[gmx-users] Sulfate ion parameters

[#SUKRITI GUPTA#]

Dear gromacs users,


I wanted to simulate sulphate ions in water using oplsaa force field but I 
couldn't find parameters for sulphur and oxygen atoms of sulphate ions in the 
oplsaa force field files. Can anyone suggest from where can I get these 
parameters?


Charmm force field has the parameters for sulphate ions, so is it possible to 
use those parameters itself for simulations? Also the partial charges given in 
charmm force field to S and O of sulphate ions do not add up to -2. (S +1.33, O 
-0.78) So how to select the correct partial charges here?


Thanks and Regards

Sukriti


[https://sixprd0111.outlook.com/owa/service.svc/s/GetFileAttachment?id=AAMkADNjYmY4NDc0LTVjMzUtNDNmOC1hYzdkLTU5NTZhODkwYjVhNwBGAACBUPJnHBz9Qb1jEGoiHu01BwCW%2B40K8EMKR52f2bViS6X0NaBFAAC1PvQTaUN0S5CzEDGS8lwUAAIr8o3VAAABEgAQAIhFug57qj9Lg6WQKih11Lg%3D=h9cz1GMp80awqK7uWU0tmwAfbhpQFtMYCkfwOWcjFqjCjKA5rnYYMRF4FV7Oec3YWfk_SWGzz4s.=3]

Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | 
Nanyang Technological University
N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798
Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | 
Web:erian.ntu.edu.sg



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[gmx-users] modeling CNT, center of mass velocity, energy minimization

[mohammad r]

Hi GROMACS users,


  I have some questions:  1-  Can I model a carbonnanotube (CNT) 
conveying fluid in GROMACS subjected to a magnetic field?2-  How can I 
check the centerof mass velocity of my system?3-  I want to calculate 
volumeand water self diffusion coefficient for 1ns, can the energy 
minimizationprocess do it? Or the equilibrium processes can do it? I want to 
draw theparameters versus time.  Thank you, Mohammad.

  
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[gmx-users] recompile gromacs 5.0.7

[Mehreen Jan]

Respected sir!
Thanks for your  response

I recompile my system(gromacs5.0.7) but the error remain same.
looking for your response to solve this issue.

thank you one again






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Re: [gmx-users] pdb2gmx generate .itp file for each molecule

[Ming Tang]

Hi ,

Maybe you can try -merge all when using pdb2gmx.
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[gmx-users] pdb2gmx generate .itp file for each molecule

[Ray Chao]

​Hi, gmx users,

I used materials studio to generate a .pdb file containing 160 PTFE chains,
and then modified the oplsaa  forcefiled as Justin did. The pdb2gmx
generated right .gro and .top files. But the problem is that it generated
one .itp file for each molecule. Since there are 160 identical molecules in
the .pdb file, each .itp file is exactly the same except that it named the
molecules as "Other", "Other2",...,"Other160". So is there any way to tell
gromacs that there are actually 160 identical molecules in the .pdb file?

Thank you so much.
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[gmx-users] Question about WHAM

[Supriyo Bhattacharya]

Hello,This question is more about the WHAM technique in general, but I take the 
liberty to ask it in this forum, hoping somebody can point me in the right 
direction.
I am calculating the free energy difference between two wells separated by an 
energy barrier using an umbrella potential restraining an inter-residue 
distance.
After running the umbrella sampling, I find that some of the histograms have 
shifted to some extent from their intended positions, with the peak shifted 
from the restraining distance value. This happens close to the barrier region. 
So, I have sampled the barrier region separately with a stronger umbrella 
potential to prevent the 'slippage'.
Now my questions are:1. Can I mix two different umbrella potentials for two 
different regions (well and barrier) in gmx wham?
2. Would it be wrong to include those simulations where the histograms shifted 
from the restraining distance in the WHAM calculations?
Many thanks in advance,Supriyo
p.s. If something is unclear in my posting, please let me know and I will try 
to clarify as much as possible.
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Re: [gmx-users] protein atoms with alternate conformations

[Irem Altan]

Thanks :)

In case anyone else wonders, the highest occupancy atom is taken.

Irem

> On Feb 23, 2016, at 3:04 PM, Mark Abraham  wrote:
> 
> Hi,
> 
> Swap them and see :-)
> 
> Mark
> 
> On Tue, 23 Feb 2016 20:55 Irem Altan  wrote:
> 
>> Hi,
>> 
>> I have a protein that contains atoms with alternate conformations:
>> 
>> ATOM856  SG ACYS A 217   7.649  52.725  28.525  0.58 12.64
>>   S
>> ATOM859  SG BCYS A 217   7.282  54.809  26.839  0.42 15.97
>>   S
>> 
>> How does pdb2gmx handle this? I checked the .gro file to see that SG ACYS
>> was chosen (judging by the coordinates). Is it because it has a slightly
>> higher occupancy or because it appears first?
>> 
>> Best,
>> Irem
>> 
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Re: [gmx-users] protein atoms with alternate conformations

[Mark Abraham]

Hi,

Swap them and see :-)

Mark

On Tue, 23 Feb 2016 20:55 Irem Altan  wrote:

> Hi,
>
> I have a protein that contains atoms with alternate conformations:
>
> ATOM856  SG ACYS A 217   7.649  52.725  28.525  0.58 12.64
>S
> ATOM859  SG BCYS A 217   7.282  54.809  26.839  0.42 15.97
>S
>
> How does pdb2gmx handle this? I checked the .gro file to see that SG ACYS
> was chosen (judging by the coordinates). Is it because it has a slightly
> higher occupancy or because it appears first?
>
> Best,
> Irem
>
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[gmx-users] protein atoms with alternate conformations

[Irem Altan]

Hi,

I have a protein that contains atoms with alternate conformations:

ATOM856  SG ACYS A 217   7.649  52.725  28.525  0.58 12.64   S
ATOM859  SG BCYS A 217   7.282  54.809  26.839  0.42 15.97   S

How does pdb2gmx handle this? I checked the .gro file to see that SG ACYS was 
chosen (judging by the coordinates). Is it because it has a slightly higher 
occupancy or because it appears first?

Best,
Irem

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Re: [gmx-users] Protein-ligand system simulations with GROMACS

[Dries Van Rompaey]

Hi,

These questions are quite specific to your problem. There's no way we can
predict what equilibration time will suffice for your system. Your
simulation time also depends on what the aim of your simulations is and
what you hope to observe. That said, current simulations are generally a
couple of hundred nanoseconds in length. Keep in mind that it's probably
best to perform several simulations - one simulation will only tell you so
much. Repeatability of your observations is important.

You might want to consider using a dodecahedron rather than a cubic box -
the cubic box will require more water molecules to fill completely. As for
the parameters, read the literature. A good starting point is the paper
describing the amber99sb ildn parametrisation. It's also a good idea to
check what parameters have been described in the literature by people
performing similar simulations.

Good luck!
On 23 Feb 2016 8:39 p.m., "Guillem Prats Ejarque" <
guillem.prats.ejar...@uab.cat> wrote:

> Dear colleagues,
>
> I'm starting to use GROMACS and I'm simulating a system between an RNA
> binding protein and a small RNA ligand (a dinucleotide, ~60 atoms) in a
> cubic box. I set  AMBER99SB-ILDN protein, nucleic AMBER94 as a forcefield,
> with a tip3p water model.
>
> This was only to put you in context. My question is, which parameters
> should I take into account with my system during the production run? Which
> should be the duration of the run? And what about the equilibration?
>
> Thanks a lot for your attention,
>
> Guillem
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[gmx-users] Protein-ligand system simulations with GROMACS

[Guillem Prats Ejarque]

Dear colleagues,

I'm starting to use GROMACS and I'm simulating a system between an RNA binding 
protein and a small RNA ligand (a dinucleotide, ~60 atoms) in a cubic box. I 
set  AMBER99SB-ILDN protein, nucleic AMBER94 as a forcefield, with a tip3p 
water model.

This was only to put you in context. My question is, which parameters should I 
take into account with my system during the production run? Which should be the 
duration of the run? And what about the equilibration?

Thanks a lot for your attention,

Guillem
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Re: [gmx-users] Segmentation fault during equilibration

[Mark Abraham]

Hi,

As normal, even for coarse-grained simulations, equilibration may require
bigger rearrangements for some starting conditions than others. The usual
advice for http://www.gromacs.org/Documentation/Terminology/Blowing_Up still
applies - particularly to try smaller time steps while relaxing what might
be large forces.

