 2 [file em.mdp]:
The sum of the two largest charge group radii (16.704304) is larger than
rlist (1.20)



Which is the ignored using maxwarn option.

When getting to the em step:

Fatal error:

step 25: Water molecule starting at atom 31535 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.




What is the best approach here to correct this?

Thanks!

Sergio Manzetti

[ http://www.fjordforsk.no/logo_hr2.jpg ]

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ]
Midtun
6894 Vangsnes
Norge
Org.nr. 911 659 654
Tlf: +47 57695621
[ http://www.oekolab.com/ | Økolab  ] | [ http://www.nanofact.no/ | Nanofactory 
 ] | [ http://www.aq-lab.no/ | AQ-Lab  ] | [ http://www.phap.no/ | FAP ]

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Re: [gmx-users] Topology generation of molecules

[Smith, Micholas D.]

Channa,

What are you trying to use the Topology for? MD or Analysis of a trajectory 
from some other piece of software? Justin is right, if you want to run MD than 
you can't just use one force-field server to generate another, as each one has 
will give output for different force-fields and each force-field may (read: 
will) lead to different dynamics. However: If you are just trying to analyze a 
trajectory your built with some other software (like NAMD), you can use 
topotools ( https://sites.google.com/site/akohlmey/software/topotools ) to 
convert a psf into a gromacs topology with "non-sense" force-field parameters 
but the correct bond, dihedrial and angle portion of the topology file, which 
will let you use grompp to make a *.tpr for the analysis tools.

-Micholas

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


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

Sent: Tuesday, June 20, 2017 7:58 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Topology generation of molecules

On 6/20/17 12:21 AM, Abid Channa wrote:
> If PRODRG is not giving suitable results . Can I use Antechamber output in 
> GROMACS for the topology generation of molecules ?  .

PRODRG is for GROMOS, Antechamber is for AMBER.  You can't simply replace one
with the other because the force fields are totally different.  Parametrize your
molecule in a manner consistent with the parent biomolecular force field, or
find the program/server that is consistent with that force field.

-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] Alternatives to COMPASS forcefield

[Smith, Micholas D.]

OPLS/AA maybe?

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


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Bruno 
Escribano 
Sent: Wednesday, June 14, 2017 12:10 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Alternatives to COMPASS forcefield

Dear All,

we are trying to setup simulations for a polymer material that in the
past has been studied with other softwares using the COMPASS forcefield.

I understand that this forcefield is not available in GROMACS, but can
anybody recommend a different forcefield that would produce similar
results to COMPASS.

Thank you in advance.
Best regards,
Bruno

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Re: [gmx-users] How to improve the performance of simulation in HPC (finding optimal number of nodes and processors)

[Smith, Micholas D.]

Perhaps try something like:

(in your PBS Script)
-l nodes=8:ppn=28 (request for 8 nodes with all cores)
source (your source stuff here)

mpirun -n 56 -npernode 7 gmx_mpi mdrun -ntomp 4 (your run stuff here).

This should give you 7 mpi ranks per node, with each rank using 5 openMP 
threads, which give reasonable speed. Let me know if that works.

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


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Santhosh Kumar 
Nagarajan 
Sent: Friday, June 02, 2017 1:49 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] How to improve the performance of simulation in HPC 
(finding optimal number of nodes and processors)

Dear users,

I am simulating a protein having 285 residues in a Gromacs environment
installed in our University's HPC. Gromacs version: gmx, version 2016.3.

I have tried to run the simulation using the standard
"select=1:ncpus=28:mpiprocs=28" provided by our HPC admin (in pbs script).
The same number of nodes and processors is given by the users of various
other software (like VASP, Mathematica), which run perfectly. But when I
tried to give the same number, the simulation was running too slow
(approximately one ns per day). So I tried to change the number of nodes
and processors, but nothing seems to improve the performance.

For example:
Many times I got fatal errors, saying,

###Using 6 MPI threads
Using 28 OpenMPI threads per tMPI thread

WARNING: Oversubscribing the available 28 logical CPU cores with 168
threads. This will cause considerable performance loss!

Fatal error: Your choice of number of MPI ranks and amount of resources
result in using 28 OpenMP threads per rank, which is most likely
insufficient. The optimum is usually between 1 and 6 threads per rank. If
you want to run with this setup, specify the -ntomp option. But we suggest
to change the number of MPI ranks (option -ntmpi).###

After this, I have added the "-ntomp option", which skipped the warning.
But didn't improve the performance.
Recently I tried "select=1:ncpus=6:mpiprocs=56, which runs the simulation
using 4 MPI threads and 6 OpenMP threads. I think this is a too low
performance for our HPC, as other software runs with better performance.

Below, I am providing the pbs.sh file which I have used to run the
simulation in HPC. Can anyone please help me, what I am doing wrong.

###PBS file used

#i/bin/bash
#PBS -N my_protein_name
#PBS -q work-01
#PBS -l select=1:ncpus=28:mpiprocs=28
#PBS -j oe
#PBS -V
cd $PBS_O_WORKDIR
cat $PBS_NODEFILE>./pbsnodelist
CORES='cat./pbsnodelist|wc -1'
source /opt/software/intel/parallel_studi_xe_2017.2.050/psxevars.sh intel64
gmx mdrun -ntmpi 28 -deffnm md_0_1

###


Specifications of the HPC:

One master node+40 computer nodes
40X2x Intel Xeon E5-2680v4
(28 threads for one E5-2680)
10 TB RAM
40 TB Hard disk

Master
1X2XE5-2650v4
(24 threads for E5-2650)
128 GB RAM
80TB Hard Disk

Thank you

Regards
--
Santhosh Kumar Nagarajan
PhD Research Scholar
Department of Genetic Engineering
SRM University
Kattankulathur
Chennai - 603203
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Re: [gmx-users] REMD analysis of trajectories

[Smith, Micholas D.]

Ouyang,

Each Replica corresponds to 1 temperature in Gromacs (unlike other software 
packages). If you want to have continuous trajectories (i.e. follow the motion 
of one replica through temperature exchanges) then you have to demux. But the 
demux is really only useful (in my experience) with use of the retired 
g_kinetics tool.


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


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

Sent: Thursday, June 01, 2017 10:53 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] REMD analysis of trajectories

Hi,

What did you learn from the first sentence of the link I gave you?

Mark

On Thu, Jun 1, 2017 at 3:20 PM YanhuaOuyang <15901283...@163.com> wrote:

> Do you mean  that the original trajectories REMD generated are belong to
> "one trajectory per temperature" (i.e. the md2.xtc is a trajectory at 298K)?
>
>
>
> Ouyang
>
>
>
>
> At 2017-06-01 21:00:52, "Mark Abraham"  wrote:
> >Hi,
> >
> >That's what you already have. See
> >http://www.gromacs.org/Documentation/How-tos/REMD#Post-Processing
> >
> >Mark
> >
> >On Thu, Jun 1, 2017 at 5:37 AM YanhuaOuyang <15901283...@163.com> wrote:
> >
> >> Hi,
> >>I have run a 100ns-REMD of protein, which has 20 replicas (i.e.
> >> remd1.xtc, remd2.xtc, ..., remd20.xtc).  I want to analyze a trajectory
> at
> >> specific temperature  such as a trajectory at experiment temperature
> 298K
> >> rather than analyzing the continuous trajectory. I have known GROMACS
> >> exchange coordinate when REMD running. Do I just analyze remd2.xtc of
> >> replica 2(T=298K) if I want to analyze a trajectory at 298K? Do I need
> to
> >> do something else on the trajectories to get a trajectory at specific
> >> temperature(i.e. 298K)?
> >>
> >> Best regards,
> >> Ouyang
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
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> >> posting!
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> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
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Re: [gmx-users] Poor GPU Performance with GROMACS 5.1.4

[Smith, Micholas D.]

Try just using your equivalent of:

mpirun -n 2 -npernode 2 gmx_mpi mdrun (your run stuff here) -ntomp 4 -gpu_id 00

That may speed it up. 

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


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

Sent: Wednesday, May 24, 2017 3:08 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Poor GPU Performance with GROMACS 5.1.4

Hello,

I'm using GROMACS 5.1.4 on 8 CPUs and 1 GPU for a system of ~8000 atoms in
a dodecahedron box, and I'm having trouble getting good performance out of
the GPU. Specifically it appears that there is significant performance loss
to wait times ("Wait + Comm. F" and "Wait GPU nonlocal"). I have pasted the
relevant parts of the log file below. I suspect that I have set up my
ranks/threads badly, but I am unsure where the issue is. I have tried
changing the local variable OMP_NUM_THREADS from 1 to 2 per the note
generated by GROMACS, but this severely slows down the simulation to the
point where it takes 10 minutes to get a few picoseconds.

I have tried browsing through the mailing lists, but I haven't found a
solution to this particular problem.

Any help is appreciated,
Dan






GROMACS:  gmx mdrun, VERSION 5.1.4
Executable:   /home/dkozuch/programs/gromacs_514_gpu/bin/gmx_514_gpu
Data prefix:  /home/dkozuch/programs/gromacs_514_gpu
Command line:
  gmx_514_gpu mdrun -deffnm 1ucs_npt -ntomp 1

GROMACS version:VERSION 5.1.4
Precision:  single
Memory model:   64 bit
MPI library:MPI
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
GPU support:enabled
OpenCL support: disabled
invsqrt routine:gmx_software_invsqrt(x)
SIMD instructions:  AVX2_256
FFT library:fftw-3.3.4-sse2-avx
RDTSCP usage:   enabled
C++11 compilation:  disabled
TNG support:enabled
Tracing support:disabled
Built on:   Mon May 22 18:29:21 EDT 2017
Built by:   dkoz...@tigergpu.princeton.edu [CMAKE]
Build OS/arch:  Linux 3.10.0-514.16.1.el7.x86_64 x86_64
Build CPU vendor:   GenuineIntel
Build CPU brand:Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
Build CPU family:   6   Model: 79   Stepping: 1
Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt
lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd
rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
C compiler: /usr/bin/cc GNU 4.8.5
C compiler flags:-march=core-avx2-Wextra
-Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall
-Wno-unused -Wunused-value -Wunused-parameter  -O3 -DNDEBUG
-funroll-all-loops -fexcess-precision=fast  -Wno-array-bounds
C++ compiler:   /usr/bin/c++ GNU 4.8.5
C++ compiler flags:  -march=core-avx2-Wextra
-Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function
 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  -Wno-array-bounds
Boost version:  1.53.0 (external)
CUDA compiler:  /usr/local/cuda-8.0/bin/nvcc nvcc: NVIDIA (R) Cuda
compiler driver;Copyright (c) 2005-2016 NVIDIA Corporation;Built on
Sun_Sep__4_22:14:01_CDT_2016;Cuda compilation tools, release 8.0, V8.0.44
CUDA compiler flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=comp
ute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-
gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_
50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-
gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_
61,code=sm_61;-gencode;arch=compute_60,code=compute_60;-
gencode;arch=compute_61,code=compute_61;-use_fast_math;;
;-march=core-avx2;-Wextra;-Wno-missing-field-initializers;-
Wpointer-arith;-Wall;-Wno-unused-function;-O3;-DNDEBUG;-
funroll-all-loops;-fexcess-precision=fast;-Wno-array-bounds;
CUDA driver:8.0
CUDA runtime:   8.0


Number of logical cores detected (28) does not match the number reported by
OpenMP (1).
Consider setting the launch configuration manually!

