[gmx-users] poor average exchange ratio for each replica

[YanhuaOuyang]

Dear Grimacs users,
I did use the equation:Ti=T0*ek*i  to generate a temperature distribution, 
after a 2-ns  REMD, I check the md.log file. I find the average exchange ratio 
for each replica is poor. the average exchange ratio is as below

Replica exchange statistics
Repl  499 attempts, 250 odd, 249 even
Repl  average probabilities:
Repl 0123456789   10   11   12   13   
14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   
30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
Repl  .07  .08  .05  .05  .06  .06  .06  .06  .06  .05  .05  .04  .03  .05  
.03  .03  .03  .01  .03  .02  .04  .02  .02  .02  .01  .02  .02  .01  .01  .01  
.01  .01  .01  .01  .01  .02  .01  .01  .02  .00  .02  .00  .02  .02  .01

Repl  number of exchanges:
Repl 0123456789   10   11   12   13   
14   15   16   17   18   19   20   21   22   23   24   25   26   27   28   29   
30   31   32   33   34   35   36   37   38   39   40   41   42   43   44   45
Repl   14   20   13   12   16   14   15   17   14   159   128   13  
  757256   10646253163  
  332345234242443

 the temperature distribution: 270.00 272.84 275.77 278.79 281.91 285.12 288.43 
291.84 295.36 299.00 302.75 306.61 310.60 314.72 318.97 323.36 327.89 332.56 
337.39 342.38 347.52 352.83 358.32 363.98 369.82 375.86 382.09 388.51 395.15 
401.99 409.05 416.33 423.84 431.59 439.58 447.81 456.29 465.04 474.05 483.34 
492.92 502.78 512.96 523.45 534.28 545.46.

the temperature is reasonable, but the acceptance ratio is far from 0.2-0.3. So 
I get a another temperature distribution with the 
website:http://origami.phys.rpi.edu/racc/rate_of_acceptance.php 
  ,the average 
exchange ratio still is  less than 0.05. 
I really do not know how to improve the situation. What should I do in the next 
step? How should I improve such a low exchange ratio?

best regards,
Ouyang



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[gmx-users] Software inconsistency error: pme_loadbal_do called at an interval != nstlist

[Yorquant Wang]

Dear All,

I recently met a error:"Software inconsistency error: pme_loadbal_do called
at an interval != nstlist" when I try to restart one of jobs.
I used GMX 5.1.2  on K80 GPU nodes with haswell CPU.

Is there anyone know how to solve this error?
Thank you very much!

cheer​s
Yukun Wang

below is the output log files:

   :-) GROMACS - gmx mdrun, VERSION 5.1.2 (-:

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

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

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

GROMACS:  gmx mdrun, VERSION 5.1.2
Executable:   /lustre/usr/gromacs/5.1-icc15-impi5-gpu/bin/gmx_mpi
Data prefix:  /lustre/usr/gromacs/5.1-icc15-impi5-gpu
Command line:
  gmx_mpi mdrun -deffnm 200DPPC-16-WT_COO-_150mV_2 -append -cpi -v
-resethway -noconfout

No previous checkpoint file present, assuming this is a new run.

Number of logical cores detected (16) does not match the number reported by
OpenMP (8).
Consider setting the launch configuration manually!

Running on 1 node with total 16 cores, 16 logical cores, 2 compatible GPUs
Hardware detected on host gpu35 (the node of MPI rank 0):
  CPU info:
Vendor: GenuineIntel
Brand:  Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz
SIMD instructions most likely to fit this hardware: AVX_256
SIMD instructions selected at GROMACS compile time: AVX_256
  GPU info:
Number of GPUs detected: 2
#0: NVIDIA Tesla K20m, compute cap.: 3.5, ECC: yes, stat: compatible
#1: NVIDIA Tesla K20m, compute cap.: 3.5, ECC: yes, stat: compatible