You could also compile better to suit this machine and get higher
performance ;-)

Mark

On Tue, Feb 23, 2016 at 5:06 PM Yasser Almeida <
yasser.almeida.hernan...@chemie.uni-hamburg.de> wrote:

> Hi all,
>
> I am running an equilibration of a membrane/protein coarse grained
> system and got this Segmentation fault error.
>
> ---
> Reading file equilibration.protein_DPPC.tpr, VERSION 4.6.5 (single
> precision)
> Using 8 MPI threads
> Compiled acceleration: SSE4.1 (Gromacs could use AVX_256 on this
> machine, which is better)
> starting mdrun 'Protein in INSANE! Membrane UpperLeaflet>DPPC=1
> LowerLeaflet>DPPC=1'
> 25000 steps,500.0 ps.
> step 0
> Step 3, time 0.06 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.01, max 0.03 (between atoms 204 and 205)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>   30 31   32.70.1950   0.1950  0.1950
>
> Step 4, time 0.08 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 195678.573993, max 1044637.687500 (between atoms 30 and 31)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>   30 31   90.00.1950 203704.5469  0.1950
> Wrote pdb files with previous and current coordinates
> Segmentation fault (core dumped)
> ---
>
> This is the mdp file:
> ---
> dt =  0.02
> nsteps   =  25000
> nstxout  =  0
> nstvout  =  0
> nstlog   =  100
> nstxtcout =  100
> xtc-precision =  100
> rlist =  1.4
> coulombtype =  shift
> rcoulomb =  1.2
> epsilon_r =  15
> vdw-type =  shift
> rvdw-switch =  0.9
> rvdw =  1.2
> tcoupl   =  v-rescale
> tc-grps  =  Protein_DPPC W_Ion
> tau-t =  1.0 1.0
> ref-t =  323 323
> Pcoupl   =  berendsen
> Pcoupltype =  semiisotropic
> tau-p =  10.0 10.0
> compressibility  =  3e-4 3e-4
> ref-p =  1.0 1.0
> refcoord_scaling =  com
> ---
>
> I've used this settings before with similar protein/membrane systems
> without problem.
>
> Any thoughts?
> Thanks in advance
>
> Yasser
>
> --
> Yasser Almeida Hernández
> PhD student
> Institute of Biochemistry and Molecular Biology
> Department of Chemistry
> University of Hamburg
> Martin-Luther-King-Platz 6
> 20146 Hamburg
> Germany
> +49 40 42838 2845
> yasser.almeida.hernan...@chemie.uni-hamburg.de
> office: Grindelallee 117, room 250c
>
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[gmx-users] Segmentation fault during equilibration

[Yasser Almeida]

Hi all,

I am running an equilibration of a membrane/protein coarse grained 
system and got this Segmentation fault error.


---
Reading file equilibration.protein_DPPC.tpr, VERSION 4.6.5 (single 
precision)

Using 8 MPI threads
Compiled acceleration: SSE4.1 (Gromacs could use AVX_256 on this 
machine, which is better)
starting mdrun 'Protein in INSANE! Membrane UpperLeaflet>DPPC=1 
LowerLeaflet>DPPC=1'

25000 steps,500.0 ps.
step 0
Step 3, time 0.06 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.01, max 0.03 (between atoms 204 and 205)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 30 31   32.70.1950   0.1950  0.1950

Step 4, time 0.08 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 195678.573993, max 1044637.687500 (between atoms 30 and 31)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
 30 31   90.00.1950 203704.5469  0.1950
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)
---

This is the mdp file:
---
dt =  0.02
nsteps   =  25000
nstxout  =  0
nstvout  =  0
nstlog   =  100
nstxtcout =  100
xtc-precision =  100
rlist =  1.4
coulombtype =  shift
rcoulomb =  1.2
epsilon_r =  15
vdw-type =  shift
rvdw-switch =  0.9
rvdw =  1.2
tcoupl   =  v-rescale
tc-grps  =  Protein_DPPC W_Ion
tau-t =  1.0 1.0
ref-t =  323 323
Pcoupl   =  berendsen
Pcoupltype =  semiisotropic
tau-p =  10.0 10.0
compressibility  =  3e-4 3e-4
ref-p =  1.0 1.0
refcoord_scaling =  com
---

I've used this settings before with similar protein/membrane systems 
without problem.


Any thoughts?
Thanks in advance

Yasser

--
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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Re: [gmx-users] Huge conformational change of ATP molecules

[Mark Abraham]

Hi,

Indeed that seems to short. So if one has excluded natural processes, the
artificial ones remain the only possible ones... Your process does have to
include a custom index group, for example... see
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Mark

On Tue, Feb 23, 2016 at 4:56 PM Zheng Ruan  wrote:

> Hi Mark,
>
> Thank you for the suggestions, but I don't think it is because of the PBC
> artifacts. I do centered my protein and ligand with  "-center -pbc mol"
> option. The protein itself looks fine without any breaking. It's just the
> ATP that moves out and stays at the outer surface of the protein. I don't
> think it's possible in such a short time scale (20ns).
>
> Best,
> Ruan
>
> On Tue, Feb 23, 2016 at 4:32 AM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > It sounds like you are observing artefacts from
> >
> >
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
> >
> > Mark
> >
> > On Tue, Feb 23, 2016 at 6:18 AM Zheng Ruan  wrote:
> >
> > > Hi Gromacs Users,
> > >
> > > I'm running 20ns MD simulation of a protein kinase with ATP bond. I use
> > > amber99sb-ildn force field with parameters of ATP derived from the
> > database
> > > of Richard Bryce.
> > >
> > > What surprised me is that the ATP molecules displays a huge flexibility
> > and
> > > conformational change. First, it slipped out from the starting binding
> > > pocket. In addition, the plane of adenine ring and ribose sugar rotate
> to
> > > about 180 degree after 10ns, making the ATP molecule looks weird. I
> never
> > > run a MD of a protein with ligand before. Is this something normal?
> What
> > > are possible causes for this? Maybe I should try some other ATP protein
> > > complex to see if the same thing happens? Thank you!
> > >
> > > Ruan
> > > --
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Re: [gmx-users] Huge conformational change of ATP molecules

[Zheng Ruan]

Hi Mark,

Thank you for the suggestions, but I don't think it is because of the PBC
artifacts. I do centered my protein and ligand with  "-center -pbc mol"
option. The protein itself looks fine without any breaking. It's just the
ATP that moves out and stays at the outer surface of the protein. I don't
think it's possible in such a short time scale (20ns).

Best,
Ruan

On Tue, Feb 23, 2016 at 4:32 AM, Mark Abraham 
wrote:

> Hi,
>
> It sounds like you are observing artefacts from
>
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
>
> Mark
>
> On Tue, Feb 23, 2016 at 6:18 AM Zheng Ruan  wrote:
>
> > Hi Gromacs Users,
> >
> > I'm running 20ns MD simulation of a protein kinase with ATP bond. I use
> > amber99sb-ildn force field with parameters of ATP derived from the
> database
> > of Richard Bryce.
> >
> > What surprised me is that the ATP molecules displays a huge flexibility
> and
> > conformational change. First, it slipped out from the starting binding
> > pocket. In addition, the plane of adenine ring and ribose sugar rotate to
> > about 180 degree after 10ns, making the ATP molecule looks weird. I never
> > run a MD of a protein with ligand before. Is this something normal? What
> > are possible causes for this? Maybe I should try some other ATP protein
> > complex to see if the same thing happens? Thank you!
> >
> > Ruan
> > --
> > 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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>
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Re: [gmx-users] confusion on energy for a system of protein sovated in water

[Justin Lemkul]

On 2/22/16 10:03 PM, Ming Tang wrote:

Thanks Justin,

How about LJ and Coulomb  energy?

I want to see the trend of protein energy only. I defined 2 energy group: 
protein and SOL in .mdp file. Then, I saw LJ and Coulomb: protein-ptrotein 
option when using g_energy. Are they VDW and Coulomb force within the protein 
only?



The "protein energy" usually tells you nothing.  Unless you're doing a more 
rigorous calculation like MM/PBSA, I wouldn't try to base anything off of these 
quantities.  They're not free energies and they're totally force field-dependent 
results.  From your previous post, I'm assuming you're using GROMOS96, which, 
while parametrized against free energies of solvation, does not guarantee that 
such short-range interaction energies actually correspond to something 
physically useful (unlike, e.g. CHARMM, which is directly parametrized against 
QM water interaction energies).


-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] gmx sasa versus g_sas

[Justin Lemkul]

On 2/23/16 9:45 AM, Sara Del Galdo wrote:

Hi Gromacs users,

I am using gromacs tool g_sas to calculate protein excluded volumes and I
noticed that it provides significant different excluded volume values when
compared to the new version gmx sasa tool. Does anyone know the reason of
this and which of the two tool is more reliable?


As I recall, gmx sasa prints a prominent warning about the changes that have 
been made to the program with respect to atomic radii.  That should explain 
everything :)


-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] gmx sasa versus g_sas

[Sara Del Galdo]

Hi Gromacs users,

I am using gromacs tool g_sas to calculate protein excluded volumes and I
noticed that it provides significant different excluded volume values when
compared to the new version gmx sasa tool. Does anyone know the reason of
this and which of the two tool is more reliable?
Thanks in advance.