Running on 1 node with total 28 logical cores, 1 compatible GPU
Hardware detected on host tiger-i23g10 (the node of MPI rank 0):
  CPU info:
Vendor: GenuineIntel
Brand:  Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
Family:  6  model: 79  stepping:  1
CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt
lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd
rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
SIMD instructions most likely to fit this hardware: AVX2_256
SIMD instructions selected at GROMACS compile time: AVX2_256
  GPU info:
Number of GPUs detected: 1
#0: NVIDIA Tesla P100-PCIE-16GB, compute cap.: 6.0, ECC: yes, stat:
compatible


For o

Re: [gmx-users] Calculating number of molecules to add in simulation box

[Smith, Micholas D.]

0.67 moles/L * 2440.78 nm^3  = 0.67 moles* 2.4408*x10^-21

0.67*6.022141x10^23 molecules * 2.4408*x10^-21 = 0.67 * 1470 molecules

0.67 * 1470 = 984.9 molecules

You would need ~985 molecules in your box to fulfill your molar concentration.


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Pandya, Akash 

Sent: Thursday, May 18, 2017 8:52 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Calculating number of molecules to add in simulation box

Hi all,

I'm trying to calculate the number of Glycine molecules to add into the 
simulation box. The molar concentration of glycine I'm using is 0.67M. My 
simulation box size is 2nm and the box volume is 2440.78nm^3. How would I 
calculate the number of glycine molecules to fulfil this molar concentration?


Best wishes,

Akash

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Re: [gmx-users] MD at different pH

[Smith, Micholas D.]

Thank you for pointing out António Baptista and Miguel Machuqueiro's groups. I 
hadn't intended to exclude them

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


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

Sent: Thursday, May 04, 2017 9:12 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] MD at different pH

P.S.: By "fully integrated" I meant that their modifications to Gromacs
were never submitted/added to the main public distribution. Their method is
obviously integrated with Gromacs, otherwise it wouldn't run, so it was a
poor choice of words. Plus it requires third-party software for the
Poisson-Boltzmann/Monte Carlo steps.

On Thu, May 4, 2017 at 3:02 PM, João Henriques  wrote:

> Technically, Helmut Grubmüller's group is not the only performing
> constant-pH MD using Gromacs. António Baptista and Miguel Machuqueiro's
> groups in Portugal have done it with explicit solvent since 2002:
>
> http://aip.scitation.org/doi/abs/10.1063/1.1497164
>
> It is not fully integrated in Gromacs, making it difficult to use for
> someone outside the group, but I thought their names had to be mentioned
> given their extensive contribution to this field since its early days.
>
> /J
>
> On Thu, May 4, 2017 at 2:44 PM, Smith, Micholas D. 
> wrote:
>
>> Although this is the gromacs mailing list, it should be mentioned that
>> "constant" pH simulations do exist...you just have to use a different MD
>> simulation packages (such as Amber or CHARMM) to allow protonation states
>> to change on the fly. See the following:
>>
>> http://pubs.acs.org/doi/abs/10.1021/ct2006314
>>
>> https://link.springer.com/article/10.1007/s00894-012-1680-0
>>
>> https://www.nature.com/articles/srep22523
>>
>> https://www.ncbi.nlm.nih.gov/pubmed/16878971?dopt=Abstract&holding=npg
>>
>> https://www.ncbi.nlm.nih.gov/pubmed/21687785?dopt=Abstract&holding=npg
>> (Ok So I was wrong, you can do it in gromacs, but you have to hack at the
>> lamba-dynamics stuff)
>>
>>
>> https://www.ncbi.nlm.nih.gov/pubmed/22694266?dopt=Abstract&holding=npg
>>
>>
>> In general; however, Justin is right. It is much easier, and efficient to
>> just assign the protonation states at the onset and keep them fixed so that
>> you have a "fixed-pH"; however, if the sites are known to transistion from
>> protontated to deprotonated frequently in your solvent, than a  CpHMD
>> simulation can be used.
>>
>> Good Luck!
>>
>> ===
>> Micholas Dean Smith, PhD.
>> Post-doctoral Research Associate
>> University of Tennessee/Oak Ridge National Laboratory
>> Center for Molecular Biophysics
>>
>> 
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin
>> Lemkul 
>> Sent: Thursday, May 04, 2017 8:29 AM
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] MD at different pH
>>
>> On 5/4/17 1:02 AM, Anu George wrote:
>> > Through the simulation, I am trying to find out if the binding free
>> energy of the drug-protein complex is strong enough for the drug to be a
>> good inhibitor of the protein.
>> > so, does the pH of the simulation matter as in reality the active
>> monomer exists in acidic pH conditions?
>>
>> You have to model whatever the realistic conditions are, whether that's
>> in vivo
>> or in vitro.  This is part of good experimental design.  If your target
>> exists
>> in a mildly acidic microenvironment, that's what you should model.
>> Binding
>> thermodynamics do depend on protonation states (in some cases, quite
>> strongly)
>> so if you model one state and try to relate it to data that exist in
>> another,
>> you're comparing apples to oranges and you've wasted a lot of time and
>> resources.
>>
>> Also, dispel with the notion of "pH of the simulation" because such a
>> thing does
>> not exist.  You'll be modeling a constant protonation state and there are
>> no
>> dissociable protons floating around.  You're going to do a simulation
>> using the
>> dominant protonation state of a given set of molecules at a corresponding
>> experimental pH.
>>
>> -Justin
>>
>> > Thanks
>> > Anu George
>> >
>> > 

Re: [gmx-users] MD at different pH

[Smith, Micholas D.]

Although this is the gromacs mailing list, it should be mentioned that 
"constant" pH simulations do exist...you just have to use a different MD 
simulation packages (such as Amber or CHARMM) to allow protonation states to 
change on the fly. See the following:

http://pubs.acs.org/doi/abs/10.1021/ct2006314

https://link.springer.com/article/10.1007/s00894-012-1680-0

https://www.nature.com/articles/srep22523

https://www.ncbi.nlm.nih.gov/pubmed/16878971?dopt=Abstract&holding=npg

https://www.ncbi.nlm.nih.gov/pubmed/21687785?dopt=Abstract&holding=npg 
(Ok So I was wrong, you can do it in gromacs, but you have to hack at the 
lamba-dynamics stuff)


https://www.ncbi.nlm.nih.gov/pubmed/22694266?dopt=Abstract&holding=npg


In general; however, Justin is right. It is much easier, and efficient to just 
assign the protonation states at the onset and keep them fixed so that you have 
a "fixed-pH"; however, if the sites are known to transistion from protontated 
to deprotonated frequently in your solvent, than a  CpHMD simulation can be 
used.

Good Luck!

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


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

Sent: Thursday, May 04, 2017 8:29 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] MD at different pH

On 5/4/17 1:02 AM, Anu George wrote:
> Through the simulation, I am trying to find out if the binding free energy of 
> the drug-protein complex is strong enough for the drug to be a good inhibitor 
> of the protein.
> so, does the pH of the simulation matter as in reality the active monomer 
> exists in acidic pH conditions?

You have to model whatever the realistic conditions are, whether that's in vivo
or in vitro.  This is part of good experimental design.  If your target exists
in a mildly acidic microenvironment, that's what you should model.  Binding
thermodynamics do depend on protonation states (in some cases, quite strongly)
so if you model one state and try to relate it to data that exist in another,
you're comparing apples to oranges and you've wasted a lot of time and 
resources.

Also, dispel with the notion of "pH of the simulation" because such a thing does
not exist.  You'll be modeling a constant protonation state and there are no
dissociable protons floating around.  You're going to do a simulation using the
dominant protonation state of a given set of molecules at a corresponding
experimental pH.

-Justin

> Thanks
> Anu George
>
> - Original Message -
> From: "Justin Lemkul" 
> To: gmx-us...@gromacs.org
> Sent: Wednesday, May 3, 2017 8:15:33 PM
> Subject: Re: [gmx-users] MD at different pH
>
>
>
> On 5/3/17 10:04 AM, Anu George wrote:
>> Thanks Justin for the information.
>> But I had a further question regarding the simulation-if the active monomer 
>> exists only in the acidic pH, then will carrying out a simulation of the 
>> monomer with a drug  at neutral pH help?
>
> That depends on what your scientific goals/questions are and what you are
> actually trying to model.
>
> -Justin
>
>> regards,
>> Anu George
>>
>> - Original Message -
>> From: "Justin Lemkul" 
>> To: gmx-us...@gromacs.org
>> Sent: Wednesday, May 3, 2017 5:37:33 PM
>> Subject: Re: [gmx-users] MD at different pH
>>
>>
>>
>> On 5/2/17 11:31 PM, Anu George wrote:
>>> Dear Gromacs users,
>>> I am working on a tetramer(human beta-2 tryptase) protein which exist as an 
>>> active monomer at an acidic pH of about 6..If I have to do a molecular 
>>> dynamic simulation of the monomer with a small molecule,  should the 
>>> simulation be carried out  at this pH ? what are the steps I should follow?
>>
>> Calculate the pKa values for titratable residues and select their dominant
>> protonation states at that pH when running pdb2gmx.
>>
>> -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] Replica exchange simulations more than number of processor

[Smith, Micholas D.]

You can try over assignment of cores, but that will be horribly slow. Or use 
more than 1 node (if you can get it).

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


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Мижээ 
Батсайхан 
Sent: Friday, April 14, 2017 4:16 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Replica exchange simulations more than number of   
processor

Dear gmx users,

I would like to simulate folding of a peptides. I have only 12 core
processor, and I assumed the number of replica using temperature generator
as following link
http://folding.bmc.uu.se/remd/.

The number of replica is about 60. How can I solve this problem? Can you
advice me, please?

Best regards,
Mijee
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Re: [gmx-users] Protein-surface interaction during flow

[Smith, Micholas D.]

Christopher makes a good point.

Thermal motion will likely take over, but if you use a long enough initial 
push, you should also induce a local velocity field in the solvent around the 
protein which will allow some drifting. Alternatively you could give a kick to 
both the solvent and protein.



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


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Christopher 
Neale 
Sent: Tuesday, January 31, 2017 11:15 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] Protein-surface interaction during flow

flow the solvent and let the protein respond freely to that?

My guess is that the initial velocities will be lost fairly quickly to thermal 
noise if you try the suggestion of giving it a kick and then simply letting it 
go.


— original message —

I am trying to simulate a flow of protein over and along a surface
structure. To do this, I have a box which is very long in its x
direction, relatively small in its y direction and its z dimension is
limited by an artificially created surface. These proteins will move
in the positive x direction, starting at around x=0, and move towards
the surface structure. At this point the protein will either pass
along the structure, or adhere to it through LJ/Coulomb interactions.
There will also be interactions between the (many) proteins flowing.
Essentially, I’m trying to create a flow.

However, I’m unsure on how to do this. If I set the proteins as a
acc-grps, they will continue to accelerate even after they have
adhered to the surface, essentially pulling them off. Is there a way
to set acc-grps for a specific amount of time or distance? After which
their velocities will guide them towards the surface structure? Or can
I give these proteins a starting velocity after which they just flow?
Any ideas?

Mark
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Re: [gmx-users] Protein-surface interaction during flow

[Smith, Micholas D.]

Hi Mark,

The gro file will not store the velocities, but a *.trr file will (for all 
frames, provided you set velocities to be saved in your mdp file). The cpt 
files will only have the velocities for the last step that was check-pointed. 
Your command is correct though otherwise. If you want to get velocities from a 
frame other than the last one you will need to record that frame to a file (gmx 
trjconv can be used for this) and read it into grompp with the -t flag.

