[gmx-users] umbrella sampling, LINCS WARNING

[rose rahmani]

Hello;

I'm doing umbrella sampling, protein is getting closer to ZnS, but i get
some step files and run crashed just 107sec to end. Would it be because of
protein got very close to ZnS? Would you please help me?

With regards


-
this is pullf.xvg

0.  -0.000579208
0.0020  2.45011
0.0040  4.89696
0.0060  7.35804
0.0080  9.82449
0.0100  12.2863
0.0120  14.7352
0.0140  17.1628
0.0160  19.5634

.
.
.
1956.0480   -100532
1956.0500   -100532
1956.0520   -100531
1956.0540   -100530
1956.0560   -100529
1956.0580   -100528
1956.0600   -100527
1956.0620   -100526
---
this is pullx.xvg

0.  4.287   1.73577
0.1000  4.287   1.72023
0.2000  4.287   1.73131
0.3000  4.287   1.75326
0.4000  4.287   1.77348
0.5000  4.287   1.76939
0.6000  4.287   1.75636
0.7000  4.287   1.73677
0.8000  4.287   1.71755
0.9000  4.287   1.70901
1.  4.287   1.72336

.
.
.

1953.2000   4.287   0.324765
1953.3000   4.287   0.323972
1953.4000   4.287   0.326929
1953.5000   4.287   0.323881
1953.6000   4.287   0.323358
1953.7000   4.287   0.325145
1953.8000   4.287   0.32516
1953.9000   4.287   0.324791
1954.   4.287   0.325144
1954.1000   4.287   0.324902
1954.2000   4.287   0.324985
1954.3000   4.287   0.324877
1954.4000   4.287   0.323429
1954.5000   4.287   0.32637
1954.6000   4.287   0.324941
1954.7000   4.

---
this is md_pull.mdp;

integrator   = md
dt   = 0.002
nsteps   = 100
nstxout  = 5000
nstvout  = 5000
nstfout  = 500
nstlog   = 500
nstenergy= 1000
nstxtcout= 1000
nstlist  = 10
rlist= 1.5
coulombtype  = pme
rcoulomb = 1.5
vdwtype  = Switch
rvdw_switch  = 1.0
rvdw = 1.2
pcoupl   = no
gen_vel  = no
constraints  = h-bonds
ns_type  = grid
pbc  = xy
freezegrps   = WAL ZnS
freezedim= Y Y Y Y Y Y
energygrp-excl   = WAL WAL ZnS ZnS
energygrps   = SOL WAL ZnS Protein NA CL
nwall= 2
wall-atomtype= C C
wall-type= 9-3
wall-density = 150 150
wall-ewald-zfac  = 3
ewald-geometry   = 3dc
fourierspacing   = 0.12
tcoupl   = v-rescale
tc-grps  = System
tau-t= 0.1
ref-t= 300

; Pull code
pull= umbrella
pull_ngroups= 1
pull_group0 = ZnS
pull_group1 = Protein
pull_geometry   = direction
pull_vec1   = 0 0 1
pull_dim= N N Y
pull_rate1  = -0.011; 1 nm per  ns
pull_k1 = 5000
pull_start  = yes
pull_nstxout= 50

--
This is pull.job


Step 978195, time 1956.39 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.04, max 0.10 (between atoms 782 and 780)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
770769   61.40.1090   0.1090  0.1090
779778   42.00.1010   0.1010  0.1010

Step 978197, time 1956.39 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.429802, max 1.468930 (between atoms 783 and 780)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
773771   90.00.1112   0.1202  0.1090
770769   32.80.1090   0.1090  0.1090
779778   90.00.1010   0.1232  0.1010
783780   90.00.1090   0.2691  0.1090
Wrote pdb files with previous and current coordinates

Step 978198, time 1956.4 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 2.212948, max 5.521000 (between atoms 773 and 771)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
773771   90.00.1202   0.7108  0.1090
772771   47.80.1105   0.1031  0.1090
770769   90.00.1090   0.1142  0.1090
779778   90.00.1232   0.6381  0.1010
783780   57.80.2691   0.1086  0.1090
Wrote pdb files with previous and current coordinates

Step 978199, time 1956.4 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.451943, max 1.210712 (between atoms 770 and 769)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
773771   90.00.7108   0.1628  0.1090
772771   36.80.1031   0.1131  0.1090
770769   90.00.1142   0.2410  0.1090
779778   56.60.6381   0.1010  0.1010

Re: [gmx-users] Related to REMD

[ISHRAT JAHAN]

Hi Sudip
For doing REMD,I have generated the five seed conformation using trjconv
command. I have taken only 10 temperature from the temperature generating
tool, now i want to know whether i have to generate different .tpr file
using one conformation at all temperature or all conformations at all
temperature. Will you please tell me what to do as i am unable to
understand?
Thanks in advance