Reading file 200DPPC-16-WT_COO-_150mV_2.tpr, VERSION 5.0.4 (single
precision)
Note: file tpx version 100, software tpx version 103
Changing nstlist from 25 to 40, rlist from 1.038 to 1.08

The number of OpenMP threads was set by environment variable
OMP_NUM_THREADS to 8
Using 2 MPI processes
Using 8 OpenMP threads per MPI process

On host gpu35 2 compatible GPUs are present, with IDs 0,1
On host gpu35 2 GPUs auto-selected for this run.
Mapping of GPU IDs to the 2 PP ranks in this node: 0,1


NOTE: GROMACS was configured without NVML support hence it can not exploit
  application clocks of the detected Tesla K20m GPU to improve
performance.
  Recompile with the NVML library (compatible with the driver used) or
set application clocks manually.


Non-default thread affinity set probably by the OpenMP library,
disabling internal thread affinity

WARNING: This run will generate roughly 38667 Mb of data


NOTE: DLB will not turn on during the first phase of PME tuning

starting mdrun '200dppc_membrane_16Maculatin-WT-COO-'
100 steps, 2000.0 ps (continuing from step 268830925, 537661.8
ps).

---
Program gmx mdrun, VERSION 5.1.2
Source code file:
/home/rpm/rpmbuild/BUILD/gromacs-5.1.2/src/gromacs/ewald/pme-load-balancing.cpp,
line: 947

Software inconsistency error:
pme_loadbal_do called at an interval != nstlist
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---


---
Program gmx mdrun, VERSION 5.1.2
Source code file:
/home/rpm/rpmbuild/BUILD/gromacs-5.1.2/src/gromacs/ewald/pme-load-balancing.cpp,
line: 947

Software inconsistency error:
pme_loadbal_do called at an interval != nstlist
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Halting parallel program gmx mdrun on rank 1 out of 2
Halting parallel program gmx mdrun on rank 0 out of 2
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
srun: error: gpu35: tasks 

Re: [gmx-users] fe4s4

[Ullmann, Thomas]

A good starting point to get an idea of the challenges posed by
iron sulfur clusters are the publications of Louis Noodleman.

Good luck,
Thomas.

--
R. Thomas Ullmann, PhD
Theoretical & Computational Biophysics
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11
37077 Göttingen, Germany
thomas.ullm...@mpibpc.mpg.de
www.bisb.uni-bayreuth.de/People/ullmannt
--


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Nilkanta 
Chowdhury [nil5...@gmail.com]
Sent: Saturday, May 28, 2016 2:19 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] fe4s4

will you please guide me. how can I do this?
On May 28, 2016 5:11 PM, "Justin Lemkul"  wrote:

>
>
> On 5/28/16 3:59 AM, Nilkanta Chowdhury wrote:
>
>> Hello friends,
>>   I want to simulate a protein  molecule boud with a
>> Fe4S4 molecule, in gromacs. How do i generet the topology og this fe4s4
>> molecule.
>>
>
> You need to obtain/derive parameters for it.  That's not a simple species
> to deal with.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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Re: [gmx-users] Fwd: Conversion from GROMACS .top .itp to CHARMM .psf .par combo

[Michael Shirts]

Try ParmEd.

http://parmed.github.io/ParmEd/html/index.html

On Sat, May 28, 2016 at 7:57 AM, Sourav Ray  wrote:
> Hello
>
> Currently I have a combination of:
>
> 1. .pdb file (four copies of a monomer)
> 2. .itp file defining the topology of one monomer (applied on all four with
> the help of the .top file described below).
> 3. .top file listing the constituents of the entire pdb:
>
> 
>
> #include "martini_v2.2P.itp"
>
> #include "Protein_A.itp"
>
> [ system ]
> ; name
> Martini system from fa_qpr.pdb
>
> [ molecules ]
> ; namenumber
> Protein_A  1
> Protein_A  1
> Protein_A  1
> Protein_A  1
>
> -
>
> It would be really helpful if someone could refer to a software or script
> maybe that takes the .top and .itp files as input and converts them to .psf
> and .par/.prm files.
>
> Thanks and regards
> Sourav
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[gmx-users] Suggestion required for calculation of membrane contact sites and Lipid binding strength