But yeah, the command gmx grompp -f new.mdp -c last_frame.gro -o new.tpr -t 
old.cpt will give you a "new" simulation with the velocities your "new" initial 
velocities.

Happy Simulating.

-Micholas

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


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Kamps, M. 

Sent: Tuesday, January 31, 2017 4:27 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Protein-surface interaction during flow

Dear Micholas,

Thanks for your reply and suggestions!

Your idea at point 2, how can I do this? The forces and velocities are
stored in the .edr files, while the final velocities and positions are
also stored in the output .gro file right? This means I should run a
simulation just long enough that the proteins reach a desired point,
after which I can use the final .gro  or the .edr files?
I then need to continue (extend) my simulation, while creating a new
.tpr file via the new .mdp file, effectively using this command:

gmx grompp -f new.mdp -c old.tpr -o new.tpr -t old.cpt
mdrun -s new.tpr
(http://www.gromacs.org/Documentation/How-tos/Extending_Simulations)

Will this continue my simulation with the 'previous' velocities? Since
none of these files will input any .edr or .gro files?

Mark
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Re: [gmx-users] Protein-surface interaction during flow

[Smith, Micholas D.]

Hi Mark,

There are two ways I see you could do this:

1) Perform multiple simulations at different accelerations (i.e. different 
applied forces)
2) Pick the acceleration you want, start a simulation, calculate the velocity 
of your protein every few steps, and once you have it, then stop, and use the 
velocities and positions at the end of the initial "push" segment as new 
initial conditions for a new run without the accel. group.

The first choice is something akin to dragging the protein across the surface 
(in which case you could likely use the pull code with you setting a maximum 
pull-force) and you can measure/quantify the adherence strength directly. The 
second choice using a prolonged impulse. 

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


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Kamps, M. 

Sent: Monday, January 30, 2017 9:17 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Protein-surface interaction during flow

Dear GMX users,

I am trying to simulate a flow of protein over and along a surface
structure. To do this, I have a box which is very long in its x
direction, relatively small in its y direction and its z dimension is
limited by an artificially created surface. These proteins will move
in the positive x direction, starting at around x=0, and move towards
the surface structure. At this point the protein will either pass
along the structure, or adhere to it through LJ/Coulomb interactions.
There will also be interactions between the (many) proteins flowing.
Essentially, I’m trying to create a flow.

However, I’m unsure on how to do this. If I set the proteins as a
acc-grps, they will continue to accelerate even after they have
adhered to the surface, essentially pulling them off. Is there a way
to set acc-grps for a specific amount of time or distance? After which
their velocities will guide them towards the surface structure? Or can
I give these proteins a starting velocity after which they just flow?
Any ideas?

Mark
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Re: [gmx-users] Force Fields Selection

[Smith, Micholas D.]

Hi Azeem,

At this point in time, it is pretty much a trial and error kind method. You may 
have some luck with a literature search to see if anyone has performed a 
benchmark on your system, or a similar one, and that may guide you a bit. 

-Micholas

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


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

Sent: Thursday, December 22, 2016 8:51 AM
To: gromacs.org_gmx-users
Subject: [gmx-users] Force Fields Selection

Hi all,

What are criteria for choosing the force fields?

Is choosing a force field for a particular protein molecule, a trial
and error method based?

Thanks in advance

Azeem
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Re: [gmx-users] How to decrease the time gap between frames of an already made simulation

[Smith, Micholas D.]

Marko,

2fs timestep is your integration timestep, not necessarily your frame saving 
rate. This is defined by your integration step multiplied by the nstxout term 
in your simulation mdp file. In order to save every integration step you would 
need to have dt = 0.001 (picseconds) and nstxout = 1000 .

-Micholas

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


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

Sent: Tuesday, October 18, 2016 3:56 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] How to decrease the time gap between frames of an 
already made simulation

Micholas, I think it should be 2fs the timestep if you are reffering to that? I 
have the .trr file its 95gb, I should be able to make a xtc with 1ps step right?

Marko
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Re: [gmx-users] How to decrease the time gap between frames of an already made simulation

[Smith, Micholas D.]

Hi Marko,

Unless you saved your trajectory at a 1picosecond/frame saving rate, you won't 
be able to reduce the "gap" from 20ps to 1ps.

-Micholas

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


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

Sent: Tuesday, October 18, 2016 9:33 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] How to decrease the time gap between frames of an already 
made simulation

Hello,

could you please advise regarding the correct command for  decreaseing the time 
gap between frames of an already made simulation, from 20ps to 1ps.

I tried these commands but they didn't work:

gmx trjconv -s md.tpr -f md.trr -o md1pico.xtc -tu ps -skip 500
gmx trjconv -f md.trr -o md1pico.xtc -timestep 1

And various similair commands to those...

But seems it isn't the correct way to go about it...
Can you guys help?

Cheers,
Marko


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Re: [gmx-users] changing the location of a molecule in a box

[Smith, Micholas D.]

HI Anurag Dobhal,

If it is already split into two regions when you simulate without the protein, 
load the system in something like VMD, define a sphere between the two solvents 
that can hold your protein, record the residue ids for the water/chloroform in 
that sphere region, delete these from your .gro file, and place your protein in 
that position using a text editor. Then use editconf to make sure all of the 
atom numberings are resolved. Then run a short NPT simulation with the protein 
fixed in place to let the solvent molecules relax around it (since you may have 
created voids during the placement/removal of solvent molecules). 

There may be more direct ways, but that's how others I've worked with have made 
void regions to place proteins in specific locations for initial simulation 
starting configurations.

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


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

Sent: Friday, September 09, 2016 6:55 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se; gmx-us...@gromacs.org
Subject: Re: [gmx-users] changing the location of a molecule in a box

Dear Gromacs users,

I am working on a biphasic system where I have taken chloroform and water
as two solvents. I want to locate my protien at the center of the box such
that half of the protien is solvated in water and other half in the
chloroform.

How can I acheive the desired placement of the protien.

Thank You




*Anurag Dobhal*
*Graduate Student (Bioprocess Technology)*


On Fri, Sep 9, 2016 at 4:24 PM, Anurag Dobhal <
anurag.dob...@nano-medicine.co.in> wrote:

> Dear Gromacs users,
>
> I am working on a biphasic system where I have taken chloroform and water
> as two solvents. I want to locate my protien at the center of the box such
> that half of the protien is solvated in water and other half in the water.
>
> How can I acheive the desired placement of the protien.
>
> Thank You
>
>
>
> *Anurag Dobhal*
> *Graduate Student (Bioprocess Technology)*
>
>
>

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Re: [gmx-users] high pressure and temperatures: force field parameters

[Smith, Micholas D.]

My apologies, I had intended for my response to be addressed to Mohsen, not 
Sotririos. 

-Micholas



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Smith, 
Micholas D. 
Sent: Thursday, September 08, 2016 3:44 PM
To: Discussion list for GROMACS users
Subject: [UNTRUSTED] Re: [gmx-users] high pressure and temperatures: force  
field   parameters

Hi Sotririos,

I am not sure if anyone has ever done a detailed study of the extremes for each 
force-field; however, I can say from personal experience that what would be 
considered high (relative to physiological) temperature (~450K) simulations 
seem to perform relatively well for systems of with organic liquids in them. 
For instance binary systems that exhibit closed miscibility gaps can (such as 
Tetrahydrofuran-Water systems) experimentally, can have these same gaps/phase 
separation behaviors observed in MD simulations (even with TIP3P) with common 
force-fields (given a large enough simulation box).

I am inclined to believe that so long as you near not too close to a phase 
transition for your system, the standard force-fields will be at least 
reasonable approximations; that being said, this is more of an opinion gleened 
from experience simulating biopolymers at moderately high temps, than from any 
rigorous test. To be honest, it would be an interesting paper if someone did 
test the temperature and pressure bounds of force-field validity for protein 
behaviour.

When in doubt, you can always try to hunt down an experimentalist who may be 
able to inform you of some type of macroscopic/mesoscopic behavior that only 
occurs near the temperature/pressure you are interested for a similar system 
and see if you can get simulation results that are consistent with this before 
running your protein of interest under those cases.

Interesting question though...I'll have to take a longer literature search to 
see what that brings up.

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


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Mohsen 
Ramezanpour 
Sent: Thursday, September 08, 2016 3:27 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] high pressure and temperatures: force field
parameters

Hi Sotirios,

I totally agree with what you said. However, I am not interested in
breaking bonds or forming bonds (e.g. in plasma case)

To clarify the question, here is an example:

How if you want to check the effect of high temperature on protein
structure (folding and unfolding problem)? Or if you want to do a simulated
annealing! How much are you allowed to raise the temperature?!
(for now, lets assume unfolding and folding can happen in allowed time
scales. Lets focus on ff validity for a moment)

Is the ff developed for proteins are valid in high temperatures? We know
they are working well in physiological range. However, there are some cases
of interest where high T happens.

Hope it is clear now. The same for pressure.

Cheers
Mohsen

On Thu, Sep 8, 2016 at 10:42 AM, Sotirios Dionysios I. Papadatos <
si.papada...@edu.cut.ac.cy> wrote:

> I am not aware on your question per se, but just to give you food for
> thought. Force fields are not based on real values of let's say force
> constants. You can't produce for example 'plasma' at least with the default
> ff, if you overheat. So it not a matter of a ff not being accurate for high
> values of T or P, rather than a ff is made to reproduce - simulate the
> physical properties of a system as close as possible to real life
> conditions. Now, if you are interested in simulating on such high values,
> you should search if there is a literature on how to simulate in such
> environments specifically.
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mohsen
> Ramezanpour 
> Sent: Thursday, September 8, 2016 2:47:07 AM
> To: Discussion list for GROMACS users
> Subject: [gmx-users] high pressure and temperatures: force field parameters
>
> Dear gromacs users,
>
> Force field parameters are not usually parametrized for high pressures and
> temperatures.
>
> say for P=500 bar! or for T=500 K
>
> Although we can do simulations, but we cannot trust on the results.
>
> Is there any maximum (or range ) defined somewhere in the literature (which
> I am not aware of) we should not go further in simulations?
> I searched but I did not get any good answer for it.
>
> The best way would be to check the force field validity by comparing the
> simulations (with that FF) in desired high T and P with some available
> experime

Re: [gmx-users] high pressure and temperatures: force field parameters

[Smith, Micholas D.]

Hi Sotririos,

I am not sure if anyone has ever done a detailed study of the extremes for each 
force-field; however, I can say from personal experience that what would be 
considered high (relative to physiological) temperature (~450K) simulations 
seem to perform relatively well for systems of with organic liquids in them. 
For instance binary systems that exhibit closed miscibility gaps can (such as 
Tetrahydrofuran-Water systems) experimentally, can have these same gaps/phase 
separation behaviors observed in MD simulations (even with TIP3P) with common 
force-fields (given a large enough simulation box). 

I am inclined to believe that so long as you near not too close to a phase 
transition for your system, the standard force-fields will be at least 
reasonable approximations; that being said, this is more of an opinion gleened 
from experience simulating biopolymers at moderately high temps, than from any 
rigorous test. To be honest, it would be an interesting paper if someone did 
test the temperature and pressure bounds of force-field validity for protein 
behaviour.