Sara
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Re: [gmx-users] Regarding installation problem

[Mark Abraham]

Hi,

That's still going to need an updated binutils, though.

Mark

On Tue, Feb 23, 2016 at 3:40 PM Szilárd Páll  wrote:

> AVX is supported even by gcc 4.4.7 (although admittedly I'm not sure if
> it's functional), so you may want to try -DGMX_SIMD=AVX_256, that will
> waste your hardware a bit less.
>
> --
> Szilárd
>
> On Tue, Feb 23, 2016 at 3:02 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > You can probably use any GROMACS version, if you want it to run slowly
> and
> > generate less science for you. Just use cmake -DGMX_SIMD=SSE4.1.
> >
> > Mark
> >
> > On Tue, Feb 23, 2016 at 2:47 PM SOUVIK MONDAL 
> > wrote:
> >
> > > Which version of gromacs will be suitable for gcc version 4.4.7?
> > >
> > >
> > >
> > > - Original Message -
> > > From: "Mark Abraham" 
> > > To: gmx-us...@gromacs.org
> > > Sent: Tuesday, February 23, 2016 6:05:13 PM
> > > Subject: Re: [gmx-users] Regarding installation problem
> > >
> > > Hi,
> > >
> > > The simplest thing is to get the latest version of gcc that your
> > operating
> > > system (e.g. Linux distribution) supports. Sadly, people often sell
> > compute
> > > systems based on "mature, stable, reliable" versions of software, but
> > with
> > > modern hardware, which automatically means that everything is out of
> date
> > > and their users have to do all of this useless work. But do talk to
> your
> > > system administrators to get some up to date tools installed for you.
> > >
> > > Mark
> > >
> > > On Tue, Feb 23, 2016 at 12:55 PM SOUVIK MONDAL 
> > > wrote:
> > >
> > > > Can u tell what are compilers I need to up-to-date?
> > > >
> > > > - Original Message -
> > > > From: "Mark Abraham" 
> > > > To: gmx-us...@gromacs.org
> > > > Sent: Tuesday, February 23, 2016 4:50:52 PM
> > > > Subject: Re: [gmx-users] Regarding installation problem
> > > >
> > > > Hi,
> > > >
> > > > On Tue, Feb 23, 2016 at 11:54 AM SOUVIK MONDAL <
> m.sou...@iitkgp.ac.in>
> > > > wrote:
> > > >
> > > > > After doing cmake .. -DGMX_BUILD_OWN_FFTW=ON
> > > -DREGRESSIONTEST_DOWNLOAD=ON
> > > > > the output in that ternimal comes as follows
> > > > >
> > > > > - The C compiler identification is GNU 4.4.7
> > > > > -- The CXX compiler identification is GNU 4.4.7
> > > > >
> > > >
> > > > This compiler version was designed several years before your hardware
> > > model
> > > > was released, so it will not work very well. Please get an up-to-date
> > > > compiler for your distribution, as the install guide suggests :-)
> > > >
> > > > -- Check for working C compiler: /usr/bin/cc
> > > > > -- Check for working C compiler: /usr/bin/cc -- works
> > > > > -- Detecting C compiler ABI info
> > > > > -- Detecting C compiler ABI info - done
> > > > > -- Detecting C compile features
> > > > > -- Detecting C compile features - done
> > > > > -- Check for working CXX compiler: /usr/bin/c++
> > > > > -- Check for working CXX compiler: /usr/bin/c++ -- works
> > > > > -- Detecting CXX compiler ABI info
> > > > > -- Detecting CXX compiler ABI info - done
> > > > > -- Detecting CXX compile features
> > > > > -- Detecting CXX compile features - done
> > > > > -- Looking for NVIDIA GPUs present in the system
> > > > > -- Could not detect NVIDIA GPUs
> > > > > -- No compatible CUDA toolkit found (v4.0+), disabling native GPU
> > > > > acceleration
> > > > > -- Checking for GCC x86 inline asm
> > > > > -- Checking for GCC x86 inline asm - supported
> > > > > -- Detecting best SIMD instructions for this CPU
> > > > > -- Detected best SIMD instructions for this CPU - AVX2_256
> > > > > -- Try OpenMP C flag = [-fopenmp]
> > > > > -- Performing Test OpenMP_FLAG_DETECTED
> > > > > -- Performing Test OpenMP_FLAG_DETECTED - Success
> > > > > -- Try OpenMP CXX flag = [-fopenmp]
> > > > > -- Performing Test OpenMP_FLAG_DETECTED
> > > > > -- Performing Test OpenMP_FLAG_DETECTED - Success
> > > > > -- Found OpenMP: -fopenmp
> > > > > -- Performing Test CFLAGS_WARN
> > > > > -- Performing Test CFLAGS_WARN - Success
> > > > > -- Performing Test CFLAGS_WARN_EXTRA
> > > > > -- Performing Test CFLAGS_WARN_EXTRA - Success
> > > > > -- Performing Test CFLAGS_WARN_UNDEF
> > > > > -- Performing Test CFLAGS_WARN_UNDEF - Success
> > > > > -- Performing Test CFLAGS_WARN_REL
> > > > > -- Performing Test CFLAGS_WARN_REL - Success
> > > > > -- Performing Test CFLAGS_EXCESS_PREC
> > > > > -- Performing Test CFLAGS_EXCESS_PREC - Failed
> > > > > -- Performing Test CFLAGS_COPT
> > > > > -- Performing Test CFLAGS_COPT - Success
> > > > > -- Performing Test CFLAGS_NOINLINE
> > > > > -- Performing Test CFLAGS_NOINLINE - Success
> > > > > -- Performing Test CXXFLAGS_WARN
> > > > > -- Performing Test CXXFLAGS_WARN - Success
> > > > > -- Performing Test CXXFLAGS_WARN_EXTRA
> > > > > -- Performing Test CXXFLAGS_WARN_EXTRA - Success
> > > > > -- Performing Test CXXFLAGS_WARN_UNDEF
> > > > > -- 

Re: [gmx-users] Regarding installation problem

[Szilárd Páll]

AVX is supported even by gcc 4.4.7 (although admittedly I'm not sure if
it's functional), so you may want to try -DGMX_SIMD=AVX_256, that will
waste your hardware a bit less.

--
Szilárd

On Tue, Feb 23, 2016 at 3:02 PM, Mark Abraham 
wrote:

> Hi,
>
> You can probably use any GROMACS version, if you want it to run slowly and
> generate less science for you. Just use cmake -DGMX_SIMD=SSE4.1.
>
> Mark
>
> On Tue, Feb 23, 2016 at 2:47 PM SOUVIK MONDAL 
> wrote:
>
> > Which version of gromacs will be suitable for gcc version 4.4.7?
> >
> >
> >
> > - Original Message -
> > From: "Mark Abraham" 
> > To: gmx-us...@gromacs.org
> > Sent: Tuesday, February 23, 2016 6:05:13 PM
> > Subject: Re: [gmx-users] Regarding installation problem
> >
> > Hi,
> >
> > The simplest thing is to get the latest version of gcc that your
> operating
> > system (e.g. Linux distribution) supports. Sadly, people often sell
> compute
> > systems based on "mature, stable, reliable" versions of software, but
> with
> > modern hardware, which automatically means that everything is out of date
> > and their users have to do all of this useless work. But do talk to your
> > system administrators to get some up to date tools installed for you.
> >
> > Mark
> >
> > On Tue, Feb 23, 2016 at 12:55 PM SOUVIK MONDAL 
> > wrote:
> >
> > > Can u tell what are compilers I need to up-to-date?
> > >
> > > - Original Message -
> > > From: "Mark Abraham" 
> > > To: gmx-us...@gromacs.org
> > > Sent: Tuesday, February 23, 2016 4:50:52 PM
> > > Subject: Re: [gmx-users] Regarding installation problem
> > >
> > > Hi,
> > >
> > > On Tue, Feb 23, 2016 at 11:54 AM SOUVIK MONDAL 
> > > wrote:
> > >
> > > > After doing cmake .. -DGMX_BUILD_OWN_FFTW=ON
> > -DREGRESSIONTEST_DOWNLOAD=ON
> > > > the output in that ternimal comes as follows
> > > >
> > > > - The C compiler identification is GNU 4.4.7
> > > > -- The CXX compiler identification is GNU 4.4.7
> > > >
> > >
> > > This compiler version was designed several years before your hardware
> > model
> > > was released, so it will not work very well. Please get an up-to-date
> > > compiler for your distribution, as the install guide suggests :-)
> > >
> > > -- Check for working C compiler: /usr/bin/cc
> > > > -- Check for working C compiler: /usr/bin/cc -- works
> > > > -- Detecting C compiler ABI info
> > > > -- Detecting C compiler ABI info - done
> > > > -- Detecting C compile features
> > > > -- Detecting C compile features - done
> > > > -- Check for working CXX compiler: /usr/bin/c++
> > > > -- Check for working CXX compiler: /usr/bin/c++ -- works
> > > > -- Detecting CXX compiler ABI info
> > > > -- Detecting CXX compiler ABI info - done
> > > > -- Detecting CXX compile features
> > > > -- Detecting CXX compile features - done
> > > > -- Looking for NVIDIA GPUs present in the system
> > > > -- Could not detect NVIDIA GPUs
> > > > -- No compatible CUDA toolkit found (v4.0+), disabling native GPU
> > > > acceleration
> > > > -- Checking for GCC x86 inline asm
> > > > -- Checking for GCC x86 inline asm - supported
> > > > -- Detecting best SIMD instructions for this CPU
> > > > -- Detected best SIMD instructions for this CPU - AVX2_256
> > > > -- Try OpenMP C flag = [-fopenmp]
> > > > -- Performing Test OpenMP_FLAG_DETECTED
> > > > -- Performing Test OpenMP_FLAG_DETECTED - Success
> > > > -- Try OpenMP CXX flag = [-fopenmp]
> > > > -- Performing Test OpenMP_FLAG_DETECTED
> > > > -- Performing Test OpenMP_FLAG_DETECTED - Success
> > > > -- Found OpenMP: -fopenmp
> > > > -- Performing Test CFLAGS_WARN
> > > > -- Performing Test CFLAGS_WARN - Success
> > > > -- Performing Test CFLAGS_WARN_EXTRA
> > > > -- Performing Test CFLAGS_WARN_EXTRA - Success
> > > > -- Performing Test CFLAGS_WARN_UNDEF
> > > > -- Performing Test CFLAGS_WARN_UNDEF - Success
> > > > -- Performing Test CFLAGS_WARN_REL
> > > > -- Performing Test CFLAGS_WARN_REL - Success
> > > > -- Performing Test CFLAGS_EXCESS_PREC
> > > > -- Performing Test CFLAGS_EXCESS_PREC - Failed
> > > > -- Performing Test CFLAGS_COPT
> > > > -- Performing Test CFLAGS_COPT - Success
> > > > -- Performing Test CFLAGS_NOINLINE
> > > > -- Performing Test CFLAGS_NOINLINE - Success
> > > > -- Performing Test CXXFLAGS_WARN
> > > > -- Performing Test CXXFLAGS_WARN - Success
> > > > -- Performing Test CXXFLAGS_WARN_EXTRA
> > > > -- Performing Test CXXFLAGS_WARN_EXTRA - Success
> > > > -- Performing Test CXXFLAGS_WARN_UNDEF
> > > > -- Performing Test CXXFLAGS_WARN_UNDEF - Success
> > > > -- Performing Test CXXFLAGS_WARN_REL
> > > > -- Performing Test CXXFLAGS_WARN_REL - Success
> > > > -- Performing Test CXXFLAGS_EXCESS_PREC
> > > > -- Performing Test CXXFLAGS_EXCESS_PREC - Failed
> > > > -- Performing Test CXXFLAGS_COPT
> > > > -- Performing Test CXXFLAGS_COPT - Success
> > > > -- Performing Test CXXFLAGS_NOINLINE
> > > > 

Re: [gmx-users] Regarding installation problem

[Mark Abraham]

Hi,

You can probably use any GROMACS version, if you want it to run slowly and
generate less science for you. Just use cmake -DGMX_SIMD=SSE4.1.

Mark

On Tue, Feb 23, 2016 at 2:47 PM SOUVIK MONDAL  wrote:

> Which version of gromacs will be suitable for gcc version 4.4.7?
>
>
>
> - Original Message -
> From: "Mark Abraham" 
> To: gmx-us...@gromacs.org
> Sent: Tuesday, February 23, 2016 6:05:13 PM
> Subject: Re: [gmx-users] Regarding installation problem
>
> Hi,
>
> The simplest thing is to get the latest version of gcc that your operating
> system (e.g. Linux distribution) supports. Sadly, people often sell compute
> systems based on "mature, stable, reliable" versions of software, but with
> modern hardware, which automatically means that everything is out of date
> and their users have to do all of this useless work. But do talk to your
> system administrators to get some up to date tools installed for you.
>
> Mark
>
> On Tue, Feb 23, 2016 at 12:55 PM SOUVIK MONDAL 
> wrote:
>
> > Can u tell what are compilers I need to up-to-date?
> >
> > - Original Message -
> > From: "Mark Abraham" 
> > To: gmx-us...@gromacs.org
> > Sent: Tuesday, February 23, 2016 4:50:52 PM
> > Subject: Re: [gmx-users] Regarding installation problem
> >
> > Hi,
> >
> > On Tue, Feb 23, 2016 at 11:54 AM SOUVIK MONDAL 
> > wrote:
> >
> > > After doing cmake .. -DGMX_BUILD_OWN_FFTW=ON
> -DREGRESSIONTEST_DOWNLOAD=ON
> > > the output in that ternimal comes as follows
> > >
> > > - The C compiler identification is GNU 4.4.7
> > > -- The CXX compiler identification is GNU 4.4.7
> > >
> >
> > This compiler version was designed several years before your hardware
> model
> > was released, so it will not work very well. Please get an up-to-date
> > compiler for your distribution, as the install guide suggests :-)
> >
> > -- Check for working C compiler: /usr/bin/cc
> > > -- Check for working C compiler: /usr/bin/cc -- works
> > > -- Detecting C compiler ABI info
> > > -- Detecting C compiler ABI info - done
> > > -- Detecting C compile features
> > > -- Detecting C compile features - done
> > > -- Check for working CXX compiler: /usr/bin/c++
> > > -- Check for working CXX compiler: /usr/bin/c++ -- works
> > > -- Detecting CXX compiler ABI info
> > > -- Detecting CXX compiler ABI info - done
> > > -- Detecting CXX compile features
> > > -- Detecting CXX compile features - done
> > > -- Looking for NVIDIA GPUs present in the system
> > > -- Could not detect NVIDIA GPUs
> > > -- No compatible CUDA toolkit found (v4.0+), disabling native GPU
> > > acceleration
> > > -- Checking for GCC x86 inline asm
> > > -- Checking for GCC x86 inline asm - supported
> > > -- Detecting best SIMD instructions for this CPU
> > > -- Detected best SIMD instructions for this CPU - AVX2_256
> > > -- Try OpenMP C flag = [-fopenmp]
> > > -- Performing Test OpenMP_FLAG_DETECTED
> > > -- Performing Test OpenMP_FLAG_DETECTED - Success
> > > -- Try OpenMP CXX flag = [-fopenmp]
> > > -- Performing Test OpenMP_FLAG_DETECTED
> > > -- Performing Test OpenMP_FLAG_DETECTED - Success
> > > -- Found OpenMP: -fopenmp
> > > -- Performing Test CFLAGS_WARN
> > > -- Performing Test CFLAGS_WARN - Success
> > > -- Performing Test CFLAGS_WARN_EXTRA
> > > -- Performing Test CFLAGS_WARN_EXTRA - Success
> > > -- Performing Test CFLAGS_WARN_UNDEF
> > > -- Performing Test CFLAGS_WARN_UNDEF - Success
> > > -- Performing Test CFLAGS_WARN_REL
> > > -- Performing Test CFLAGS_WARN_REL - Success
> > > -- Performing Test CFLAGS_EXCESS_PREC
> > > -- Performing Test CFLAGS_EXCESS_PREC - Failed
> > > -- Performing Test CFLAGS_COPT
> > > -- Performing Test CFLAGS_COPT - Success
> > > -- Performing Test CFLAGS_NOINLINE
> > > -- Performing Test CFLAGS_NOINLINE - Success
> > > -- Performing Test CXXFLAGS_WARN
> > > -- Performing Test CXXFLAGS_WARN - Success
> > > -- Performing Test CXXFLAGS_WARN_EXTRA
> > > -- Performing Test CXXFLAGS_WARN_EXTRA - Success
> > > -- Performing Test CXXFLAGS_WARN_UNDEF
> > > -- Performing Test CXXFLAGS_WARN_UNDEF - Success
> > > -- Performing Test CXXFLAGS_WARN_REL
> > > -- Performing Test CXXFLAGS_WARN_REL - Success
> > > -- Performing Test CXXFLAGS_EXCESS_PREC
> > > -- Performing Test CXXFLAGS_EXCESS_PREC - Failed
> > > -- Performing Test CXXFLAGS_COPT
> > > -- Performing Test CXXFLAGS_COPT - Success
> > > -- Performing Test CXXFLAGS_NOINLINE
> > > -- Performing Test CXXFLAGS_NOINLINE - Success
> > > -- gcc 4.4.7 detected, using -O3, will apply workaround for
> optimization
> > > bug (disable with GMX_DISABLE_GCC44_BUG_WORKAROUND)
> > > -- Looking for include file unistd.h
> > > -- Looking for include file unistd.h - found
> > > -- Looking for include file pwd.h
> > > -- Looking for include file pwd.h - found
> > > -- Looking for include file dirent.h
> > > -- Looking for include file dirent.h - found
> > > -- Looking for include file 

Re: [gmx-users] Regarding installation problem

[SOUVIK MONDAL]

Which version of gromacs will be suitable for gcc version 4.4.7?