[Antara mazumdar]

Dear Gromacs users,

Can anyone suggest me a way to find the membrane contact sites i.e. the
lipids that are making contact with protein residues with respect to time
from a  membrane protein simulation? I have calculated the distance and
contact of protein residues from upper leaflet atoms of bilayer already
with a cutoff between 0.5 nm and 0.7 nm.

I have the lipid numbers in the log file from g_hbond as well as g_dist.
Should i be taking all these into account or a cutoff needs to be taken and
can this be calculated wrt time?

Secondly, has anyone found out the lipid binding strength from membrane
protein simulations? Can we call the frequency of a protein residue to make
a contact as its lipid binding strength? Here also, is there some way to
find the binding strength wrt time?

Thanks!!
Kind Regards,
Antara

--
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Systems biology group
CSIR-Institute of Genomics & Integrative Biology
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New Delhi -  110020
M : +91-9717970040
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[gmx-users] Fwd: Conversion from GROMACS .top .itp to CHARMM .psf .par combo

[Sourav Ray]

Hello

Currently I have a combination of:

1. .pdb file (four copies of a monomer)
2. .itp file defining the topology of one monomer (applied on all four with
the help of the .top file described below).
3. .top file listing the constituents of the entire pdb:



#include "martini_v2.2P.itp"

#include "Protein_A.itp"

[ system ]
; name
Martini system from fa_qpr.pdb

[ molecules ]
; namenumber
Protein_A  1
Protein_A  1
Protein_A  1
Protein_A  1

-

It would be really helpful if someone could refer to a software or script
maybe that takes the .top and .itp files as input and converts them to .psf
and .par/.prm files.

Thanks and regards
Sourav
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Re: [gmx-users] fe4s4

[Mark Abraham]

Hi,

Very likely, anybody who knows how to do this has already published
literature on what they did, and how well it worked. This would be another
useful place to start searching.

Mark

On Sat, May 28, 2016 at 2:19 PM Nilkanta Chowdhury 
wrote:

> will you please guide me. how can I do this?
> On May 28, 2016 5:11 PM, "Justin Lemkul"  wrote:
>
> >
> >
> > On 5/28/16 3:59 AM, Nilkanta Chowdhury wrote:
> >
> >> Hello friends,
> >>   I want to simulate a protein  molecule boud with a
> >> Fe4S4 molecule, in gromacs. How do i generet the topology og this fe4s4
> >> molecule.
> >>
> >
> > You need to obtain/derive parameters for it.  That's not a simple species
> > to deal with.
> >
> > -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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> >
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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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Re: [gmx-users] fe4s4

[Nilkanta Chowdhury]

will you please guide me. how can I do this?
On May 28, 2016 5:11 PM, "Justin Lemkul"  wrote:

>
>
> On 5/28/16 3:59 AM, Nilkanta Chowdhury wrote:
>
>> Hello friends,
>>   I want to simulate a protein  molecule boud with a
>> Fe4S4 molecule, in gromacs. How do i generet the topology og this fe4s4
>> molecule.
>>
>
> You need to obtain/derive parameters for it.  That's not a simple species
> to deal with.
>
> -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
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> posting!
>
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>
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>
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Re: [gmx-users] Adaptive Biasing Force method

[Justin Lemkul]

On 5/28/16 6:33 AM, khourshaeisha...@mech.sharif.ir wrote:





Dear GROMACS users


Is there any way� to employ the adaptive biasing force (ABF) method
with GROMACS ?! If so,� could you please introduce me a tutorial or
article about it ? I really appreciate it.