When in doubt, you can always try to hunt down an experimentalist who may be 
able to inform you of some type of macroscopic/mesoscopic behavior that only 
occurs near the temperature/pressure you are interested for a similar system 
and see if you can get simulation results that are consistent with this before 
running your protein of interest under those cases.

Interesting question though...I'll have to take a longer literature search to 
see what that brings up.

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


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Mohsen 
Ramezanpour 
Sent: Thursday, September 08, 2016 3:27 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] high pressure and temperatures: force field
parameters

Hi Sotirios,

I totally agree with what you said. However, I am not interested in
breaking bonds or forming bonds (e.g. in plasma case)

To clarify the question, here is an example:

How if you want to check the effect of high temperature on protein
structure (folding and unfolding problem)? Or if you want to do a simulated
annealing! How much are you allowed to raise the temperature?!
(for now, lets assume unfolding and folding can happen in allowed time
scales. Lets focus on ff validity for a moment)

Is the ff developed for proteins are valid in high temperatures? We know
they are working well in physiological range. However, there are some cases
of interest where high T happens.

Hope it is clear now. The same for pressure.

Cheers
Mohsen

On Thu, Sep 8, 2016 at 10:42 AM, Sotirios Dionysios I. Papadatos <
si.papada...@edu.cut.ac.cy> wrote:

> I am not aware on your question per se, but just to give you food for
> thought. Force fields are not based on real values of let's say force
> constants. You can't produce for example 'plasma' at least with the default
> ff, if you overheat. So it not a matter of a ff not being accurate for high
> values of T or P, rather than a ff is made to reproduce - simulate the
> physical properties of a system as close as possible to real life
> conditions. Now, if you are interested in simulating on such high values,
> you should search if there is a literature on how to simulate in such
> environments specifically.
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mohsen
> Ramezanpour 
> Sent: Thursday, September 8, 2016 2:47:07 AM
> To: Discussion list for GROMACS users
> Subject: [gmx-users] high pressure and temperatures: force field parameters
>
> Dear gromacs users,
>
> Force field parameters are not usually parametrized for high pressures and
> temperatures.
>
> say for P=500 bar! or for T=500 K
>
> Although we can do simulations, but we cannot trust on the results.
>
> Is there any maximum (or range ) defined somewhere in the literature (which
> I am not aware of) we should not go further in simulations?
> I searched but I did not get any good answer for it.
>
> The best way would be to check the force field validity by comparing the
> simulations (with that FF) in desired high T and P with some available
> experimental data, even if these systems are not the same with what you are
> interested in. If they are valid, so, we might do predictions for our
> system of interest in those T and P range. Well, this also can be argued,
> because, the force field might not work properly for our specific molecules
> in question.
>
> Please let me know your opinion
>
> Thanks in advance
>
> Cheers
> Mohsen
>
>
> --
> *Rewards work better than punishment ...*
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists

Re: [gmx-users] Ethanol Co-ordinate file

[Smith, Micholas D.]

Here is an ethanol *.gro file for a single molecule:

Ethanol, t= 0.00
9
  240ETOHC11   0.229   0.252   0.170
  240ETOHO12   0.092   0.290   0.184
  240ETOH   HO13   0.102   0.380   0.218
  240ETOH   H114   0.297   0.339   0.155
  240ETOH   H125   0.230   0.180   0.085
  240ETOHC26   0.269   0.172   0.293
  240ETOH   H217   0.198   0.089   0.311
  240ETOH   H228   0.285   0.241   0.379
  240ETOH   H239   0.369   0.126   0.274
   0.46000   0.45000   0.45000

You can use gmx insert-molecule or gmx solvate to generate a small box of these 
and then run a short md to relax it to generate a solvent box for solvating 
molecules.

-Micholas

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


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

Sent: Wednesday, August 03, 2016 11:45 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] Ethanol Co-ordinate file

Dear List,

Can someone help me locating Ethanol solvent co-ordinate file? I looked up
on Virtualchemistry.org and around, no luck yet.

many thanks,
Suru
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Re: [gmx-users] GPU Not Being Utilized during mdrun

[Smith, Micholas D.]

Quick question, what is your integration stepsize? 

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


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Vito 
Spadavecchio 
Sent: Thursday, July 14, 2016 2:28 PM
To: gmx-us...@gromacs.org
Subject: [gmx-users] GPU Not Being Utilized during mdrun

Hello

After building GROMACS with GPU support and running some simple MD, I am
only getting ~20ns/day (which is what I would expect to get out of my
i7-6700k cpu only. My machine currently has a 1080 GTX in it, which should
even on moderately large systems, be getting ~100ns/day)

 I've tried launching a mdrun with with the following command:

  gmx mdrun -deffnm md_0_1 -gpu_id 0 -nb gpu



With the following in my md.mdp file:

; Neighborsearching

cutoff-scheme   = Verlet



The top of the log file for the mdrun notes:

Running on 1 node with total 4 cores, 8 logical cores, 1 compatible GPU
> Hardware detected:
>   CPU info:
> Vendor: GenuineIntel
> Brand:  Intel(R) Core(TM) i7-6700K CPU @ 4.00GHz
> SIMD instructions most likely to fit this hardware: AVX2_256
> SIMD instructions selected at GROMACS compile time: AVX2_256
>   GPU info:
> Number of GPUs detected: 1
> #0: NVIDIA GeForce GTX 1080, compute cap.: 6.1, ECC:  no, stat:
> compatible
> Reading file md_0_1.tpr, VERSION 5.1.2 (single precision)
> Changing nstlist from 10 to 40, rlist from 1 to 1.099
> Using 1 MPI thread
> Using 8 OpenMP threads
> 1 GPU user-selected for this run.
> Mapping of GPU ID to the 1 PP rank in this node: 0
>

The output of *nvidia-smi *on my machine is:

hu Jul 14 11:25:04 2016
>
> +-+
> | NVIDIA-SMI 367.27 Driver Version: 367.27
>|
>
> |---+--+--+
> | GPU  NamePersistence-M| Bus-IdDisp.A | Volatile Uncorr.
> ECC |
> | Fan  Temp  Perf  Pwr:Usage/Cap| Memory-Usage | GPU-Util  Compute
> M. |
>
> |===+==+==|
> |   0  GeForce GTX 1080Off  | :01:00.0  On |
>  N/A |
> | 30%   41CP8 7W / 180W |730MiB /  8113MiB |  3%
>  Default |
>
> +---+--+--+
>
>
>
> +-+
> | Processes:   GPU
> Memory |
> |  GPU   PID  Type  Process name   Usage
>|
>
> |=|
> |0  1035G   /usr/lib/xorg/Xorg
> 424MiB |
> |0  2132G   compiz
> 103MiB |
> |0  5296G   ...s-passed-by-fd --v8-snapshot-passed-by-fd
>  59MiB |
> |0 14079G   ...s-passed-by-fd --v8-snapshot-passed-by-fd
>  31MiB |
> |0 14234G   ...ing 108MiB |
>
> +-+


and output of *nvcc --version* is:

nvcc: NVIDIA (R) Cuda compiler driver
> Copyright (c) 2005-2015 NVIDIA Corporation
> Built on Tue_Aug_11_14:27:32_CDT_2015
> Cuda compilation tools, release 7.5, V7.5.17


Does anyone have any ideas what the problem might be?

Thanks!
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Re: [gmx-users] Running all the processors in HPC

[Smith, Micholas D.]

Was gromacs built with mpi? or OpenMP?

If mpi you need to run mdrun through the mpirun executable (search the internet 
for how to run mpi-jobs)

-Micholas

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


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Santhosh Kumar 
Nagarajan 
Sent: Monday, June 27, 2016 12:15 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] Running all the processors in HPC

Hi,
I am trying to run a 'Protein-Ligand' complex in our university's HPC.
There are 32 processors in the cluster. But, while running mdrun it runs in
only one CPU. How to cluster all the processors in the HPC? I have searched
internet with no luck.

The version is 4.6. I also tried running logged in as root.

Best regards,

Santhosh.
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Re: [gmx-users] Cross correlation map of residues

[Smith, Micholas D.]

If you want coloured images you can always use the xpm2ps tool. It will map the 
.xpm generated into a postscript file with the expected coloring.


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


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

Sent: Friday, June 03, 2016 6:00 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Cross correlation map of residues

Hi,

@Tsjerk: I just installed GROMACS-3.3 and implemented g_correlation tool.
Unfortunately this tool generates the colorless correlation matrix (.xpm)
on atoms. Whereas I would like to have the colourful correlation matrix on
residues (not based on atoms). I think there is no way to get the colourful
correlation matrix on residues by g_correlation tool?

@Florent: The R package bio3d is complex :( It would be good if you share
on the user list such a code to generate the correlation matrix?

Cheers,

On 3 June 2016 at 11:27, Florent Hédin  wrote:

> Hi,
>
> In case you really want to produce something similar, I have a solution (
> 2 in fact ;-) )
>
> This plot is easy to produce with the R package bio3d, unfortunately it
> only supports charmm/namd dcd and amber ncdf trajectory types.
>
> The first option : would be to use vmd for converting a gmx trajectory to,
> for example, dcd. Then follow the bio3d tutorials of R.
>
> The second option is : R is really modular, you can write a piece of C
> code reading the gromacs trajectory and returning it (frame by frame) to R.
> This code is compiled as a shared library, and in R you would just easily
> load it. I already have some code doing that, if interested I can share it.
> On long term I plan to put this piece of code directly into a R package.
>
> Regards,
>
> Florent Hédin
>
>
> On 03/06/16 08:02, Tsjerk Wassenaar wrote:
>
>> Hi Qasim,
>>
>> The plot you refer to is the result of NMA on C-alpha only. So g_covar
>> -xpma using only C-alpha atoms should come close. You might also want to
>> try the g_correlation tool mentioned earlier on the list, but again with a
>> selection of only C-alpha atoms.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Fri, Jun 3, 2016 at 1:50 AM, Qasim Pars  wrote:
>>
>> Dear gmx users,
>>>
>>> I need to get the cross correlation map of all residues belonging to a
>>> protein (like this figure
>>>
>>> http://thegrantlab.org/bio3d/vignettes/Bio3D_nma/figures/ex1C-dccmplot.png
>>> ).
>>> Is there any tool to get such a plot with GROMACS?
>>>
>>> By the way, gmx covar -xpma gives the cross correlation for each atom
>>> pair
>>> but it is not what I want.
>>>
>>> Any suggestions will be appreciated.
>>>
>>> --
>>> Qasim Pars
>>> --
>>> 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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>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
>>
>>
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>



--
Qasim Pars
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Re: [gmx-users] Deprotonated Asp and Glu

[Smith, Micholas D.]

Best thing to do would be to check the *.gro and *.top files and see if it 
really is deprotonated.

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


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

Sent: Tuesday, May 24, 2016 8:33 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Deprotonated Asp and Glu

The charge on Asp amd Glu seems 0 and hydrogens are present in time frames and 
cluster.pdb. But I deprotonated during pd2gmx.

Sent from my iPhone

> On 24-May-2016, at 6:00 pm, sun  wrote:
>
> Hello
> I have simulated a protein ligand complex and analyzed the trajectory. After 
> visualization of time frames and clusters.pdb; It occurs to me that the Asp 
> and Glu are nit deprotonated although during pdb2gmx I used -inter command 
> and deprotonated both residue according to pH 7. Can anyone tell me if this 
> possible during visualization? or what might the problem be? My protein is 
> Amyloid beta peptide (1-42) and ligand is a small organic molecule (35 
> atoms), Gromacs 5.0 and ff Gromos96 43A1.
> With Regards
> Suniba
>
> Sent from my iPhone
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Re: [gmx-users] Choosing water molecules and box type and dimensions

[Smith, Micholas D.]