On Tue, Jan 2, 2018 at 4:55 PM, Sudip Das  wrote:

> Hi Ishrat,
>
>
> On Tue, Jan 2, 2018 at 4:14 PM, ISHRAT JAHAN  wrote:
>
> > Dear all,
> > I am trying to do REMD simulation. I had equillbrated the system for 5ns
> > and extracted the seed conformation at 3ns using the command-
> > gmx trjconv -f traj.trr -o 3ns.gro -s topol.tpr -dump 3000 -pbc mol
> > I had used temperature generator for REMD simulation from
> > folding.bmc.uu.se/remd with transition probability of 0.25 in
> temperature
> > range of 290-400K.it gives too many replica and i want only 10 replica.
>
> will anyone tell me what criteria should be taken for taking 10 replicas
> >
>
> It seems that your system size is reasonably large. You can try using
> replica exchange with solute scaling (REST2 method) which is basically
> comes under Hamiltonian replica exchange. It will reduce the number of
> replicas by scaling the potential energy surface with respect to effective
> temperature of the corresponding replica.
>
>
> > and also tell how to extract the one seed conformation from multiple seed
> > conformation which i had generated using above command.
> >
>
> See the several options under the module trjconv by typing the command:
> gmx trjconv -h
>
>
> Regards,
> Sudip
>
>
> Thanks in advance
> > --
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[gmx-users] Defining single, double and triple bonds

[SUVANKAR GHOSH]

Hi, Is there any option to define single, double and triple bonds in my
topology.

-- 
Suvankar Ghosh
Research Scholar,
Computational Structural Biology Lab,
Dept. of Biosciences and Bioengineering (BSBE),
Indian Institute of Technology Guwahati (IITG)
Guwahati 781039, Assam, India
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[gmx-users] 1st CfP: 4th Symposium on Big Data Visual and Immersive Analytics (BDVA): 17.-19.10.2018 Konstanz

[Björn Sommer]

*** 4th International Symposium on Big Data Visual and Immersive
Analytics (BDVA 2018) ***
*** 1st Call for Papers * Konstanz, Germany * 17th to 19th October 2018 ***

The BDVA 2018 Symposium is calling for contributions in the area of
Visual Analytics and Immersive Analytics of Big Data. Submit your work
and be part of a vibrant venue that will bring together an exciting
programme with internationally renowned keynote speakers, special
sessions, and workshops:

http://bdva.net

Visual Analytics plays a major role in the analysis and decision-making
processes for science, industry, and government organisations. Immersive
Analytics combines the well-established field of Visual Analytics with
Virtual and Augmented Reality to empower multi-sensory experiences.
Recent immersive technologies bring promising opportunities to interact
with Big Data, coming from geo-science, biomedical applications,
collective behaviour, text mining, crime analysis, among others.

Symposium topics include but are not limited to:
- Immersive Analytics
- Foundations of Immersive Analytics
- Immersive Storytelling
- Scalable Visual Analytics
- Volunteer Geographic Information
- Virtual and Augmented Reality for Analytics
- Visual Analytics of High-dimensional Data
- Big Data Management, Transformation, and Presentation
- Machine Learning and Data Mining for Big Data Visual Analytics
- Analytical Reasoning and Sense-making on Big Data
- Human-Computer Interaction on Big Data
- High Performance Computing for Visualisation
- Context-driven User Querying
- Semantics-driven Visual Analytics
 
** Submission Info **
Authors are invited to submit original and unpublished regular papers up
to 8 pages that report novel and mature work. Paper quality versus
length will be assessed based on a contribution-per-page judgment. The
symposium proceedings will be submitted for inclusion in IEEE Xplore. It
is a condition of publication that accepted papers are presented by one
of the authors. All accepted papers will be presented during the
symposium. Presenters must register before the camera-ready deadline to
avoid withdrawal from the symposium proceedings and programme. All
Submissions are due on 24 June 2018.

Your publicity and organising chairs,
Alfie Abdul-Rahman, Alexandra Diehl, Björn Sommer
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Re: [gmx-users] warning:Long Bond

[Saleheh Heidari]

Hi Justin

Thanks for your reply. As you said I checked the atom numbers which gave
the long bond warning, and there was no problem with the intra-residual
bonds in all the residues, but the warning was given for the inter-residual
bonds, i.e. the bond between the last atom of a residue and the first atom
of the next residue. I also checked the pdb file by visualizing it with VMD
and it looked correct. Should I continue and ignore the warnings assuming
that the structure returns to the proper conformation after minimization?

I would greatly appreciate your help.