Available features are described in the manual.  Tutorials are found via Google.

-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] fe4s4

[Justin Lemkul]

On 5/28/16 3:59 AM, Nilkanta Chowdhury wrote:

Hello friends,
  I want to simulate a protein  molecule boud with a
Fe4S4 molecule, in gromacs. How do i generet the topology og this fe4s4
molecule.


You need to obtain/derive parameters for it.  That's not a simple species to 
deal with.


-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] amidated C-terminal residue of peptide

[Justin Lemkul]

Please don't reply to the entire digest.

On 5/28/16 2:09 AM, kamakshi sikka wrote:

Dear Justin,


Charmm GUI created the topology file for the membrane only..I am asking for
C-terminal amidated peptide topology file. pdb2gmx command does not give
topology file here because of C-terminal amide residue which is missing in
the residue database. Please help.



CHARMM-GUI can build the entire membrane-protein complex, you just need to carry 
out a few more steps.


Otherwise, the patching is simple.  Choose the CT2 C-terminus type if using our 
CHARMM36 port.  That builds a C-terminal amide.


-Justin

--
==

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

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

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

==
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[gmx-users] Adaptive Biasing Force method

[khourshaeishargh]

Dear GROMACS users


Is there any way� to employ the adaptive biasing force (ABF) method
with GROMACS ?! If so,� could you please introduce me a tutorial or
article about it ? I really appreciate it.


best regards, Ali

==

Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir)

Department of Mechanical Engineering

Sharif University of Technology, Tehran, Iran

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Re: [gmx-users] query on performance of GTX 1080 in gromacs

[Jagannath Mondal]

Dear Mark

   I will appreciate if you share your experience, once you tested with GTX
1080. I can wait for your response.

Jagannath


On Fri, May 27, 2016 at 10:36 PM, Mark Abraham 
wrote:

> Hi,
>
> Yes, we expect it to work, but we haven't tried it yet. NVIDIA didn't
> manage to give us any early access, in practice. We have some cards, but
> perhaps no actual run until early next week.
>
> Mark
>
> On Fri, 27 May 2016 18:22 Jagannath Mondal 
> wrote:
>
> > Dear Gromacs users
> >
> >   I just wanted to check whether latest GPU of NVIDIA GTX 1080 has been
> > tested by any one for its compatibility/performance with gromacs.
> >
> > I have used GTX 980 Ti and have found it compatible with gromacs with a
> > significant performance boosting. I wanted to check if the latest release
> > of NVIDIA GTX 1080 will work with Gromacs.
> >
> > I will appreciate your feedback.
> >
> > Jagannath
> > --
> > 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!
>
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>
> * For (un)subscribe requests visit
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[gmx-users] fe4s4

[Nilkanta Chowdhury]

Hello friends,
  I want to simulate a protein  molecule boud with a
Fe4S4 molecule, in gromacs. How do i generet the topology og this fe4s4
molecule.
thank you..
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 145, Issue 109

[kamakshi sikka]

Dear Justin,


Charmm GUI created the topology file for the membrane only..I am asking for
C-terminal amidated peptide topology file. pdb2gmx command does not give
topology file here because of C-terminal amide residue which is missing in
the residue database. Please help.


Regards
Kamakshi Sikka



On Fri, May 27, 2016 at 8:40 PM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:

> Send gromacs.org_gmx-users mailing list submissions to
> gromacs.org_gmx-users@maillist.sys.kth.se
>
> To subscribe or unsubscribe via the World Wide Web, visit
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> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> Today's Topics:
>
>1. NMA problems with mass-weighting -m option (Ravasio Riccardo)
>2. NEMD (khourshaeisha...@mech.sharif.ir)
>3. Re: Lipid Head group Orientation (Chandan Choudhury)
>4. Re: NEMD (Mark Abraham)
>5. Output of g energy (khourshaeisha...@mech.sharif.ir)
>6. Re: amidated C-terminal residue of peptide (Justin Lemkul)
>7. Re: Distance restraint and pull code (Justin Lemkul)
>
>
> --
>
> Message: 1
> Date: Fri, 27 May 2016 13:49:17 +
> From: Ravasio Riccardo 
> To: "gromacs.org_gmx-users@maillist.sys.kth.se"
> 
> Subject: [gmx-users] NMA problems with mass-weighting -m option
> Message-ID: <1464356957471.73...@epfl.ch>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear gmx users,
>
>
> After performing Normal Mode Analysis, I would like to print a non
> mass-weighted spectrum, but both with option -m false and with -m true I
> get mass-weighted eigenvalues and eigenvectors. Why? I'm using version
> 5.1.2. I looked at the source code, but it was of version 3.2.0: maybe the
> -m option was forgotten in the last version? Or, what am I doing wrong?
>
>
> I'm using the usual following commands:
>
>
> gmx_d grompp -v -f nma.mdp -c $STRUCT-vacuum-min$((sample-1)).gro -p
> $STRUCT.top -o $STRUCT-vacuum-nma.tpr
>
>
> gmx_d mdrun -v -s $STRUCT-vacuum-nma.tpr -mtx $STRUCT-vacumm-nma.mtx
>
>
> gmx_d nmeig -f $STRUCT-vacumm-nma.mtx -s $STRUCT-vacuum-nma.tpr -m true
> -last 3693
>
>
> I tried to put also 0/1 or yes/no, but nothing changes.
>
>
> I thank you for your kindness and for your help.
>
>
> Best regards,
>
>
> Riccardo
>
>
> --
>
> Message: 2
> Date: Fri, 27 May 2016 18:20:12 +0430
> From: khourshaeisha...@mech.sharif.ir
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] NEMD
> Message-ID:
> 
> Content-Type: text/plain;charset=UTF-8
>
> Dear Gromacs users
> I am a M.Sc student at Sharif university in field of mechanical
> engineering. for my M.Sc thesis I'm using GROMACS and for a part of it, I
> need to use NEMD. I searched Internet but unfortunately found nothing
> related to gromacs ( I mean Example, article and ...). So could anyone
> please
> introduce me something relevant to NEMD part of GROMACS like tutorial,
> article  or anything else?
> I really appreciate it.
>
> best  regards, Ali
>
> ==
>
> Ali khourshaei shargh (khourshaeisha...@mech.sharif.ir)
>
> Department of Mechanical Engineering
>
> Sharif University of Technology, Tehran, Iran
>
>
> --
>
> Message: 3
> Date: Fri, 27 May 2016 10:33:29 -0400
> From: Chandan Choudhury 
> To: gmx-users 
> Subject: Re: [gmx-users] Lipid Head group Orientation
> Message-ID:
> <
> cahesojwzbp-pmyx-ghsmhgebhc16hm3qraeplyc9ky-h5wb...@mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Nidhin!
>
> I wrote a code some time ago on the the orientation of lipid molecules
> which was the specific to the problem addressed at
> http://pubs.acs.org/doi/full/10.1021/bm4011408. If you need, I can share.
>
> Chandan
>
> On Thu, May 26, 2016 at 7:50 PM, Nidhin Thomas <
> nidhin.thomas0...@gmail.com>
> wrote:
>
> > Hi GROMACS Users,
> >
> > This question was asked before in the forum. But I could not find a
> > complete answer. So I?m asking again. Is there any command in GROMACS
> that
> > can give the orientation of lipid head groups of all lipids averaged over
> > time?
> >
> > I wrote a code which takes the co-ordinates of P and N atoms at each time
> > frames and gives the orientation of P-N vector averaged over the time. I
> > was wondering if there is any command in GROMACS that can provide this
> data
> > directly ?
> >
> > I used g_sgangle command to obtain the angles of one lipid