@Justin,

As I recall it was the standard TIP3P, so that it could be compared across the 
force-fields. The biggest difference found in this work between water models 
was the number of water-protein hydrogen bonds are altered, but peptide-peptide 
contacts and structure, regardless of water model, were largely influenced by 
the force-field choice, not the water choice. Now it should be noted that the 
peptide used was an IDP and has a substantial amount of charged residues for 
being as small as it is, so your mileage may vary. Also, this work did not test 
the newest Charmm forcefield so recent notes about the water model choice for 
that may be different (as you have pointed out).

And I would agree for lipid systems the water model is likely going to matter a 
whole heck of a lot more. But for aggregation-related IDPs (like the one used 
in the study) it seems that the force-field choice is really what causes the 
largest deviations in structural sampling.

-Micholas


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

Sent: Friday, April 29, 2016 11:12 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Choosing water molecules and box type and dimensions

On 4/29/16 10:20 AM, Smith, Micholas D. wrote:
> Just to add, a study (http://pubs.acs.org/doi/full/10.1021/acs.jcim.5b00308 ) 
> comparing the 7 force-fields and 3 common water models (for each force-field, 
> except gromos) and found that at least for sampling protein behavior, TIP3P, 
> TIP4P, and SPC/E can all be interchanged between Charmm27, OPLSAA, and Amber 
> force-fields with only minor deviations from one another; i.e. if you compare 
> water models for a given force-field the differences are fairly small.
>

Was the TIP3P used in the CHARMM simulations the CHARMM-modified TIP3P, or
standard?  It makes a difference.  It's an even more profound difference in the
case of lipids, but it is important for the proteins nonetheless, as we have
recently discovered.

-Justin

> -Micholas
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  on behalf of abhijit 
> Kayal 
> Sent: Friday, April 29, 2016 10:07 AM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Choosing water molecules and box type and dimensions
>
> Justin, as always is absolutely right.  The paper that I have suggested  is
> just compare the different water models with the bulk properties. And the
> bio molecular forcefields are compatible with particular type water
> model. Like charmm force field is compatible with TIP3P water.
>
> On Fri, Apr 29, 2016 at 6:53 AM, Justin Lemkul  wrote:
>
>>
>>
>> On 4/29/16 9:51 AM, zeineb SI CHAIB wrote:
>>
>>> Dear all,
>>>
>>> Thank your for your answers.
>>>
>>> @ Justin,
>>>
>>> Where can I found informations related to the compatibility of one water
>>> type with the force field that I choose for my protein? in other words
>>> "where can I found information about the water type that had been used for
>>> the parametrisation of my Force field"?
>>>
>>>
>> Read the primary literature for the force field you're using.  That's of
>> course the first step, otherwise you wouldn't have chosen a force field
>> yet, right? :)
>>
>> Then look for subsequent citations of that force field in application
>> studies related to water.  There are a few for each force field, but
>> generally the water model is considered part of the force field and it is
>> rare to deviate from this model.  Don't do it unless you have a really,
>> really good reason.
>>
>> -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
>>
>> ==
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
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>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to g

Re: [gmx-users] Choosing water molecules and box type and dimensions

[Smith, Micholas D.]

Just to add, a study (http://pubs.acs.org/doi/full/10.1021/acs.jcim.5b00308 ) 
comparing the 7 force-fields and 3 common water models (for each force-field, 
except gromos) and found that at least for sampling protein behavior, TIP3P, 
TIP4P, and SPC/E can all be interchanged between Charmm27, OPLSAA, and Amber 
force-fields with only minor deviations from one another; i.e. if you compare 
water models for a given force-field the differences are fairly small.

-Micholas


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

Sent: Friday, April 29, 2016 10:07 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Choosing water molecules and box type and dimensions

Justin, as always is absolutely right.  The paper that I have suggested  is
just compare the different water models with the bulk properties. And the
bio molecular forcefields are compatible with particular type water
model. Like charmm force field is compatible with TIP3P water.

On Fri, Apr 29, 2016 at 6:53 AM, Justin Lemkul  wrote:

>
>
> On 4/29/16 9:51 AM, zeineb SI CHAIB wrote:
>
>> Dear all,
>>
>> Thank your for your answers.
>>
>> @ Justin,
>>
>> Where can I found informations related to the compatibility of one water
>> type with the force field that I choose for my protein? in other words
>> "where can I found information about the water type that had been used for
>> the parametrisation of my Force field"?
>>
>>
> Read the primary literature for the force field you're using.  That's of
> course the first step, otherwise you wouldn't have chosen a force field
> yet, right? :)
>
> Then look for subsequent citations of that force field in application
> studies related to water.  There are a few for each force field, but
> generally the water model is considered part of the force field and it is
> rare to deviate from this model.  Don't do it unless you have a really,
> really good reason.
>
> -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
>
> ==
> --
> 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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>



--
Abhijit kayal
Research Scholar
Theoretical Chemistry
IIT Kanpur
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Re: [gmx-users] Constant Density

[Smith, Micholas D.]

Hi Anthony,

One possible way I can think of to get the water to redistribute is to perform 
some temperature annealing of just the solvent, i.e. raise the temperature 
every so many steps to a max ~500K then quickly quench (lower the temperature) 
the solvent back to the physiological regime. Repeat this a few cycles to make 
sure you've redistributed the water as you expect. Just make sure to hold the 
protein fixed with restraints. After it has done a few cycles (maybe 5 or so), 
try running with NVT at the proper temperature for both protein+solvent 
(typical NVT simulation). You should note that the water will not remain 
"uniformly" distributed; though, as it will tend toward its equilibrium values 
so your system should be considered non-equilibrium MD (thought the extent of 
how long it takes to relax to the standard state, may allow you to approximate 
it as quasi-equilibrium)

There may be other ways to do this as well.

-Micholas


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Nash, Anthony 

Sent: Tuesday, April 26, 2016 9:29 AM
To: gmx-us...@gromacs.org
Subject: [gmx-users] Constant Density

Hi all,

At the risk of bending the rules of thermodynamics, I¹m wondering whether
Gromacs can maintain density of a water box (0.750 g/L density of water in
a collagen fibril environment) whilst applying an NPT ensemble?

gmx_d solvate, fills up to 2/3 of my truncated oct cell, with my protein
at the centre. An NVT simulation does not redistribute the water. To do
this I need to perform an NPT run, but even so this rapidly shrinks the
box.

I have considering looking up the necessary pressure value for this
density, however I¹m a bit uncertain whether this maintains any
physiological realism for the protein itself.

I¹ve tried googling with little success.

Any thoughts are appreciated.
Thanks
Anthony

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Re: [gmx-users] MARTINI simulation of protein-protein recognition

[Smith, Micholas D.]

Hi James,

My guess is that running a two (unbound) protein simulation with the MARTINI 
force-field will be the same as if it was all atom. Build two separate protein 
topologies (with Martini force-fields) as *.itp files to include in your *.top 
and go from there. The topology file is what grompp uses to determine bonding, 
so if the topology file doesn't have the two proteins bound, they won't be. If 
I remember correctly, you can see an example (all-atom) topology file to work 
with if you use pdb2gmx for a pdb that contains 2 chains (with the proper flag 
the chains will be split).

-Micholas

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


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of James 
Starlight 
Sent: Monday, April 18, 2016 9:43 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] MARTINI simulation of protein-protein recognition

It seems like smth very complicated :)

I just need to put two different proteins in the system - one in the
membrane (A) and one in the water (B) and simulate it independently 10
times to collect statistics about associations of A and B during those
runs. The problems that I don't know how to put 2 different unbound
proteins in the MARTINI system.

James

2016-04-18 9:55 GMT+02:00 Kroon, P.C. :
> Hi,
>
> I assume you want to study the binding of your water soluble protein to
> your membrane(protein). DAFT was created to do just this. DOI:
> 10.1021/ct5010092
>
> Peter
>
> On Fri, Apr 15, 2016 at 3:37 PM, James Starlight 
> wrote:
>
>> Dear Gromacs users!
>>
>> I am looking for some tutorial for the MARTINI simulation of
>> protein-protein recognition dealing with the big membrane protein
>> simulated within the membrane and its assosiation with the small water
>> soluble protein. The question - is it possible in existing Martini
>> system conisdted of only membrane protein solvated in membrane with
>> water to
>> i) increase box size on Z
>> ii)add some water
>> iii) put another water soluble protein in new space (on the distance
>> of the initial membrane protein complex)
>> iv) edit topology of new system and run new md
>>
>> assuming that i,ii and iv are trivial the problem here is the iii step :-)
>>
>> or alternatively if I would like to run new simulation with those 2
>> proteins (in the unbound form) how I can prepare such complex system
>> consisted of big protein in membrane plus water soluble protein
>> unbound from it?
>>
>> Thanks!
>>
>> Gleb
>> --
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Re: [gmx-users] REMD of IDPs

[Smith, Micholas D.]

Very good point from João. Always remember to check that your box length is big 
enough!

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


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

Sent: Friday, April 08, 2016 8:24 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] REMD of IDPs

One small remark to Micholas' email​:

- Make sure the simulation box is big enough to allow the IDP to fully
stretch without interacting with its periodic image(s). This is non-trivial
if you build your system from a random coil. That's why I start from a
fully stretched conformation instead of a more representative conformation
of the system. Much easier to control and the time it takes to get to a
"meaningful" conformation is minimal.

/J



On Fri, Apr 8, 2016 at 2:10 PM, Smith, Micholas D.  wrote:

> Dear Yanhua,
>
> Converting a sequence into a structure is itself an "open" problem in
> computational biology/biophysics. There are ways to generate potential
> structures if you also happen to have some restraints from NMR or other
> experiments (small-angle scattering or CD-Spectra) noted in the literature,
> but getting to the "native" fold is very challenging. One program that
> tries to address the sequence to structure problem is Rosetta (
> http://robetta.bakerlab.org/ ).
>
> If you have a short IDP fragment (less than 20 residues), one thing you
> can do it use something like Schrodinger's Maestro program (its free from
> their webpage www.schrodinger.com) and use the molecule builder to "grow"
> the chain as a random coil (random phi-psi placement), save the PDB from it
> and then run MD at high temp to relax the structure into a potential
> starting structure. If it is longer, the IDP may have small structural
> segments (the chain is dominated by disorder but may have short-lived,
> meta-stable, secondary structure regions) in which case you can either try
> to build the molecule with a corresponding secondary structure distribution
> (using Maestro) or try using Rosetta and refine with energy minimization.
>
> Good Luck!
>
> ===
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of João
> Henriques 
> Sent: Friday, April 08, 2016 3:51 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] REMD of IDPs
>
> ​Dear Yanhua,
>
> To my knowledge (prior to gromacs 5.X at least), there​ are no gromacs
> tools able to turn a sequence into a PDB. The user must take care of that
> pre-processing on his/her own. I work with IDPs quite a lot, so what I can
> tell you is what I usually do. I take my fasta sequence and use PyMOL to
> construct the PDB. Then I'm able to feed the PDB to pdb2gmx.
>
> *I'm sure there are a million different ways of doing this, given that
> there are so many different protein modelling tools out there.*
>
> Here's one example using Histatin 5.
>
> - On PyMOL's command line type the following (without the quotation marks):
> "for aa in "AKRHHGYKRKFH": cmd._alt(string.lower(aa))"
>
> - This builds a fully stretched Histatin 5 3D model which can be exported
> as PDB.
>
> - Make sure to use "-ignh" on pdb2gmx, as the resulting hydrogen atom names
> are usually incompatible with the force fields I routinely use.
>
> - It's also a good idea to use "-renum" on pdb2gmx as for some reason PyMOL
> exports the PDB with residue numberings starting from no. 2.
>
> Cheers,
> João
>
>
> On Fri, Apr 8, 2016 at 4:14 AM, YanhuaOuyang <15901283...@163.com> wrote:
>
> > Hi, I have a sequence of an intrinsically disordered protein, I have no
> > idea how to start my REMD with gromacs. e.g. how to convert my sequence
> > into a pdb file
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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> >
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> Gromacs Users mailing list
>
> * Pl

Re: [gmx-users] REMD of IDPs

[Smith, Micholas D.]