Regards,

Saleheh Heydari



On Fri, Dec 22, 2017 at 3:22 AM, Justin Lemkul  wrote:

>
>
> On 12/21/17 12:09 PM, Saleheh Heidari wrote:
>
>> Dear Gromacs Users
>>
>> I am trying to run a molecular dynamics simulation with a DNA tetrahedron.
>> I am using Gromacs-2016.4 having the forcefield AMBER99SB-ILDN.
>>
>> The topology file has been successfully generated.
>>
>> However I am concerned with the following comment in the output of
>> pdb2gmx,
>> these are the gromacs output for the first chain:
>>
>> 
>> There are 4 chains and 0 blocks of water and 220 residues with 4497 atoms
>>
>>chain  #res #atoms
>>1 'A'55   1119
>>2 'B'55   1133
>>3 'C'55   1123
>>4 'D'55   1122
>>
>> All occupancies are one
>> Opening force field file
>> /usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp
>> Atomtype 67
>> Reading residue database... (amber99sb-ildn)
>> Opening force field file
>> /usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp
>> Residue 93
>> Sorting it all out...
>> Opening force field file
>> /usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/dna.rtp
>> Residue 109
>> Sorting it all out...
>> Opening force field file
>> /usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/rna.rtp
>> Residue 125
>> Sorting it all out...
>> Opening force field file
>> /usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb
>> Opening force field file
>> /usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/dna.hdb
>> Opening force field file
>> /usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/rna.hdb
>> Opening force field file
>> /usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/a
>> minoacids.n.tdb
>> Opening force field file
>> /usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/a
>> minoacids.c.tdb
>> Processing chain 1 'A' (1119 atoms, 55 residues)
>> Identified residue DT51 as a starting terminus.
>> Identified residue DT355 as a ending terminus.
>> 8 out of 8 lines of specbond.dat converted successfully
>> Opening force field file
>> /usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn
>> Opening force field file
>> /usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/dna.arn
>> Opening force field file
>> /usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/rna.arn
>> Checking for duplicate atoms
>> Generating any missing hydrogen atoms and/or adding termini.
>> Now there are 55 residues with 1747 atoms
>> Chain time...
>> Making bonds...
>> Warning: Long Bond (30-31 = 0.277244 nm)
>> Warning: Long Bond (62-63 = 0.306978 nm)
>> Warning: Long Bond (92-93 = 0.350789 nm)
>> Warning: Long Bond (124-125 = 0.320527 nm)
>> Warning: Long Bond (157-158 = 0.340453 nm)
>> Warning: Long Bond (189-190 = 0.273576 nm)
>> Warning: Long Bond (219-220 = 0.268338 nm)
>> Warning: Long Bond (251-252 = 0.277104 nm)
>> Warning: Long Bond (283-284 = 0.360828 nm)
>> Warning: Long Bond (315-316 = 0.320431 nm)
>> Warning: Long Bond (348-349 = 0.329925 nm)
>> Warning: Long Bond (381-382 = 0.334705 nm)
>> Warning: Long Bond (413-414 = 0.330311 nm)
>> Warning: Long Bond (477-478 = 0.354473 nm)
>> Warning: Long Bond (510-511 = 0.254489 nm)
>> Warning: Long Bond (542-543 = 0.659257 nm)
>> Warning: Long Bond (574-575 = 0.331438 nm)
>> Warning: Long Bond (606-607 = 0.757552 nm)
>> Warning: Long Bond (638-639 = 0.277172 nm)
>> Warning: Long Bond (670-671 = 0.307023 nm)
>> Warning: Long Bond (700-701 = 0.296372 nm)
>> Warning: Long Bond (730-731 = 0.296309 nm)
>> Warning: Long Bond (760-761 = 0.350757 nm)
>> Warning: Long Bond (792-793 = 0.273076 nm)
>> Warning: Long Bond (822-823 = 0.344508 nm)
>> Warning: Long Bond (855-856 = 0.25441 nm)
>> Warning: Long Bond (887-888 = 0.360906 nm)
>> Warning: Long Bond (919-920 = 0.320435 nm)
>> Warning: Long Bond (952-953 = 0.254546 nm)
>> Warning: Long Bond (984-985 = 0.35455 nm)
>> Warning: Long Bond (1017-1018 = 0.254603 nm)
>> Warning: Long Bond (1049-1050 = 0.307071 nm)
>> Warning: Long Bond (1079-1080 = 0.344648 nm)
>> Warning: Long Bond (1112-1113 = 0.254605 nm)
>> Warning: Long Bond (1144-1145 = 0.611147 nm)
>> Warning: Long Bond (1208-1209 = 0.514416 nm)
>> Warning: Long Bond (1241-1242 = 0.254576 nm)
>> Warning: Long Bond (1273-1274 = 0.360751 nm)
>> Warning: Long Bond (1337-1338 = 0.277311 nm)
>> Warning: Long Bond (1369-1370 = 

[gmx-users] Fwd: EULA clarification

[Erik Lindahl]

Hi,

Some of you might have seen the discuss about NVIDIA license changes
targeting commercial usage of GeForce cards in very large data centers.