- Original Message -
From: "Mark Abraham" 
To: gmx-us...@gromacs.org
Sent: Tuesday, February 23, 2016 6:05:13 PM
Subject: Re: [gmx-users] Regarding installation problem

Hi,

The simplest thing is to get the latest version of gcc that your operating
system (e.g. Linux distribution) supports. Sadly, people often sell compute
systems based on "mature, stable, reliable" versions of software, but with
modern hardware, which automatically means that everything is out of date
and their users have to do all of this useless work. But do talk to your
system administrators to get some up to date tools installed for you.

Mark

On Tue, Feb 23, 2016 at 12:55 PM SOUVIK MONDAL 
wrote:

> Can u tell what are compilers I need to up-to-date?
>
> - Original Message -
> From: "Mark Abraham" 
> To: gmx-us...@gromacs.org
> Sent: Tuesday, February 23, 2016 4:50:52 PM
> Subject: Re: [gmx-users] Regarding installation problem
>
> Hi,
>
> On Tue, Feb 23, 2016 at 11:54 AM SOUVIK MONDAL 
> wrote:
>
> > After doing cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> > the output in that ternimal comes as follows
> >
> > - The C compiler identification is GNU 4.4.7
> > -- The CXX compiler identification is GNU 4.4.7
> >
>
> This compiler version was designed several years before your hardware model
> was released, so it will not work very well. Please get an up-to-date
> compiler for your distribution, as the install guide suggests :-)
>
> -- Check for working C compiler: /usr/bin/cc
> > -- Check for working C compiler: /usr/bin/cc -- works
> > -- Detecting C compiler ABI info
> > -- Detecting C compiler ABI info - done
> > -- Detecting C compile features
> > -- Detecting C compile features - done
> > -- Check for working CXX compiler: /usr/bin/c++
> > -- Check for working CXX compiler: /usr/bin/c++ -- works
> > -- Detecting CXX compiler ABI info
> > -- Detecting CXX compiler ABI info - done
> > -- Detecting CXX compile features
> > -- Detecting CXX compile features - done
> > -- Looking for NVIDIA GPUs present in the system
> > -- Could not detect NVIDIA GPUs
> > -- No compatible CUDA toolkit found (v4.0+), disabling native GPU
> > acceleration
> > -- Checking for GCC x86 inline asm
> > -- Checking for GCC x86 inline asm - supported
> > -- Detecting best SIMD instructions for this CPU
> > -- Detected best SIMD instructions for this CPU - AVX2_256
> > -- Try OpenMP C flag = [-fopenmp]
> > -- Performing Test OpenMP_FLAG_DETECTED
> > -- Performing Test OpenMP_FLAG_DETECTED - Success
> > -- Try OpenMP CXX flag = [-fopenmp]
> > -- Performing Test OpenMP_FLAG_DETECTED
> > -- Performing Test OpenMP_FLAG_DETECTED - Success
> > -- Found OpenMP: -fopenmp
> > -- Performing Test CFLAGS_WARN
> > -- Performing Test CFLAGS_WARN - Success
> > -- Performing Test CFLAGS_WARN_EXTRA
> > -- Performing Test CFLAGS_WARN_EXTRA - Success
> > -- Performing Test CFLAGS_WARN_UNDEF
> > -- Performing Test CFLAGS_WARN_UNDEF - Success
> > -- Performing Test CFLAGS_WARN_REL
> > -- Performing Test CFLAGS_WARN_REL - Success
> > -- Performing Test CFLAGS_EXCESS_PREC
> > -- Performing Test CFLAGS_EXCESS_PREC - Failed
> > -- Performing Test CFLAGS_COPT
> > -- Performing Test CFLAGS_COPT - Success
> > -- Performing Test CFLAGS_NOINLINE
> > -- Performing Test CFLAGS_NOINLINE - Success
> > -- Performing Test CXXFLAGS_WARN
> > -- Performing Test CXXFLAGS_WARN - Success
> > -- Performing Test CXXFLAGS_WARN_EXTRA
> > -- Performing Test CXXFLAGS_WARN_EXTRA - Success
> > -- Performing Test CXXFLAGS_WARN_UNDEF
> > -- Performing Test CXXFLAGS_WARN_UNDEF - Success
> > -- Performing Test CXXFLAGS_WARN_REL
> > -- Performing Test CXXFLAGS_WARN_REL - Success
> > -- Performing Test CXXFLAGS_EXCESS_PREC
> > -- Performing Test CXXFLAGS_EXCESS_PREC - Failed
> > -- Performing Test CXXFLAGS_COPT
> > -- Performing Test CXXFLAGS_COPT - Success
> > -- Performing Test CXXFLAGS_NOINLINE
> > -- Performing Test CXXFLAGS_NOINLINE - Success
> > -- gcc 4.4.7 detected, using -O3, will apply workaround for optimization
> > bug (disable with GMX_DISABLE_GCC44_BUG_WORKAROUND)
> > -- Looking for include file unistd.h
> > -- Looking for include file unistd.h - found
> > -- Looking for include file pwd.h
> > -- Looking for include file pwd.h - found
> > -- Looking for include file dirent.h
> > -- Looking for include file dirent.h - found
> > -- Looking for include file time.h
> > -- Looking for include file time.h - found
> > -- Looking for include file sys/time.h
> > -- Looking for include file sys/time.h - found
> > -- Looking for include file io.h
> > -- Looking for include file io.h - not found
> > -- Looking for include file sched.h
> > -- Looking for include file sched.h - found
> > -- Looking for include file regex.h
> > -- Looking for include file regex.h - found
> > -- Looking for posix_memalign
> > -- 

Re: [gmx-users] Regarding installation problem

[Mark Abraham]

Hi,

The simplest thing is to get the latest version of gcc that your operating
system (e.g. Linux distribution) supports. Sadly, people often sell compute
systems based on "mature, stable, reliable" versions of software, but with
modern hardware, which automatically means that everything is out of date
and their users have to do all of this useless work. But do talk to your
system administrators to get some up to date tools installed for you.

Mark

On Tue, Feb 23, 2016 at 12:55 PM SOUVIK MONDAL 
wrote:

> Can u tell what are compilers I need to up-to-date?
>
> - Original Message -
> From: "Mark Abraham" 
> To: gmx-us...@gromacs.org
> Sent: Tuesday, February 23, 2016 4:50:52 PM
> Subject: Re: [gmx-users] Regarding installation problem
>
> Hi,
>
> On Tue, Feb 23, 2016 at 11:54 AM SOUVIK MONDAL 
> wrote:
>
> > After doing cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> > the output in that ternimal comes as follows
> >
> > - The C compiler identification is GNU 4.4.7
> > -- The CXX compiler identification is GNU 4.4.7
> >
>
> This compiler version was designed several years before your hardware model
> was released, so it will not work very well. Please get an up-to-date
> compiler for your distribution, as the install guide suggests :-)
>
> -- Check for working C compiler: /usr/bin/cc
> > -- Check for working C compiler: /usr/bin/cc -- works
> > -- Detecting C compiler ABI info
> > -- Detecting C compiler ABI info - done
> > -- Detecting C compile features
> > -- Detecting C compile features - done
> > -- Check for working CXX compiler: /usr/bin/c++
> > -- Check for working CXX compiler: /usr/bin/c++ -- works
> > -- Detecting CXX compiler ABI info
> > -- Detecting CXX compiler ABI info - done
> > -- Detecting CXX compile features
> > -- Detecting CXX compile features - done
> > -- Looking for NVIDIA GPUs present in the system
> > -- Could not detect NVIDIA GPUs
> > -- No compatible CUDA toolkit found (v4.0+), disabling native GPU
> > acceleration
> > -- Checking for GCC x86 inline asm
> > -- Checking for GCC x86 inline asm - supported
> > -- Detecting best SIMD instructions for this CPU
> > -- Detected best SIMD instructions for this CPU - AVX2_256
> > -- Try OpenMP C flag = [-fopenmp]
> > -- Performing Test OpenMP_FLAG_DETECTED
> > -- Performing Test OpenMP_FLAG_DETECTED - Success
> > -- Try OpenMP CXX flag = [-fopenmp]
> > -- Performing Test OpenMP_FLAG_DETECTED
> > -- Performing Test OpenMP_FLAG_DETECTED - Success
> > -- Found OpenMP: -fopenmp
> > -- Performing Test CFLAGS_WARN
> > -- Performing Test CFLAGS_WARN - Success
> > -- Performing Test CFLAGS_WARN_EXTRA
> > -- Performing Test CFLAGS_WARN_EXTRA - Success
> > -- Performing Test CFLAGS_WARN_UNDEF
> > -- Performing Test CFLAGS_WARN_UNDEF - Success
> > -- Performing Test CFLAGS_WARN_REL
> > -- Performing Test CFLAGS_WARN_REL - Success
> > -- Performing Test CFLAGS_EXCESS_PREC
> > -- Performing Test CFLAGS_EXCESS_PREC - Failed
> > -- Performing Test CFLAGS_COPT
> > -- Performing Test CFLAGS_COPT - Success
> > -- Performing Test CFLAGS_NOINLINE
> > -- Performing Test CFLAGS_NOINLINE - Success
> > -- Performing Test CXXFLAGS_WARN
> > -- Performing Test CXXFLAGS_WARN - Success
> > -- Performing Test CXXFLAGS_WARN_EXTRA
> > -- Performing Test CXXFLAGS_WARN_EXTRA - Success
> > -- Performing Test CXXFLAGS_WARN_UNDEF
> > -- Performing Test CXXFLAGS_WARN_UNDEF - Success
> > -- Performing Test CXXFLAGS_WARN_REL
> > -- Performing Test CXXFLAGS_WARN_REL - Success
> > -- Performing Test CXXFLAGS_EXCESS_PREC
> > -- Performing Test CXXFLAGS_EXCESS_PREC - Failed
> > -- Performing Test CXXFLAGS_COPT
> > -- Performing Test CXXFLAGS_COPT - Success
> > -- Performing Test CXXFLAGS_NOINLINE
> > -- Performing Test CXXFLAGS_NOINLINE - Success
> > -- gcc 4.4.7 detected, using -O3, will apply workaround for optimization
> > bug (disable with GMX_DISABLE_GCC44_BUG_WORKAROUND)
> > -- Looking for include file unistd.h
> > -- Looking for include file unistd.h - found
> > -- Looking for include file pwd.h
> > -- Looking for include file pwd.h - found
> > -- Looking for include file dirent.h
> > -- Looking for include file dirent.h - found
> > -- Looking for include file time.h
> > -- Looking for include file time.h - found
> > -- Looking for include file sys/time.h
> > -- Looking for include file sys/time.h - found
> > -- Looking for include file io.h
> > -- Looking for include file io.h - not found
> > -- Looking for include file sched.h
> > -- Looking for include file sched.h - found
> > -- Looking for include file regex.h
> > -- Looking for include file regex.h - found
> > -- Looking for posix_memalign
> > -- Looking for posix_memalign - found
> > -- Looking for memalign
> > -- Looking for memalign - not found
> > -- Looking for _aligned_malloc
> > -- Looking for _aligned_malloc - not found
> > -- Looking for gettimeofday
> > -- Looking for gettimeofday - found
> > -- Looking for 

Re: [gmx-users] Regarding installation problem

[SOUVIK MONDAL]

Can u tell what are compilers I need to up-to-date?

- Original Message -
From: "Mark Abraham" 
To: gmx-us...@gromacs.org
Sent: Tuesday, February 23, 2016 4:50:52 PM
Subject: Re: [gmx-users] Regarding installation problem

Hi,

On Tue, Feb 23, 2016 at 11:54 AM SOUVIK MONDAL 
wrote:

> After doing cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> the output in that ternimal comes as follows
>
> - The C compiler identification is GNU 4.4.7
> -- The CXX compiler identification is GNU 4.4.7
>

This compiler version was designed several years before your hardware model
was released, so it will not work very well. Please get an up-to-date
compiler for your distribution, as the install guide suggests :-)

-- Check for working C compiler: /usr/bin/cc
> -- Check for working C compiler: /usr/bin/cc -- works
> -- Detecting C compiler ABI info
> -- Detecting C compiler ABI info - done
> -- Detecting C compile features
> -- Detecting C compile features - done
> -- Check for working CXX compiler: /usr/bin/c++
> -- Check for working CXX compiler: /usr/bin/c++ -- works
> -- Detecting CXX compiler ABI info
> -- Detecting CXX compiler ABI info - done
> -- Detecting CXX compile features
> -- Detecting CXX compile features - done
> -- Looking for NVIDIA GPUs present in the system
> -- Could not detect NVIDIA GPUs
> -- No compatible CUDA toolkit found (v4.0+), disabling native GPU
> acceleration
> -- Checking for GCC x86 inline asm
> -- Checking for GCC x86 inline asm - supported
> -- Detecting best SIMD instructions for this CPU
> -- Detected best SIMD instructions for this CPU - AVX2_256
> -- Try OpenMP C flag = [-fopenmp]
> -- Performing Test OpenMP_FLAG_DETECTED
> -- Performing Test OpenMP_FLAG_DETECTED - Success
> -- Try OpenMP CXX flag = [-fopenmp]
> -- Performing Test OpenMP_FLAG_DETECTED
> -- Performing Test OpenMP_FLAG_DETECTED - Success
> -- Found OpenMP: -fopenmp
> -- Performing Test CFLAGS_WARN
> -- Performing Test CFLAGS_WARN - Success
> -- Performing Test CFLAGS_WARN_EXTRA
> -- Performing Test CFLAGS_WARN_EXTRA - Success
> -- Performing Test CFLAGS_WARN_UNDEF
> -- Performing Test CFLAGS_WARN_UNDEF - Success
> -- Performing Test CFLAGS_WARN_REL
> -- Performing Test CFLAGS_WARN_REL - Success
> -- Performing Test CFLAGS_EXCESS_PREC
> -- Performing Test CFLAGS_EXCESS_PREC - Failed
> -- Performing Test CFLAGS_COPT
> -- Performing Test CFLAGS_COPT - Success
> -- Performing Test CFLAGS_NOINLINE
> -- Performing Test CFLAGS_NOINLINE - Success
> -- Performing Test CXXFLAGS_WARN
> -- Performing Test CXXFLAGS_WARN - Success
> -- Performing Test CXXFLAGS_WARN_EXTRA
> -- Performing Test CXXFLAGS_WARN_EXTRA - Success
> -- Performing Test CXXFLAGS_WARN_UNDEF
> -- Performing Test CXXFLAGS_WARN_UNDEF - Success
> -- Performing Test CXXFLAGS_WARN_REL
> -- Performing Test CXXFLAGS_WARN_REL - Success
> -- Performing Test CXXFLAGS_EXCESS_PREC
> -- Performing Test CXXFLAGS_EXCESS_PREC - Failed
> -- Performing Test CXXFLAGS_COPT
> -- Performing Test CXXFLAGS_COPT - Success
> -- Performing Test CXXFLAGS_NOINLINE
> -- Performing Test CXXFLAGS_NOINLINE - Success
> -- gcc 4.4.7 detected, using -O3, will apply workaround for optimization
> bug (disable with GMX_DISABLE_GCC44_BUG_WORKAROUND)
> -- Looking for include file unistd.h
> -- Looking for include file unistd.h - found
> -- Looking for include file pwd.h
> -- Looking for include file pwd.h - found
> -- Looking for include file dirent.h
> -- Looking for include file dirent.h - found
> -- Looking for include file time.h
> -- Looking for include file time.h - found
> -- Looking for include file sys/time.h
> -- Looking for include file sys/time.h - found
> -- Looking for include file io.h
> -- Looking for include file io.h - not found
> -- Looking for include file sched.h
> -- Looking for include file sched.h - found
> -- Looking for include file regex.h
> -- Looking for include file regex.h - found
> -- Looking for posix_memalign
> -- Looking for posix_memalign - found
> -- Looking for memalign
> -- Looking for memalign - not found
> -- Looking for _aligned_malloc
> -- Looking for _aligned_malloc - not found
> -- Looking for gettimeofday
> -- Looking for gettimeofday - found
> -- Looking for sysconf
> -- Looking for sysconf - found
> -- Looking for nice
> -- Looking for nice - found
> -- Looking for fsync
> -- Looking for fsync - found
> -- Looking for _fileno
> -- Looking for _fileno - not found
> -- Looking for fileno
> -- Looking for fileno - found
> -- Looking for _commit
> -- Looking for _commit - not found
> -- Looking for sigaction
> -- Looking for sigaction - found
> -- Looking for rsqrt
> -- Looking for rsqrt - not found
> -- Looking for rsqrtf
> -- Looking for rsqrtf - not found
> -- Looking for sqrtf
> -- Looking for sqrtf - found
> -- Looking for clock_gettime in rt
> -- Looking for clock_gettime in rt - found
> -- Looking for feenableexcept in m
> -- Looking for feenableexcept in m - found
> -- Checking 