Dear Yanhua,

Converting a sequence into a structure is itself an "open" problem in 
computational biology/biophysics. There are ways to generate potential 
structures if you also happen to have some restraints from NMR or other 
experiments (small-angle scattering or CD-Spectra) noted in the literature, but 
getting to the "native" fold is very challenging. One program that tries to 
address the sequence to structure problem is Rosetta ( 
http://robetta.bakerlab.org/ ). 

If you have a short IDP fragment (less than 20 residues), one thing you can do 
it use something like Schrodinger's Maestro program (its free from their 
webpage www.schrodinger.com) and use the molecule builder to "grow" the chain 
as a random coil (random phi-psi placement), save the PDB from it and then run 
MD at high temp to relax the structure into a potential starting structure. If 
it is longer, the IDP may have small structural segments (the chain is 
dominated by disorder but may have short-lived, meta-stable, secondary 
structure regions) in which case you can either try to build the molecule with 
a corresponding secondary structure distribution (using Maestro) or try using 
Rosetta and refine with energy minimization.

Good Luck! 

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


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

Sent: Friday, April 08, 2016 3:51 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] REMD of IDPs

​Dear Yanhua,

To my knowledge (prior to gromacs 5.X at least), there​ are no gromacs
tools able to turn a sequence into a PDB. The user must take care of that
pre-processing on his/her own. I work with IDPs quite a lot, so what I can
tell you is what I usually do. I take my fasta sequence and use PyMOL to
construct the PDB. Then I'm able to feed the PDB to pdb2gmx.

*I'm sure there are a million different ways of doing this, given that
there are so many different protein modelling tools out there.*

Here's one example using Histatin 5.

- On PyMOL's command line type the following (without the quotation marks):
"for aa in "AKRHHGYKRKFH": cmd._alt(string.lower(aa))"

- This builds a fully stretched Histatin 5 3D model which can be exported
as PDB.

- Make sure to use "-ignh" on pdb2gmx, as the resulting hydrogen atom names
are usually incompatible with the force fields I routinely use.

- It's also a good idea to use "-renum" on pdb2gmx as for some reason PyMOL
exports the PDB with residue numberings starting from no. 2.

Cheers,
João


On Fri, Apr 8, 2016 at 4:14 AM, YanhuaOuyang <15901283...@163.com> wrote:

> Hi, I have a sequence of an intrinsically disordered protein, I have no
> idea how to start my REMD with gromacs. e.g. how to convert my sequence
> into a pdb file
> --
> Gromacs Users mailing list
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Re: [gmx-users] Error: Lost Particles while sorting

[Smith, Micholas D.]

True, but last time I submitted a software request, the admins told me to wait 
until there was downtime.

-Mick


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

Sent: Thursday, March 31, 2016 5:26 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Error: Lost Particles while sorting

On Thu, Mar 31, 2016 at 9:25 PM, Smith, Micholas D. 
wrote:

> Hi,
>
> Good to know. I'll ask the supercomputing folks to update gromacs from
> 5.0.4 to 5.0.7 at the next scheduled downtime.
>

I don't think the machine needs to be offline just to install a version of
GROMACS. ;)


> -Micholas
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> Abraham 
> Sent: Thursday, March 31, 2016 3:22 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Error: Lost Particles while sorting
>
> Hi,
>
> I was thinking of http://redmine.gromacs.org/issues/1153 but on general
> principles that should not have showed up in 5.0. Nonetheless the early 5.0
> versions had enough GPU-related issues that you still want to follow my
> suggestion and see how you go.
>
> Mark
>
> On Thu, 31 Mar 2016 20:11 Smith, Micholas D.  wrote:
>
> > Thanks, Mark. I didn't see this bug noted in the bug list so I thought I
> > was just going crazy
> >
> > ===
> > Micholas Dean Smith, PhD.
> > Post-doctoral Research Associate
> > University of Tennessee/Oak Ridge National Laboratory
> > Center for Molecular Biophysics
> >
> > 
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> > Abraham 
> > Sent: Thursday, March 31, 2016 2:57 PM
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] Error: Lost Particles while sorting
> >
> > Hi,
> >
> > Starting a new series of calculations on the earliest of a series of
> patch
> > releases means you have chosen to accept all the bugs that have been
> fixed
> > since. ;-) This indeed looks like one of them. Get e.g. 5.0.7 installed.
> >
> > Mark
> >
> > On Thu, 31 Mar 2016 19:40 Smith, Micholas D.  wrote:
> >
> > > Dear other users (and developers)
> > >
> > >
> > > I moved some simulations that were working pretty well on one
> > > supercomputer to another (the previous one did not have gpu nodes) to
> > take
> > > advantage of some gpus, but I am now getting a sporadic error:
> > >
> > >
> > > 
> > >
> > > Program gmx_mpi, VERSION 5.0
> > > Source code file:
> > > /autofs/na4_sw/xk6/gromacs/5.0/cle5.2_gnu4.8.2/source/src/grom
> > > acs/mdlib/nbnxn_search.c, line: 728
> > >
> > > Software inconsistency error:
> > > Lost particles while sorting
> > > For more information and tips for troubleshooting, please check the
> > GROMACS
> > > website at http://www.gromacs.org/Documentation/Errors
> > >
> > > -
> > >
> > >
> > > in one of my simulations (but not the others), when I start to use more
> > 16
> > > MPI processes per simulation. I should note that I am using mdrun
> > -multidir
> > > in order to launch these simulations at the same time, and it doesn't
> > seem
> > > to be a specific simulation that it causing the issue. Additionally, it
> > is
> > > rather sporadic, sometimes the simulations will run with no problems,
> > other
> > > times it run for 2 minutes and then fails (and I get stuck back in the
> > > queue). Any ideas?
> > >
> > >
> > >
> > > ===
> > > Micholas Dean Smith, PhD.
> > > Post-doctoral Research Associate
> > > University of Tennessee/Oak Ridge National Laboratory
> > > Center for Molecular Biophysics
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> 

Re: [gmx-users] Error: Lost Particles while sorting

[Smith, Micholas D.]

Hi,

Good to know. I'll ask the supercomputing folks to update gromacs from 5.0.4 to 
5.0.7 at the next scheduled downtime. 

-Micholas


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

Sent: Thursday, March 31, 2016 3:22 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Error: Lost Particles while sorting

Hi,

I was thinking of http://redmine.gromacs.org/issues/1153 but on general
principles that should not have showed up in 5.0. Nonetheless the early 5.0
versions had enough GPU-related issues that you still want to follow my
suggestion and see how you go.

Mark

On Thu, 31 Mar 2016 20:11 Smith, Micholas D.  wrote:

> Thanks, Mark. I didn't see this bug noted in the bug list so I thought I
> was just going crazy
>
> ===
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> Abraham 
> Sent: Thursday, March 31, 2016 2:57 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Error: Lost Particles while sorting
>
> Hi,
>
> Starting a new series of calculations on the earliest of a series of patch
> releases means you have chosen to accept all the bugs that have been fixed
> since. ;-) This indeed looks like one of them. Get e.g. 5.0.7 installed.
>
> Mark
>
> On Thu, 31 Mar 2016 19:40 Smith, Micholas D.  wrote:
>
> > Dear other users (and developers)
> >
> >
> > I moved some simulations that were working pretty well on one
> > supercomputer to another (the previous one did not have gpu nodes) to
> take
> > advantage of some gpus, but I am now getting a sporadic error:
> >
> >
> > 
> >
> > Program gmx_mpi, VERSION 5.0
> > Source code file:
> > /autofs/na4_sw/xk6/gromacs/5.0/cle5.2_gnu4.8.2/source/src/grom
> > acs/mdlib/nbnxn_search.c, line: 728
> >
> > Software inconsistency error:
> > Lost particles while sorting
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> >
> > -
> >
> >
> > in one of my simulations (but not the others), when I start to use more
> 16
> > MPI processes per simulation. I should note that I am using mdrun
> -multidir
> > in order to launch these simulations at the same time, and it doesn't
> seem
> > to be a specific simulation that it causing the issue. Additionally, it
> is
> > rather sporadic, sometimes the simulations will run with no problems,
> other
> > times it run for 2 minutes and then fails (and I get stuck back in the
> > queue). Any ideas?
> >
> >
> >
> > ===
> > Micholas Dean Smith, PhD.
> > Post-doctoral Research Associate
> > University of Tennessee/Oak Ridge National Laboratory
> > Center for Molecular Biophysics
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> * Please search the archive at
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Re: [gmx-users] Error: Lost Particles while sorting

[Smith, Micholas D.]

Thanks, Mark. I didn't see this bug noted in the bug list so I thought I was 
just going crazy

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


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

Sent: Thursday, March 31, 2016 2:57 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Error: Lost Particles while sorting

Hi,

Starting a new series of calculations on the earliest of a series of patch
releases means you have chosen to accept all the bugs that have been fixed
since. ;-) This indeed looks like one of them. Get e.g. 5.0.7 installed.

Mark

On Thu, 31 Mar 2016 19:40 Smith, Micholas D.  wrote:

> Dear other users (and developers)
>
>
> I moved some simulations that were working pretty well on one
> supercomputer to another (the previous one did not have gpu nodes) to take
> advantage of some gpus, but I am now getting a sporadic error:
>
>
> 
>
> Program gmx_mpi, VERSION 5.0
> Source code file:
> /autofs/na4_sw/xk6/gromacs/5.0/cle5.2_gnu4.8.2/source/src/grom
> acs/mdlib/nbnxn_search.c, line: 728
>
> Software inconsistency error:
> Lost particles while sorting
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> -
>
>
> in one of my simulations (but not the others), when I start to use more 16
> MPI processes per simulation. I should note that I am using mdrun -multidir
> in order to launch these simulations at the same time, and it doesn't seem
> to be a specific simulation that it causing the issue. Additionally, it is
> rather sporadic, sometimes the simulations will run with no problems, other
> times it run for 2 minutes and then fails (and I get stuck back in the
> queue). Any ideas?
>
>
>
> ===
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] Error: Lost Particles while sorting

[Smith, Micholas D.]