We’ve talked a bit to NVIDIA over the holidays. They never had the
intention of targeting academic usage, but since I mentioned it was likely
very important to all of you that there is an on-the-record statement about
this, I’m very happy they came through quickly. This is an on-the-record
statement you can share.

Basically - all academic usage is fine.

Cheers,

Erik

-- 
Erik Lindahl 
Professor of Biophysics
Dept. Biochemistry & Biophysics, Stockholm University
Dept. Applied Physics, KTH Royal Institute of Technology
Science for Life Laboratory

On 3 January 2018 at 21:30:02, Mark Berger  wrote:

We have received inquiries asking whether GeForce and TITAN GPUs can be
used in academic servers. The answer is yes.

NVIDIA pioneered GPU computing with a vision of democratizing high
performance computing.
Our GPUs have become an important tool for scientists worldwide and we
support their use of GeForce and TITAN in non-commercial academic research.

Regards,
Mark Berger
Senior Alliance Manager, Life & Material Sciences
NVIDIA Corporation
---

This email message is for the sole use of the intended recipient(s) and may
contain
confidential information. Any unauthorized review, use, disclosure or
distribution
is prohibited. If you are not the intended recipient, please contact the
sender by
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[gmx-users] hydration free energy

[dgfd dgdfg]

Hi. I have calculated deltaG of hydration for my molecule in 101 steps. First 
50 steps I decoupled coulomb interactions and last 50 - vdw. After all I 
calculated resulting value by the command
gmx bar -f {0..100}/dhdl.xvg -o -oi -oh -b 500 >RESULT
and found such phrase in the output

Temperature: 300 K
Detailed results in kT (see help for explanation):
 lam_A  lam_B  DG   +/- s_A   +/- s_B   +/-   stdev   +/- 
 0  1    8.16  0.11    0.34  0.06    0.34  0.06    0.91  0.02
 1  2    7.61  0.07    0.21  0.08    0.19  0.07    0.86  0.01
...
...
...
    97 98   -0.40  0.02    0.42  0.02    0.55  0.02    0.97  0.01
    98 99   -2.11  0.03    1.16  0.03    1.84  0.06    1.75  0.03
    99    100  -17.55  0.43   13.60  0.44 62204236256674537472.00 
33302891096617504768.00  102.60 10.21
WARNING: Some of these results violate the Second Law of Thermodynamics: 
 This is can be the result of severe undersampling, or (more likely)
 there is something wrong with the simulations.

Please answer what is wrong in my simple algorythm. It is based on tutorial  
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html
 with some simplification. All necessary data attached.

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Re: [gmx-users] Trying to use AMBER parameters in GROMACS

[Crystal Vander Zanden]

Qinghua,

Thanks so much!  This worked beautifully!!!  I wish I had asked sooner
instead of struggling with these old broken codes.

I apologize for the accidental duplicate post that followed.

Thanks,
Crystal


>
> Message: 6
> Date: Wed, 3 Jan 2018 18:03:37 +0100
> From: Qinghua Liao 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] Trying to use AMBER parameters in GROMACS
> Message-ID: 
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Hello,
>
> You could try to build the system with AmberTools (it is free), choose
> the force fields available in Amber.
> Once you get the topology and coordinates files (prmtop and inpcrd), you
> can convert them into top and gro
> in Gromacs format with *parmed*. Then you can perform the simulations
> with Gromacs.
>
> import parmed as pmd
>
> #convert prmtop and inpcrd into top and gro
> amber = pmd.load_file('mol_sol.prmtop','mol_sol.inpcrd')
> #
> amber.save('mol_sol.top')
> amber.save('mol_sol.gro')
>
> You can google for more details.
>
>
> All the best,
> Qinghua
>
> On 01/03/2018 05:52 PM, Crystal Vander Zanden wrote:
> > Dear GROMACS Community,
> >
> > I am trying to parameterize my system using AMBER force fields, and then
> do
> > molecular dynamics with the GROMACS software.  I want to use the Lipid17
> > force field, which is not build into GROMACS.  Does anyone know of a way
> to
> > do this?
> >
> >
> > I have found 3 programs people have written to do this, but in short,
> none
> > of them work because the codes are too old (ca. 2003).
> >
> > 1) https://code.google.com/archive/p/amber2gmx/downloads
> > This would work, but it is written to use a command line parser package
> > that is too old and I can?t find (com.tsd.apps).
> >
> > 2) The amber2gmxrtp script build into GROMACS
> > This doesn?t work because it was written to take .in and .prep files
> (made
> > for the antiquated AMBER Prep program).  Those file types have been
> > replaced with .lib (made for Leap)
> >
> > 3)The amberconv.tgz package from the GROMACS website (
> > http://www.gromacs.org/Downloads/User_contributions/Other_software)
> > This was missing an include file when I tried to compile it.
> >
> >
> >
> > The reason for using AMBER force fields:  My system has lipids, protein,
> > and a small molecule - all of which can be well described with AMBER
> force
> > fields.  Since AMBER force fields are QM-based, it would be really easy
> to
> > parameterize the small molecule using Antechamber and low-level QM.
> > GROMACS force fields are empirically derived, so it will be much more
> > challenging to parameterize the small molecule in a way that?s consistent
> > with the rest of the force field for lipids and protein.  I plan on
> > simulating more small molecules in the future.
> >
> > I am hoping to use GROMACS because it's free, fast, and also not too
> > difficult to learn.
> >
> >
> > Thanks in advance for any advice you?re able to provide!!
> > Crystal
> >
>
>
>
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>
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> End of gromacs.org_gmx-users Digest, Vol 165, Issue 14
> **
>