Re: [gmx-users] Regarding installation problem

[Mark Abraham]

Hi,

On Tue, Feb 23, 2016 at 11:54 AM SOUVIK MONDAL 
wrote:

> After doing cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> the output in that ternimal comes as follows
>
> - The C compiler identification is GNU 4.4.7
> -- The CXX compiler identification is GNU 4.4.7
>

This compiler version was designed several years before your hardware model
was released, so it will not work very well. Please get an up-to-date
compiler for your distribution, as the install guide suggests :-)

-- Check for working C compiler: /usr/bin/cc
> -- Check for working C compiler: /usr/bin/cc -- works
> -- Detecting C compiler ABI info
> -- Detecting C compiler ABI info - done
> -- Detecting C compile features
> -- Detecting C compile features - done
> -- Check for working CXX compiler: /usr/bin/c++
> -- Check for working CXX compiler: /usr/bin/c++ -- works
> -- Detecting CXX compiler ABI info
> -- Detecting CXX compiler ABI info - done
> -- Detecting CXX compile features
> -- Detecting CXX compile features - done
> -- Looking for NVIDIA GPUs present in the system
> -- Could not detect NVIDIA GPUs
> -- No compatible CUDA toolkit found (v4.0+), disabling native GPU
> acceleration
> -- Checking for GCC x86 inline asm
> -- Checking for GCC x86 inline asm - supported
> -- Detecting best SIMD instructions for this CPU
> -- Detected best SIMD instructions for this CPU - AVX2_256
> -- Try OpenMP C flag = [-fopenmp]
> -- Performing Test OpenMP_FLAG_DETECTED
> -- Performing Test OpenMP_FLAG_DETECTED - Success
> -- Try OpenMP CXX flag = [-fopenmp]
> -- Performing Test OpenMP_FLAG_DETECTED
> -- Performing Test OpenMP_FLAG_DETECTED - Success
> -- Found OpenMP: -fopenmp
> -- Performing Test CFLAGS_WARN
> -- Performing Test CFLAGS_WARN - Success
> -- Performing Test CFLAGS_WARN_EXTRA
> -- Performing Test CFLAGS_WARN_EXTRA - Success
> -- Performing Test CFLAGS_WARN_UNDEF
> -- Performing Test CFLAGS_WARN_UNDEF - Success
> -- Performing Test CFLAGS_WARN_REL
> -- Performing Test CFLAGS_WARN_REL - Success
> -- Performing Test CFLAGS_EXCESS_PREC
> -- Performing Test CFLAGS_EXCESS_PREC - Failed
> -- Performing Test CFLAGS_COPT
> -- Performing Test CFLAGS_COPT - Success
> -- Performing Test CFLAGS_NOINLINE
> -- Performing Test CFLAGS_NOINLINE - Success
> -- Performing Test CXXFLAGS_WARN
> -- Performing Test CXXFLAGS_WARN - Success
> -- Performing Test CXXFLAGS_WARN_EXTRA
> -- Performing Test CXXFLAGS_WARN_EXTRA - Success
> -- Performing Test CXXFLAGS_WARN_UNDEF
> -- Performing Test CXXFLAGS_WARN_UNDEF - Success
> -- Performing Test CXXFLAGS_WARN_REL
> -- Performing Test CXXFLAGS_WARN_REL - Success
> -- Performing Test CXXFLAGS_EXCESS_PREC
> -- Performing Test CXXFLAGS_EXCESS_PREC - Failed
> -- Performing Test CXXFLAGS_COPT
> -- Performing Test CXXFLAGS_COPT - Success
> -- Performing Test CXXFLAGS_NOINLINE
> -- Performing Test CXXFLAGS_NOINLINE - Success
> -- gcc 4.4.7 detected, using -O3, will apply workaround for optimization
> bug (disable with GMX_DISABLE_GCC44_BUG_WORKAROUND)
> -- Looking for include file unistd.h
> -- Looking for include file unistd.h - found
> -- Looking for include file pwd.h
> -- Looking for include file pwd.h - found
> -- Looking for include file dirent.h
> -- Looking for include file dirent.h - found
> -- Looking for include file time.h
> -- Looking for include file time.h - found
> -- Looking for include file sys/time.h
> -- Looking for include file sys/time.h - found
> -- Looking for include file io.h
> -- Looking for include file io.h - not found
> -- Looking for include file sched.h
> -- Looking for include file sched.h - found
> -- Looking for include file regex.h
> -- Looking for include file regex.h - found
> -- Looking for posix_memalign
> -- Looking for posix_memalign - found
> -- Looking for memalign
> -- Looking for memalign - not found
> -- Looking for _aligned_malloc
> -- Looking for _aligned_malloc - not found
> -- Looking for gettimeofday
> -- Looking for gettimeofday - found
> -- Looking for sysconf
> -- Looking for sysconf - found
> -- Looking for nice
> -- Looking for nice - found
> -- Looking for fsync
> -- Looking for fsync - found
> -- Looking for _fileno
> -- Looking for _fileno - not found
> -- Looking for fileno
> -- Looking for fileno - found
> -- Looking for _commit
> -- Looking for _commit - not found
> -- Looking for sigaction
> -- Looking for sigaction - found
> -- Looking for rsqrt
> -- Looking for rsqrt - not found
> -- Looking for rsqrtf
> -- Looking for rsqrtf - not found
> -- Looking for sqrtf
> -- Looking for sqrtf - found
> -- Looking for clock_gettime in rt
> -- Looking for clock_gettime in rt - found
> -- Looking for feenableexcept in m
> -- Looking for feenableexcept in m - found
> -- Checking for sched.h GNU affinity API
> -- Performing Test sched_affinity_compile
> -- Performing Test sched_affinity_compile - Success
> -- Check if the system is big endian
> -- Searching 16 bit integer
> -- Looking for sys/types.h
> -- Looking for sys/types.h - 

Re: [gmx-users] Regarding installation problem

[SOUVIK MONDAL]

After doing cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
the output in that ternimal comes as follows

- The C compiler identification is GNU 4.4.7
-- The CXX compiler identification is GNU 4.4.7
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for NVIDIA GPUs present in the system
-- Could not detect NVIDIA GPUs
-- No compatible CUDA toolkit found (v4.0+), disabling native GPU acceleration
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - supported
-- Detecting best SIMD instructions for this CPU
-- Detected best SIMD instructions for this CPU - AVX2_256
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp  
-- Performing Test CFLAGS_WARN
-- Performing Test CFLAGS_WARN - Success
-- Performing Test CFLAGS_WARN_EXTRA
-- Performing Test CFLAGS_WARN_EXTRA - Success
-- Performing Test CFLAGS_WARN_UNDEF
-- Performing Test CFLAGS_WARN_UNDEF - Success
-- Performing Test CFLAGS_WARN_REL
-- Performing Test CFLAGS_WARN_REL - Success
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Failed
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_WARN
-- Performing Test CXXFLAGS_WARN - Success
-- Performing Test CXXFLAGS_WARN_EXTRA
-- Performing Test CXXFLAGS_WARN_EXTRA - Success
-- Performing Test CXXFLAGS_WARN_UNDEF
-- Performing Test CXXFLAGS_WARN_UNDEF - Success
-- Performing Test CXXFLAGS_WARN_REL
-- Performing Test CXXFLAGS_WARN_REL - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Failed
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- gcc 4.4.7 detected, using -O3, will apply workaround for optimization bug 
(disable with GMX_DISABLE_GCC44_BUG_WORKAROUND)
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file regex.h
-- Looking for include file regex.h - found
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Looking for _aligned_malloc
-- Looking for _aligned_malloc - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Looking for rsqrt
-- Looking for rsqrt - not found
-- Looking for rsqrtf
-- Looking for rsqrtf - not found
-- Looking for sqrtf
-- Looking for sqrtf - found
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for zlibVersion in /usr/lib64/libz.so
-- Looking for zlibVersion in /usr/lib64/libz.so - found
-- Found LibXml2: /usr/lib64/libxml2.so (found version "2.7.6") 
-- Looking for xmlTextWriterEndAttribute in /usr/lib64/libxml2.so
-- Looking for 

Re: [gmx-users] Regarding installation problem

[Mark Abraham]

Hi,

Yes, I know. That's its job. The only likely relevant part is very near the
end. But first I wanted to see the terminal output - what you saw on the
screen when you ran cmake.