Dear other users (and developers)


I moved some simulations that were working pretty well on one supercomputer to 
another (the previous one did not have gpu nodes) to take advantage of some 
gpus, but I am now getting a sporadic error:




Program gmx_mpi, VERSION 5.0
Source code file: /autofs/na4_sw/xk6/gromacs/5.0/cle5.2_gnu4.8.2/source/src/grom
acs/mdlib/nbnxn_search.c, line: 728

Software inconsistency error:
Lost particles while sorting
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

-


in one of my simulations (but not the others), when I start to use more 16 MPI 
processes per simulation. I should note that I am using mdrun -multidir in 
order to launch these simulations at the same time, and it doesn't seem to be a 
specific simulation that it causing the issue. Additionally, it is rather 
sporadic, sometimes the simulations will run with no problems, other times it 
run for 2 minutes and then fails (and I get stuck back in the queue). Any ideas?



===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics
-- 
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Re: [gmx-users] Problem with the mdrun_openmpi on cluster

[Smith, Micholas D.]

What is your box size (x, y, z)? 

What happens if you use half that number of nodes? 

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


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of James 
Starlight 
Sent: Monday, March 14, 2016 12:19 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] Problem with the mdrun_openmpi on cluster

Hello,

I am trying to submit job on 64 nodes on mu local cluster using below
combination of software


DO="mpiexec -np 64"
PROG="g_mdrun_openmpi"


$DO $PROG -deffnm sim


obtaining error



Program g_mdrun_openmpi, VERSION 4.5.7
Source code file:
/builddir/build/BUILD/gromacs-4.5.7/src/mdlib/domdec.c, line: 6436

Fatal error:
There is no domain decomposition for 64 nodes that is compatible with
the given box and a minimum cell size of 2.6255 nm
Change the number of nodes or mdrun option -rcon or your LINCS settings

Could someone provide me trivial sollution/

Thanks!

J.
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Re: [gmx-users] apply force on single molecule

[Smith, Micholas D.]

Yes. Take a look at the manual for information on using the Pulling code.


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


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

Sent: Tuesday, March 08, 2016 2:20 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] apply force on single molecule

Dear all,

I want look at change in potential energy profile, when i apply force on a
molecule on one end where other end fixed in a position. Is it possible do
it in gromacs. If yes, how may i proceed?

--Masrul
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Re: [gmx-users] error running grompp for ions.mdp input

[Smith, Micholas D.]

At the end of your topology file, make sure you have the correct number of 
molecules of each type 
(typically the end of the .top file will look something like:

[ molecules ]
Protein1;Number of proteins
SOL59990 ;Number of waters
Na   2 ; Number of Na ions
Cl2; Number of Cl ions

In your case you should have something like:

[ molecules ]
Protein   1 ;Number of proteins
MET (); Number of Methanol Molecules
SOL (); Number of Solvent molecules


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


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

Sent: Tuesday, February 16, 2016 8:19 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] error running grompp for ions.mdp input

hello

I'm new to gromacs I'm simulating a protein in a mixed solvent
(water/organic solvent)

*first I added my organic solvent molecule (Methanol) using gmx
insert-molecules command

*then I solvate it in water using gmx solvate command

but I went to adding atom using gmx grompp command







*I get this error : Fatal error: number of coordinates in coordinate file
(3im_solv.gro, 161232)  does not match topology (topol.top,
492074) For more information and tips for troubleshooting, please check the
GROMACS website at http://www.gromacs.org/Documentation/Errors
 *I don't know which changes I
need to apply on the topology.top file to get it updated
I tried to change the numbers in the .top file to match the number given at
the top of the coordinate 3im_solv.gro file but I still get the same error
but with different numbers.


* any help would be appreciated  *thanks
Ghada
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Re: [gmx-users] gromacs-5.1.1 installation error: libxml2 problem

[Smith, Micholas D.]

Quick clarifying question, are you sure you have the development version of the 
libxml2 package (the source with the headers and everything)?

Also this might be a good time to complain to your sys-admin to install the 
libxml2-dev library, as it is used in a lot of other programs too, and you 
would just be saving everyone a headache.


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


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Irina 
Kosheleva 
Sent: Thursday, February 11, 2016 12:08 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] gromacs-5.1.1 installation error:  libxml2 problem

Dear gmx-users.
I would like to install gromacs-5.1.1 on a cluster where I have only user 
privileges. The machine has arch linux-rhel_6-ppc64.
I would like to install it with unittest support thus I need libxml2.a compiled 
library.
The cluster does not have this library installed so I have downloaded 
libxml2-2.9.2 and compiled it with zlib support:
 ./configure --prefix=/home/ikosh/programs/autotools-bin 
--with-python-install-dir=/home/ikosh/programs/autotools-bin 
--with-zlib=/soft/libraries/alcf/current/xl/ZLIB

Now, I would like to use this static libxml2.a library to compile gromacs-5.1.1:
cmake -DCMAKE_C_COMPILER=mpixlc_r -DCMAKE_CXX_COMPILER=mpixlcxx_r 
-DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C -DGMX_SIMD=IBM_QPX 
-DFFTWF_INCLUDE_DIR=/soft/libraries/alcf/current/xl/FFTW3/include 
-DFFTWF_LIBRARY=/soft/libraries/alcf/current/xl/FFTW3/lib/libfftw3f.a 
-DLIBXML2_INCLUDE_DIR=/gpfs/vesta-home/ikosh/programs/autotools-bin/include  
-DLIBXML2_LIBRARIES=/gpfs/vesta-home/ikosh/programs/autotools-bin/lib/libxml2.a 
-DZLIB_INCLUDE_DIR=/soft/libraries/soft/libraries/alcf/current/xl/ZLIB/include 
-DZLIB=/soft/libraries/alcf/current/xl/ZLIB/lib/libz.a
-DBUILD_SHARED_LIBS=OFF -DGMX_XML=OFF -DGMX_PREFER_STATIC_LIBS=ON  
-DCMAKE_C_FLAGS="-O3 -qsmp=omp -qarch=qp -qtune=qp" 
-DCMAKE_INSTALL_PREFIX=/gpfs/vesta-home/ikosh/gromacs-5.1.1/install

--output  just the error:
-- Looking for xmlTextWriterEndAttribute in 
/home/ikosh/programs/autotools-bin/lib/libxml2.a
-- Looking for xmlTextWriterEndAttribute in 
/home/ikosh/programs/autotools-bin/lib/libxml2.a - not found
CMake Warning at CMakeLists.txt:543 (message):
  libxml2 not found.  Will build GROMACS without unit-tests.  This is not
  recommended, because the unit-tests help to verify that GROMACS functions
  correctly.  Most likely you are missing the libxml2-dev(el) package.  After
  you installed it, set GMX_BUILD_UNITTESTS=ON.

Looking at the CMakeError.log in CMakeFiles:
/soft/buildtools/cmake/3.3.0/bin/cmake -E cmake_link_script 
CMakeFiles/cmTC_09bc5.dir/link.txt --verbose=1
/soft/compilers/wrappers/xl/mpixlc_r  -Wl,-relax -O3 -qsmp=omp -qarch=qp 
-qtune=qp -qsuppress=1500-036 -qsuppress=1500-010 -qsuppress=1500-03
0 -qlanglvl=extc99 -qarch=auto -qtune=auto  
-DCHECK_FUNCTION_EXISTS=xmlTextWriterEndAttribute
CMakeFiles/cmTC_09bc5.dir/CheckFunctionExist
s.c.o  -o cmTC_09bc5  /home/ikosh/programs/autotools-bin/lib/libxml2.a
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlGzfileOpenW':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1275: undefined reference to 
`gzopen64'
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1246: undefined reference to 
`gzdopen'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`__xmlParserInputBufferCreateFilename':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:2670: undefined reference to 
`gzdirect'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlFreeZMemBuff':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1556: undefined reference to 
`deflateEnd'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlGzfileOpen_real':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1167: undefined reference to 
`gzdopen'
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1198: undefined reference to 
`gzopen64'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlGzfileClose':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1331: undefined reference to 
`gzclose'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlGzfileWrite':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1315: undefined reference to 
`gzwrite'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlZMemBuffGetContent':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1758: undefined reference to 
`deflate'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlZMemBuffAppend':
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1717: undefined reference to 
`deflate'
/home/ikosh/programs/libxml2-2.9.3/xmlIO.c:1729: undefined reference to `crc32'
/home/ikosh/programs/autotools-bin/lib/libxml2.a(xmlIO.o): In function 
`xmlGzfileRead':
/home/ikosh/pr

Re: [gmx-users] protein-protein interaction

[Smith, Micholas D.]

Run your pdb through pdb2gmx with the splitchains option. That should give you 
a good start.


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


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Mahboobeh 
Eslami 
Sent: Thursday, January 28, 2016 10:58 AM
To: Gmx-users
Subject: [gmx-users] protein-protein interaction

 hi all I have used the HEX software for docking two protein.I want to do 
molecular dynamics simulations on the obtained complex from docking process. 
should  the simulation of  protein-protein complex be done like the 
protein-ligand complex or the protein in water simulation?  How is simulated 
protein-protein complex?
Thanks so much for your help.
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Re: [gmx-users] trivial question about water molecules

[Smith, Micholas D.]

Check the original topology file without ions for the line SOL(number of 
water's here)

then check the new topology file with ions-added  for the same line and 
compare. 


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


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Marta 
Wisniewska 
Sent: Thursday, January 21, 2016 11:47 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] trivial question about water molecules

Hello Gromacs Users;

I'd like to calculate the # of replaced water molecules by sodium chloride
in my system . I added a 0.15M concentration of NaCl. How can I calculate
the number of water molecules, which are replaced by ions?

Thank you in advance,
Marta
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Re: [gmx-users] multiple nodes, GPUs on a Cray system

[Smith, Micholas D.]

Michael,

One thing to check when using such a big machine anyway is to do some more 
scaling tests (i.e. run short jobs, 10min or so, with 1 nodes, 2 nodes, 4, 
nodes, 8 nodes, 16 nodes, 32 nodes, etc..) and make sure the performance of 
your simulation is scaling as well as you think it does. Sometimes using a 
smaller number of nodes, may be helpful to overcome slow-downs due to 
inter-node communication, also, oddly enough, check how the scaling does with 
and without the gpus (use the flag -nb cpu to avoid using the gpu). Sometimes 
not using the gpus may enhance your performance scaling (its odd when this 
happens, but I have seen it from time to time).

-Micholas

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


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

Sent: Tuesday, January 19, 2016 2:38 PM
To: Discussion list for GROMACS users
Cc: Discussion list for GROMACS users
Subject: Re: [gmx-users] multiple nodes, GPUs on a Cray system

On Tue, Jan 19, 2016 at 8:19 PM, Michael Weiner  wrote:

> Micholas,
> Thanks for the quick reply.  This solved part of my problem, in that the
> system does now run, but it seems like the domain decomposition uses only
> the number of nodes, not the total number of processors (unless it’s being
> further divided later in a way not recorded in the log file).


Multi-threaded (OpenMP) parallelization makes sure that mdrun can use all
cores in a node. Unless you or the job launcher told mdrun to use a certain
number of threads, mdrun will divide all available cores among the MPI
ranks placed onto a node. So if you start one MPI rank per node
(as Micholas suggested), mdrun should be using 8 threads/rank and the log
should clearly state this.


> As a result, the simulation seems to run much more slowly than expected.


Slow simulation could be caused by other factors too, but without seeing a
log file, it's hard to tell what the reason is.


>   Do I need to manually set the domain decomposition rather than allowing
> it to happen automatically?
>

No. You should be setting the launch configuration manually, the domain
decomposition will be set based on that.