-- 
Crystal M. Vander Zanden, Ph.D.
ASERT Postdoctoral Fellow (IRACDA)
University of New Mexico, Albuquerque
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Re: [gmx-users] ligand itp file doesn't have dihedral angles that including H atom

[Mark Abraham]

Hi,

They are presumably looked up from the parameters found normally in the
force field files.

Mark

On Wed, Jan 3, 2018 at 6:22 PM MD  wrote:

> Hi Gromacs folks,
>
> I noticed the topology file of ligand from atb site doesn't have dihedral
> angles that include H. Do you know how to create a itp file that has
> hydrogen included dihedral parameters?
>
> Thanks,
>
> Ming
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[gmx-users] Using AMBER parameters in GROMACS

[Crystal Vander Zanden]

Dear GROMACS Community,

I am trying to parameterize my system using AMBER force fields, and then do
molecular dynamics with the GROMACS software.  I want to use the Lipid17
force field, which is not build into GROMACS.  Does anyone know of a way to
do this?


I have found 3 programs people have written to do this, but in short, none
of them work because the codes are too old (ca. 2003).

1) https://code.google.com/archive/p/amber2gmx/downloads
This would work, but it is written to use a command line parser package
that is too old and I can’t find (com.tsd.apps).

2) The amber2gmxrtp script build into GROMACS
This doesn’t work because it was written to take .in and .prep files (made
for the antiquated AMBER Prep program).  Those file types have been
replaced with .lib (made for Leap)

3)The amberconv.tgz package from the GROMACS website (
http://www.gromacs.org/Downloads/User_contributions/Other_software)
This was missing an include file when I tried to compile it.



The reason for using AMBER force fields:  My system has lipids, protein,
and a small molecule - all of which can be well described with AMBER force
fields.  Since AMBER force fields are QM-based, it would be really easy to
parameterize the small molecule using Antechamber and low-level QM.
GROMACS force fields are empirically derived, so it will be much more
challenging to parameterize the small molecule in a way that’s consistent
with the rest of the force field for lipids and protein.  I plan on
simulating more small molecules in the future.

I am hoping to use GROMACS because it's free, fast, and also not too
difficult to learn.

Thanks in advance for any advice you’re able to provide!!
Crystal
-- 
Crystal M. Vander Zanden, Ph.D.
ASERT Postdoctoral Fellow (IRACDA)
University of New Mexico, Albuquerque
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[gmx-users] ligand itp file doesn't have dihedral angles that including H atom

[MD]

Hi Gromacs folks,

I noticed the topology file of ligand from atb site doesn't have dihedral
angles that include H. Do you know how to create a itp file that has
hydrogen included dihedral parameters?

Thanks,

Ming
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Re: [gmx-users] Trying to use AMBER parameters in GROMACS

[Qinghua Liao]

Hello,

You could try to build the system with AmberTools (it is free), choose 
the force fields available in Amber.
Once you get the topology and coordinates files (prmtop and inpcrd), you 
can convert them into top and gro
in Gromacs format with *parmed*. Then you can perform the simulations 
with Gromacs.


import parmed as pmd

#convert prmtop and inpcrd into top and gro
amber = pmd.load_file('mol_sol.prmtop','mol_sol.inpcrd')
#
amber.save('mol_sol.top')
amber.save('mol_sol.gro')

You can google for more details.


All the best,
Qinghua

On 01/03/2018 05:52 PM, Crystal Vander Zanden wrote:

Dear GROMACS Community,

I am trying to parameterize my system using AMBER force fields, and then do
molecular dynamics with the GROMACS software.  I want to use the Lipid17
force field, which is not build into GROMACS.  Does anyone know of a way to
do this?


I have found 3 programs people have written to do this, but in short, none
of them work because the codes are too old (ca. 2003).

1) https://code.google.com/archive/p/amber2gmx/downloads
This would work, but it is written to use a command line parser package
that is too old and I can’t find (com.tsd.apps).