Mark
-- 
Gromacs Users mailing list

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http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [gmx-users] Regarding installation problem

[SOUVIK MONDAL]

The CmakeErroor.log file have following things

Performing C SOURCE FILE Test CFLAGS_EXCESS_PREC failed with the following 
output:
Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_bf3f2/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_bf3f2.dir/build.make 
CMakeFiles/cmTC_bf3f2.dir/build
gmake[1]: Entering directory 
`/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_bf3f2.dir/src.c.o
/usr/bin/cc-DCFLAGS_EXCESS_PREC -fexcess-precision=fast   -o 
CMakeFiles/cmTC_bf3f2.dir/src.c.o   -c 
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.c
cc1: error: unrecognized command line option "-fexcess-precision=fast"
gmake[1]: Leaving directory 
`/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
gmake[1]: *** [CMakeFiles/cmTC_bf3f2.dir/src.c.o] Error 1
gmake: *** [cmTC_bf3f2/fast] Error 2

Source file was:
int main(void) { return 0; }
Performing C++ SOURCE FILE Test CXXFLAGS_EXCESS_PREC failed with the following 
output:
Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_2e3fd/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_2e3fd.dir/build.make 
CMakeFiles/cmTC_2e3fd.dir/build
gmake[1]: Entering directory 
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Source file was:
int main() { return 0;}
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Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp

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CMakeFiles/cmTC_c44f7.dir/build
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/usr/bin/cc-Wundef -Wextra -Wno-missing-field-initializers 
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-Wunused-parameter -o CMakeFiles/cmTC_c44f7.dir/CheckIncludeFiles.c.o   -c 
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/CheckIncludeFiles.c
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/* */
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int main(void){return 0;}

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Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_bf2d4/fast"
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/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx
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/* */
#include 

int main(int argc, char** argv)
{
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#else
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#endif
}

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CMakeFiles/cmTC_956e1.dir/build
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/usr/bin/c++ -Wundef -Wextra -Wno-missing-field-initializers 
-Wpointer-arith -Wall -Wno-unused-function -o 
CMakeFiles/cmTC_956e1.dir/CheckSymbolExists.cxx.o -c 

[gmx-users] Post-doctoral position in Computational Physics

[Andrea Spitaleri]

Hi all,

A post-doctoral position in Computational Physics is currently available 
in the Computational mOdelling of NanosCalE and bioPhysical sysTems 
(CONCEPT) Lab 
(https://beta.iit.it/research/lines/computational-modelling-of-nanoscale-and-biophysical-systems) 
at IIT - Genoa (ITA) to work on the theory and modeling for molecular 
simulation.


More information:

https://beta.iit.it/careers/openings/opening/81-post-doctoral-position-in-computational-physics

Best

and

--
Andrea Spitaleri PhD
Istituto Computational mOdelling of NanosCalE and bioPhysical sysTems -
CONCEPT LabItaliano di Tecnologia
Via Morego, 30 16163 Genova
cell: +39 3485188790
http://www.iit.it/en/d3-people/andrea-spitaleri.html
ORCID: http://orcid.org/-0003-3012-3557

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[gmx-users] generating an initial structure with a gromacs compatible tool

[Nash, Anthony]

Hi all,
Is there a friendly Gromacs compatible tool for generating a .gro/.pdb
file using a specific forcefield topology specification within Gromacs
itself? For context:

I¹m in the process of fully parameterising five custom protein residues
for the amber forcefield from ab initio calculations. Fragment #1 has been
very successfully, with a production NPT simulation showing very little
deviation from the equilibrium ab initio structure.

Fragment #2, on the other hand, is driving me crazy. I derive partial
charges, force constants, then I take the equilibrium structure, and
replace the capped backbone ends (required for RESP) with NGLY and CGLY. I
am using Avogadro to do this, which spits out a awful .pdb file which
requires a lot of rearranging to be compatible with the atom order of the
residues inside aminoacid.rtp in the amber99sb.ff. I hold the eq_structure
fixed in avogadro and run an energy equilibrium over the new adjoining
glycine residues. All appears fine, until I run a Gromacs energy
minimisation. The entire customer residue expands gently (beyond the eq
distances, by a few angstrom), and then an NVT simulation throws out a lot
of LINCS warnings. 

I am pretty confident that this is the fault of my initial structure, in
particular the angles (I¹m going to double check the FCs). But mean while
using Avogadro to build test structures is taking forever! Any
alternatives?

Many thanks
Anthony

Dr Anthony Nash
Department of Chemistry
University College London

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Re: [gmx-users] Effect of compilers loaded at runtime

[Mark Abraham]

Hi,

Very likely not, but technically the answer can depend how the compiler
toolchain sets up things like dynamic loading of libraries. You can perhaps
explore that effect with the command line tools ldd and objdump on the gmx
executable. You could read the Intel docs, but they'll just say "yes it is
possible to see changed behaviour."

Mark

On Mon, Feb 22, 2016 at 8:06 AM Dries Van Rompaey <
dries.vanromp...@gmail.com> wrote:

> Hi,
>
> I'm wondering if the version of the intel toolchain loaded when calling
> mdrun affects results? My gromacs version was compiled with intel/2015b -
> would it matter if module intel/2016b was loaded at runtime?
>
> Thanks
>
> Dries
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Re: [gmx-users] Huge conformational change of ATP molecules

[Mark Abraham]

Hi,

It sounds like you are observing artefacts from
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Mark

On Tue, Feb 23, 2016 at 6:18 AM Zheng Ruan  wrote:

> Hi Gromacs Users,
>
> I'm running 20ns MD simulation of a protein kinase with ATP bond. I use
> amber99sb-ildn force field with parameters of ATP derived from the database
> of Richard Bryce.
>
> What surprised me is that the ATP molecules displays a huge flexibility and
> conformational change. First, it slipped out from the starting binding
> pocket. In addition, the plane of adenine ring and ribose sugar rotate to
> about 180 degree after 10ns, making the ATP molecule looks weird. I never
> run a MD of a protein with ligand before. Is this something normal? What
> are possible causes for this? Maybe I should try some other ATP protein
> complex to see if the same thing happens? Thank you!
>
> Ruan
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Re: [gmx-users] Mdrun with rdd option

[Mark Abraham]

Hi,

On Tue, Feb 23, 2016 at 6:25 AM Raju Lunkad <
r.lun...@students.iiserpune.ac.in> wrote:

> Dear Gromacs users,
> I am trying to run a simulation but I am getting the error regarding the
> domain decomposition.


Which error? People often can't help much without precise information.
Probably your system is unstable and was
http://www.gromacs.org/Documentation/Terminology/Blowing_Up and your
"solution" below is just hiding the real problem.

I ran the simulation using "rdd" option and it is
> running fine.
> Kindly tell me whether "-rdd" option will affect my simulation. If yes,
> then which values would get affected using "rdd"  option.
>

mdrun has to choose a minimum diameter for the domains in the decomposition
for various code to work well. Choosing rdd too small risks that diameter
being too small, which means that the simulation might abort if the domain
becomes too small for all the atoms in a bonded interaction to be present
in one domain (see brief description at gmx mdrun -h). But in practice
almost nobody should have any need to change these things.

Mark


> Best Regards,
> Raju Lunkad
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Re: [gmx-users] Regarding installation problem

[Mark Abraham]

Hi,

The limited information you've provided doesn't sound like it is the real
problem. What does the whole cmake terminal output say?

Mark

On Tue, Feb 23, 2016 at 7:38 AM SOUVIK MONDAL  wrote:

> Hi
>   I have found the following problem regarding gromacs 5.1.2 installation.
> I have installes cmake and ffftw before. Can you help me out?
> -- Configuring incomplete, errors occurred!
>
>
> See also "/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeOutput.log".
> See also "/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeError.log"
>
> when I opened that two log files it shows
> Performing C SOURCE FILE Test CFLAGS_EXCESS_PREC failed with the following
> output:
> Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp
>
> Run Build Command:"/usr/bin/gmake" "cmTC_bf3f2/fast"
> /usr/bin/gmake -f CMakeFiles/cmTC_bf3f2.dir/build.make
> CMakeFiles/cmTC_bf3f2.dir/build
> gmake[1]: Entering directory
> `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
> Building C object CMakeFiles/cmTC_bf3f2.dir/src.c.o
> /usr/bin/cc-DCFLAGS_EXCESS_PREC -fexcess-precision=fast   -o
> CMakeFiles/cmTC_bf3f2.dir/src.c.o   -c
> /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.c
> cc1: error: unrecognized command line option "-fexcess-precision=fast"
> gmake[1]: Leaving directory
> `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
> gmake[1]: *** [CMakeFiles/cmTC_bf3f2.dir/src.c.o] Error 1
> gmake: *** [cmTC_bf3f2/fast] Error 2
>
> Source file was:
> int main(void) { return 0; }
> Performing C++ SOURCE FILE Test CXXFLAGS_EXCESS_PREC failed with the
> following output:
> "CMakeError.log" 624L, 40593C
>
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