> Michael
>
>
> Smith, Micholas D. smithmd at ornl.gov   gromacs.org_gmx-users%40maillist.sys.kth.se
> ?Subject=Re:%20Re%3A%20%5Bgmx-users%5D%20multiple%20nodes%2C%20GPUs%20on%20a%20Cray%20system&In-Reply-To=%3C1453225487318.55448%
> 40ornl.gov%3E>
> Tue Jan 19 18:44:54 CET 2016
>
> Try this:
>
> aprun -n (number of nodes) -N 1 (1 mpi-process per node) mdrun_mpi -gpu_id
> 0 (now your job stuff here)
>
>
>
> ===
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> 
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>
>  https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>> on
> behalf of Michael Weiner  https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>>
> Sent: Tuesday, January 19, 2016 12:14 PM
> To: gromacs.org_gmx-users at maillist.sys.kth.se <
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>
> Subject: [gmx-users] multiple nodes, GPUs on a Cray system
>
> Hello.  I am trying to run Gromacs on ORNL’s Titan supercomputer (Cray
> XK7).  Specifically, I wish to run a large system across multiple nodes
> while employing GPUs with Gromacs 4.6.6.  However, I cannot figure out the
> appropriate way to call mdrun in order for this to work.  Within a
> submission script, I have tried many combinations of flags for aprun and
> mdrun, none of which work.
> Most specifically, if I request 50 nodes of 16 cores each and use this
> command:
> aprun -n 800 -N 16 mdrun_mpi
> I get the following error: “Incorrect launch configuration: mismatching
> number of PP MPI processes and GPUs per node.  mdrun_mpi was started with
> 16 PP MPI processes per node, but only 1 GPU were detected.”
> I have also tried with the -n flag equal to the number of nodes, but then
> it decomposes only to that many domains, rather than one per processor.
> The “mdrun_mpi” command seems to be the only way of calling mdrun on the
> machine.
> I would appreciate any help with figuring out the appropriate flags to use
> for aprun and mdrun.
> Thank you.
> Michael Weiner
>
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can

Re: [gmx-users] multiple nodes, GPUs on a Cray system

[Smith, Micholas D.]

Try this:

aprun -n (number of nodes) -N 1 (1 mpi-process per node) mdrun_mpi -gpu_id 0 
(now your job stuff here)



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


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

Sent: Tuesday, January 19, 2016 12:14 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] multiple nodes, GPUs on a Cray system

Hello.  I am trying to run Gromacs on ORNL’s Titan supercomputer (Cray XK7).  
Specifically, I wish to run a large system across multiple nodes while 
employing GPUs with Gromacs 4.6.6.  However, I cannot figure out the 
appropriate way to call mdrun in order for this to work.  Within a submission 
script, I have tried many combinations of flags for aprun and mdrun, none of 
which work.
Most specifically, if I request 50 nodes of 16 cores each and use this command:
aprun -n 800 -N 16 mdrun_mpi
I get the following error: “Incorrect launch configuration: mismatching number 
of PP MPI processes and GPUs per node.  mdrun_mpi was started with 16 PP MPI 
processes per node, but only 1 GPU were detected.”
I have also tried with the -n flag equal to the number of nodes, but then it 
decomposes only to that many domains, rather than one per processor.  The 
“mdrun_mpi” command seems to be the only way of calling mdrun on the machine.
I would appreciate any help with figuring out the appropriate flags to use for 
aprun and mdrun.
Thank you.
Michael Weiner

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Re: [gmx-users] genion with Na or Ca

[Smith, Micholas D.]

At low concentrations (just a single Ca2+) you shouldn't expect any huge 
differences, though the Ca2+ may stick around the protein surface a little bit 
longer than the Na+ ions which may alter how one of the charged residues is 
hydrated. If the protein is of a modest size (not a small fragment), than any 
modifications to the hydration of a single residue likely will not be a huge 
driving factor to your dynamics...though this is not guaranteed.  

When in doubt, run both simulation conditions and compare.

-Micholas

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


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

Sent: Tuesday, January 12, 2016 7:41 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] genion with Na or Ca

On 1/12/16 3:19 AM, Turgay Cakmak wrote:
> Hi all,
>
>
> I have a quick question about neutralizing the system. I have a solvated
> system that contains a charged protein of -2q. Is there a major difference
> betwen adding 2 Na ions and a single  Ca ion to neutralize the system
> (using genion)?
>

For the purposes of neutralization, probably not, but note that additive force
fields do not deal well with divalent ions.  Na+ or K+ are preferable if only
being used for simple balancing of charge.

-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] Help calculation on cluster

[Smith, Micholas D.]

Try:

echo "0" | g_mmpbsa -f traj.xtc -s topol.tpr -i mmpbsa.mdp -n index.ndx -nomme 
-pbsa -nodecomp -apol apolar.xvg -nodiff

In your submission file. Where "0" is the index number of the group you are 
interested in.

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


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

Sent: Friday, December 18, 2015 3:04 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Help calculation on cluster

Thanks for your reply Micholas, I ask my system admins but he told me that for 
queuing the job I need to enter the selected group in the command line. My 
command is g_mmpbsa -f traj.xtc -s topol.tpr -i mmpbsa.mdp -n index.ndx -nomme 
-pbsa -nodecomp -apol apolar.xvg -nodiff
My question was if I can add something to this command in order to select the 
atom group I  wanted to use instead of selecting it from the group list that 
appears after the job is submitted?
Mishelle

> From: smit...@ornl.gov
> To: gmx-us...@gromacs.org
> Date: Fri, 18 Dec 2015 19:47:22 +
> Subject: Re: [gmx-users] Help calculation on cluster
>
> Not really the best place to ask this question (check with your system 
> admins), but
>
> You could run your command from a "screen session".
>
> Just run screen when you first log into the machine, go about your business 
> setting up your simulation and then start it. Once it is running, type 
> control-a-d to detach from the session. It will continue to run until 
> completion, or the computer crashes, whether you close the terminal or not. 
> And you can always re-attach to the screen session to see what is going on 
> from a new terminal if you need to.
>
> Ideally, though, you would just submit your job to a queuing system and wait 
> for it to finish...be sure to check with your sys. admins.
>
>
> ===
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  on behalf of Mishelle Oña 
> 
> Sent: Friday, December 18, 2015 2:40 PM
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] Help calculation on cluster
>
> Hi,
> I am doing some simulations in a cluster. I want to know if there is an 
> option to run the simulation in order that I can close the terminal?. I tried 
> to make  sbatch but the problem is that when I entered the command there is a 
> step to choose the system and with sbatch I could not choose this option.
> Thank youMishelle
> --
> Gromacs Users mailing list
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>
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Re: [gmx-users] Help calculation on cluster

[Smith, Micholas D.]

Not really the best place to ask this question (check with your system admins), 
but

You could run your command from a "screen session". 

Just run screen when you first log into the machine, go about your business 
setting up your simulation and then start it. Once it is running, type 
control-a-d to detach from the session. It will continue to run until 
completion, or the computer crashes, whether you close the terminal or not. And 
you can always re-attach to the screen session to see what is going on from a 
new terminal if you need to.

Ideally, though, you would just submit your job to a queuing system and wait 
for it to finish...be sure to check with your sys. admins.


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


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

Sent: Friday, December 18, 2015 2:40 PM
To: gmx-us...@gromacs.org
Subject: [gmx-users] Help calculation on cluster

Hi,
I am doing some simulations in a cluster. I want to know if there is an option 
to run the simulation in order that I can close the terminal?. I tried to make  
sbatch but the problem is that when I entered the command there is a step to 
choose the system and with sbatch I could not choose this option.
Thank youMishelle
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Re: [gmx-users] constraining secondary structure gmx 5

[Smith, Micholas D.]

Hi, 

If the molecules have been parameterized in OPLS/Amber and Charmm, going from 
Charmm to OPLS/Amber is pretty straightforward, you just to build a topology 
using the OPLS/Amber atom-types instead of Charmm that correspond to your 
system (its just an elaborate find/replace exercise). For peptides it is even 
easier, as you can take your pdb of your peptide and run it through gmx pdb2gmx 
and select OPLS or Amber instead of Charmm as your force-field and it will 
generate a .gro file of your peptide and a topology file for the peptide with 
the proper atomtypes for the force-field.

-Micholas

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


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Yoav 
Atsmon-Raz 
Sent: Thursday, December 10, 2015 11:37 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] constraining secondary structure gmx 5

Thanks for your reply Micholas,

The secondary structure constraints are used to "guide" the structure to a 
known minimum so to speak and that particular structure is of interest to me. I 
never worked with OPLS or Amber, is the process of working with them equivalent 
to using charmm via gromacs? At least for the time being, working with 
something that I know will give me the results I'm interested in seems 
preferable to trying out alternative software that I never tried before.


-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Smith, 
Micholas D.
Sent: Thursday, December 10, 2015 9:32 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] constraining secondary structure gmx 5

Hi,

I haven't tried to restrain secondary structure; however, it may be possible by 
using a combination of dihedral, angle, and distance restraints (see section 
4.3 in the manual). If you look up the DSSP . It would likely be cumbersome, 
but it may be do-able. The question is if the results from your simulation 
would be meaningful after all of these restraints were added. Perhaps it would 
be useful to see if you can build your system using OPLS or Amber instead of 
CHARMM and determine if the peptide's structure still "falls-apart".

Good Luck

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


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Yoav 
Atsmon-Raz 
Sent: Thursday, December 10, 2015 11:03 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] constraining secondary structure gmx 5

I've been trying to run a gromacs simulation of alternating d/l cyclical 
peptides (yes I know this is a dead horse that's been beat one time to many...) 
and after a lot of experimentation I managed to get an initial setup working 
via charmm gui. However, as the simulation progresses the structure becomes 
completely unstable which doesn't fit the experimental results that I'm 
familiar with in the literature. I was wondering if there is any way to 
manually constrain a secondary structure on a per residue basis beyond the 
definitions in the posre file. The reason I'm asking this is that I'm aware 
that this is possible in CHARMM and NAMD but I can't seem to find anything 
detailing this in the gromacs manual.

Thanks to anyone responding to this!
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Re: [gmx-users] constraining secondary structure gmx 5

[Smith, Micholas D.]

Hi,

I haven't tried to restrain secondary structure; however, it may be possible by 
using a combination of dihedral, angle, and distance restraints (see section 
4.3 in the manual). If you look up the DSSP . It would likely be cumbersome, 
but it may be do-able. The question is if the results from your simulation 
would be meaningful after all of these restraints were added. Perhaps it would 
be useful to see if you can build your system using OPLS or Amber instead of 
CHARMM and determine if the peptide's structure still "falls-apart".

Good Luck 

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


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Yoav 
Atsmon-Raz 
Sent: Thursday, December 10, 2015 11:03 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] constraining secondary structure gmx 5

I've been trying to run a gromacs simulation of alternating d/l cyclical 
peptides (yes I know this is a dead horse that's been beat one time to many...) 
and after a lot of experimentation I managed to get an initial setup working 
via charmm gui. However, as the simulation progresses the structure becomes 
completely unstable which doesn't fit the experimental results that I'm 
familiar with in the literature. I was wondering if there is any way to 
manually constrain a secondary structure on a per residue basis beyond the 
definitions in the posre file. The reason I'm asking this is that I'm aware 
that this is possible in CHARMM and NAMD but I can't seem to find anything 
detailing this in the gromacs manual.

Thanks to anyone responding to this!
--
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