2) The amber2gmxrtp script build into GROMACS
This doesn’t work because it was written to take .in and .prep files (made
for the antiquated AMBER Prep program).  Those file types have been
replaced with .lib (made for Leap)

3)The amberconv.tgz package from the GROMACS website (
http://www.gromacs.org/Downloads/User_contributions/Other_software)
This was missing an include file when I tried to compile it.



The reason for using AMBER force fields:  My system has lipids, protein,
and a small molecule - all of which can be well described with AMBER force
fields.  Since AMBER force fields are QM-based, it would be really easy to
parameterize the small molecule using Antechamber and low-level QM.
GROMACS force fields are empirically derived, so it will be much more
challenging to parameterize the small molecule in a way that’s consistent
with the rest of the force field for lipids and protein.  I plan on
simulating more small molecules in the future.

I am hoping to use GROMACS because it's free, fast, and also not too
difficult to learn.


Thanks in advance for any advice you’re able to provide!!
Crystal



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[gmx-users] Trying to use AMBER parameters in GROMACS

[Crystal Vander Zanden]

Dear GROMACS Community,

I am trying to parameterize my system using AMBER force fields, and then do
molecular dynamics with the GROMACS software.  I want to use the Lipid17
force field, which is not build into GROMACS.  Does anyone know of a way to
do this?


I have found 3 programs people have written to do this, but in short, none
of them work because the codes are too old (ca. 2003).

1) https://code.google.com/archive/p/amber2gmx/downloads
This would work, but it is written to use a command line parser package
that is too old and I can’t find (com.tsd.apps).

2) The amber2gmxrtp script build into GROMACS
This doesn’t work because it was written to take .in and .prep files (made
for the antiquated AMBER Prep program).  Those file types have been
replaced with .lib (made for Leap)

3)The amberconv.tgz package from the GROMACS website (
http://www.gromacs.org/Downloads/User_contributions/Other_software)
This was missing an include file when I tried to compile it.



The reason for using AMBER force fields:  My system has lipids, protein,
and a small molecule - all of which can be well described with AMBER force
fields.  Since AMBER force fields are QM-based, it would be really easy to
parameterize the small molecule using Antechamber and low-level QM.
GROMACS force fields are empirically derived, so it will be much more
challenging to parameterize the small molecule in a way that’s consistent
with the rest of the force field for lipids and protein.  I plan on
simulating more small molecules in the future.

I am hoping to use GROMACS because it's free, fast, and also not too
difficult to learn.


Thanks in advance for any advice you’re able to provide!!
Crystal

-- 
Crystal M. Vander Zanden, Ph.D.
ASERT Postdoctoral Fellow (IRACDA)
University of New Mexico, Albuquerque
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[gmx-users] regarding rdf

[Neha Gupta]

Hi,

I take the following steps to perform rdf calculation for my organic
molecule.

min, min2, eql, eql2 and prd.

In order to check, whether my molecule is intact, I generate .pdb of the
entire system after each step.

Till eql step, my molecule remains intact.

After eql2, the molecule breaks.


I make use of the following code for eql :

integrator   = md
dt   = 0.002 ; 2 fs
nsteps   = 50; 1.0 ns

nstenergy= 200
nstlog   = 2000
nstxout-compressed   = 1

continuation = yes
constraint-algorithm = lincs
constraints  = h-bonds

cutoff-scheme= Verlet

coulombtype  = PME
rcoulomb = 1.0

vdwtype  = Cut-off
rvdw = 1.0
DispCorr = EnerPres

tcoupl   = Nose-Hoover
tc-grps  = LIG  Water
tau-t= 2.0   2.0
ref-t= 298.15   298.15
nhchainlength= 1

pcoupl   = Parrinello-Rahman
tau_p= 2.0
compressibility  = 4.46e-5
ref_p= 1.0


How to fix it?

Thanks,
Neha
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[gmx-users] calculation of surface tension

[kordzadeh]

Hi all
I want to calculate surface  tension in lipid bilayer. I read manual and 
mailing list message and I have some question:
for calclation surface tension we should use Berendsen barostate with 
semiisotropic coupling , in mdp file:
; Pressure coupling is on
pcoupl = Berendsen ; Pressure coupling on in NPT
pcoupltype = semiisotropic ; uniform scaling of box vectors
tau_p =  2 ; time constant, in ps
ref_p = -100 1.0 ; reference pressure, in bar
compressibility = 4.5e-5  0 ; isothermal compressibility of 
water, bar^-1
How should  I find lateral pressure in xy plane? 
 we should set comressibility zero in Z direction, becase the length of box is 
constant, is that right? 
I read in this article 
Incorporation of Surface Tension into Molecular Dynamics Simulation of an 
Interface: A Fluid Phase Lipid Bilayer Membrane
lateral pressure is calculated by this:
boundary lateral pressure
= 1 - surface tension/55 A
= 1 - (56 dynes/cm)/55 X 10 - 8cm
= _-108 dynes/cm2
= - --100 atmospheres.
but in that equation I need surface tension, whereas  I want to calculate it.
should I run system under NPT condition and when the pressure converges ,I can 
calculate correctt surface tension?
does the pressure converge to 1 bar?
Any suggestion will be appreciated.
Thanks
Azadeh

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Re: [gmx-users] situation where ligand is connected to amino acid

[Justin Lemkul]

On 1/2/18 9:40 PM, Zheng Ruan wrote:

Hi Ming and Justin,

I have the same situation in which my protein has a cysteine residue
covalently linked to a drug. I'm regularly using amber99sb-ildn force
field. Is there existing tools that can help parameterize the modified
residue? Thank you!


Sure, antechamber, RED (PyRED) server, etc.

-Justin


Ruan

On Tue, Jan 2, 2018 at 8:04 PM, Justin Lemkul  wrote:



On 1/2/18 2:59 PM, MD wrote:


Hi Gromacs folks,

I want to simulation a protein complexed with a ligand. However, the
protein covalently bonded with the ligand via N-C bond. The ligand has a
size of 27 atoms. The solution I could think of now is to create a
modified
amino acid which includes both the amino acid side chain and the connected
ligand in rtp and make modifications in ffbonded.itp accordingly.

I wonder if there is another route to get this done?


Your approach is correct.

-Justin

--
==

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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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Assistant Professor
Virginia Tech Department of Biochemistry

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

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[gmx-users] RADIAL DISTRIBUTION FUNCTION

[Neha Gupta]

Hi,

I want to calculate radial distribution function for my organic molecule.

How to proceed?

How to write codes for RDF?

Thanks,
Neha
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Re: [gmx-users] Error while installing GROMACS-2018-rc1

[Yongchul Chung]

Well, celebrated too soon. I received the following error message during
"make check" step.



NOTE: The GPU has >25% less load than the CPU. This imbalance causes

  performance loss.


   Core t (s)   Wall t (s)(%)

   Time:0.0340.034  100.0

 (ns/day)(hour/ns)

Performance:   53.5840.448

Opened
/Users/ygchung/Desktop/codes/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr
as single precision energy file

Reading energy frame 20 time0.020 Reading file
/Users/ygchung/Desktop/codes/gromacs/build/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr,
VERSION 2018-rc1-dev-20180103-871f2f460-unknown (single precision)

Can not increase nstlist because an NVE ensemble is used

Using 1 MPI thread

1 GPU auto-selected for this run.

Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:

  PP:0

Compilation of source file
/Users/ygchung/Desktop/codes/gromacs/src/gromacs/mdlib/nbnxn_ocl/
nbnxn_ocl_kernels.cl failed!

-- Used build options: -DWARP_SIZE_TEST=64 -D_AMD_SOURCE_
-DGMX_OCL_FASTGEN_ADD_TWINCUT -DEL_EWALD_ANA -DEELNAME=_ElecEw
-DVDWNAME=_VdwLJ -DCENTRAL=22 -DNBNXN_GPU_NCLUSTER_PER_SUPERCLUSTER=8
-DNBNXN_GPU_CLUSTER_SIZE=8 -DNBNXN_GPU_JGROUP_SIZE=4
-DGMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY=4 -DNBNXN_MIN_RSQ=3.82e-07f
-DIATYPE_SHMEM -cl-fast-relaxed-math
-I/Users/ygchung/Desktop/codes/gromacs/src/gromacs/mdlib/nbnxn_ocl

--LOG START---

:80:10: fatal error: 'nbnxn_ocl_kernel_pruneonly.clh' file
not found

#include "nbnxn_ocl_kernel_pruneonly.clh"

 ^

---LOG END


---

Program: mdrun-test, version 2018-rc1-dev-20180103-871f2f460-unknown

Source file: src/gromacs/gpu_utils/ocl_compiler.cpp (line 502)

Function:cl_program gmx::ocl::compileProgram(FILE *, const std::string
&, const std::string &, cl_context, cl_device_id, ocl_vendor_id_t)


Internal error (bug):

Failed to compile NBNXN kernels for GPU #AMD Radeon Pro 560 Compute Engine

  Could not build OpenCL program, error was CL_BUILD_PROGRAM_FAILURE


For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors

---


  Start 33: MdrunMpiTests

33/39 Test #33: MdrunMpiTests    Passed2.69 sec

  Start 34: regressiontests/simple

34/39 Test #34: regressiontests/simple ...   Passed2.33 sec

  Start 35: regressiontests/complex

35/39 Test #35: regressiontests/complex ..   Passed   53.42 sec

  Start 36: regressiontests/kernel

36/39 Test #36: regressiontests/kernel ...   Passed   32.33 sec

  Start 37: regressiontests/freeenergy

37/39 Test #37: regressiontests/freeenergy ...   Passed5.70 sec

  Start 38: regressiontests/pdb2gmx

38/39 Test #38: regressiontests/pdb2gmx ..   Passed   15.66 sec

  Start 39: regressiontests/rotation

39/39 Test #39: regressiontests/rotation .   Passed3.10 sec


97% tests passed, 1 tests failed out of 39


Label Time Summary:

GTest  =  19.86 sec*proc (33 tests)

IntegrationTest=  18.38 sec*proc (3 tests)

MpiTest=   2.73 sec*proc (3 tests)

UnitTest   =   1.48 sec*proc (30 tests)


Total Test time (real) = 132.48 sec


The following tests FAILED:

32 - MdrunTests (Failed)

Errors while running CTest

make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8

make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2

make[1]: *** [CMakeFiles/check.dir/rule] Error 2

make: *** [check] Error 2




On Wed, Jan 3, 2018 at 7:42 PM, Yongchul Chung <ch...@northwestern.edu>
wrote:

> Thanks, I have successfully installed the release-2018 version of GROMACS
> on Macbook Pro 2017 HighSierra.
>
>
> On Tue, Jan 2, 2018 at 1:43 PM, Mark Abraham <mark.j.abra...@gmail.com>
> wrote:
>
>> Hi,
>>
>> Thanks, we have found and prepared a fix for an issue that looks very
>> similar (https://gerrit.gromacs.org/#/c/7400). Apparently the Mac OpenCL
>> compilation cannot tolerate any extra spaces in the command used to
>> compile
>> the kernels used on the device.
>>
>> You could either compile GROMACS without OpenCL support for now, or if you
>> would like to see if we have fixed the issue for you, that link enables
>> you
>> to download a tarball that contains the fix! We'd love to hear that it
>> works.
>>
>> Mark
>>
>> On Mon, Jan 1, 2018, 20:05 Yongchul Chung <ch...@northwestern.edu> wrote:
>>
>> > I am trying to install the latest GROMACS on Macbook Pro 2017 15-inch
>> (High
>> > Sierr

Re: [gmx-users] Error while installing GROMACS-2018-rc1

[Yongchul Chung]

Thanks, I have successfully installed the release-2018 version of GROMACS
on Macbook Pro 2017 HighSierra.


On Tue, Jan 2, 2018 at 1:43 PM, Mark Abraham 
wrote:

> Hi,
>
> Thanks, we have found and prepared a fix for an issue that looks very
> similar (https://gerrit.gromacs.org/#/c/7400). Apparently the Mac OpenCL
> compilation cannot tolerate any extra spaces in the command used to compile
> the kernels used on the device.
>
> You could either compile GROMACS without OpenCL support for now, or if you
> would like to see if we have fixed the issue for you, that link enables you
> to download a tarball that contains the fix! We'd love to hear that it
> works.
>
> Mark
>
> On Mon, Jan 1, 2018, 20:05 Yongchul Chung  wrote:
>
> > I am trying to install the latest GROMACS on Macbook Pro 2017 15-inch
> (High
> > Sierra) and got the following error message when issuing "make" command
> > during the installation steps.
> >
> > My command for cmake was: cmake .. -DGMX_BUILD_OWN_FFTW=ON
> > -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON -DGMX_USE_OPENCL=ON
> >
> > Thanks in advance for the help.
> >
> > [ 91%] Building CXX object
> >
> > src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_
> ocl/nbnxn_ocl_data_mgmt.cpp.o
> >
> > In file included from
> >
> > /Users/ygchung/Desktop/codes/gromacs-2018-rc1/src/gromacs/
> mdlib/nbnxn_ocl/nbnxn_ocl_data_mgmt.cpp:54:
> >
> > In file included from
> >
> > /Users/ygchung/Desktop/codes/gromacs-2018-rc1/src/gromacs/
> gpu_utils/oclutils.h:46:
> >
> > In file included from
> >
> > /Users/ygchung/Desktop/codes/gromacs-2018-rc1/src/gromacs/
> gpu_utils/gmxopencl.h:61:
> >
> > In file included from
> > /System/Library/Frameworks/OpenCL.framework/Headers/opencl.h:16:
> >
> > In file included from
> > /System/Library/Frameworks/OpenCL.framework/Headers/gcl.h:23:
> >
> > */usr/include/dispatch/dispatch.h:38:45: **error: **expected value in
> > expression*
> >
> > #if !defined(HAVE_UNISTD_H) || HAVE_UNISTD_H
> >
> > *^*
> >
> > 1 error generated.
> >
> > make[2]: ***
> >
> > [src/gromacs/CMakeFiles/libgromacs.dir/mdlib/nbnxn_
> ocl/nbnxn_ocl_data_mgmt.cpp.o]
> > Error 1
> >
> > make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> >
> > make: *** [all] Error 2
> > --
> > Gromacs Users mailing list
> >
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> >
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