Re: [gmx-users] Question about nsttcouple

[Mark Abraham]

Hi,

Sorry, it looks like the documentation is wrong in that case. Developers
are fond of doing fancy things and not remembering all the things that
depend on it. I imagine that nsttcouple gets 10 chosen, and only later is
nstlist changed. The interpretation and behaviour of nstlist have
unfortunately changed over many years...

Mark

On Thu, Nov 8, 2018 at 12:38 AM minky son  wrote:

> Thank you for reply
>
> [ Input values in mdp file ]
> nstlist = 10
> nsttcouple = -1
>
> After gmx mdrun, ‘nstlist’ is automatically changed from 10 to 50.
>
> I expected that both ‘nstlist’ and ‘nsttcouple’ would be changed to 50,
> because ‘nsttcouple=-1’ means ‘nsttcouple=nstlist’.
> But, nstlist =50 and nsttcouple= 10 were written in log file.
> Which value was used for nsttcouple? 10 or 50?
>
> I’m not sure, because .log file shows input mdp parameter values, not
> automatically changed values (GROMACS 2018).
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Re: [gmx-users] Periodic saving of checkpoint file

[Mark Abraham]

Hi,

Looks OK. The details don't matter, as you are anyway changing ensemble.

Mark

On Thu, Nov 8, 2018 at 2:39 AM Nicolas Cheron <
nicolas.cheron.bou...@gmail.com> wrote:

> Hi Mark,
>
> Thank you for your answer. I didn't know this option. From what I have
> read, eneconv is for reading parameters for Nose-Hoover or
> Parrinello-Rahman coupling. Thus, if I am doing first an NVT simulation
> with the velocity-rescale thermostat or a Langevin dynamics, I don't need
> the .edr file, right ? Can you please confirm that this is enough to
> prepare the tpr from the time 50ps of the NVT simulation:
>
> gmx grompp -v -f NVE.mdp -n Index.ndx -o NVE.tpr -c NVT.gro -t NVT.trr
> -time 50 -p Protein.top -po NVE_mdout.mdp
>
> Thank you
>
>
> Le lun. 5 nov. 2018 à 17:50, Mark Abraham  a
> écrit :
>
> > Hi,
> >
> > Since you are anyway intending to change the ensemble, you can just use
> > nstxout, nstvout and nstenergy to write output every 10ps. That content
> is
> > equivalent to that of the checkpoint. Use trjconv and eneconv afterwards
> to
> > split those up, and use them as inputs to grompp -e -t along with the
> > regular inputs.
> >
> > Mark
> >
> > On Mon, Nov 5, 2018 at 5:14 PM Nicolas Cheron <
> > nicolas.cheron.bou...@gmail.com> wrote:
> >
> > > Dear all,
> > >
> > > I would like to run a long NVT simulation and save a checkpoint file
> > every
> > > 10ps (in order to then run short NVE simulations from each checkpoint).
> > Is
> > > there a way to save a .cpt file every 10ps in an automatic way?
> > >
> > > I can do it with other program, for example with Amber "ntwr=-5000"
> will
> > > save a new restart file every 5000 steps. For now with Gromacs, the
> only
> > > thing I have found is to write a loop where at each step I extend the
> > > simulation time of 10ps with convert-tpr, perform the 10ps simulation,
> > save
> > > the .cpt, and then loop again.
> > >
> > > Thanks for your help.
> > >
> > > Nicolas
> > > --
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 175, Issue 28 - start the simulation of the last stopping point.

[Mark Abraham]

Hi,

Those were not the commands you issued. What commands did you issue?

Mark

On Fri, Nov 9, 2018 at 7:12 AM Edjan Silva 
wrote:

> Dear Paul,
>
> Thank you for your help. However, when you run the command:
>
> $ gmx convert-tpr -s previous.tpr -extend timetoextendby -o next.tpr
> $ gmx mdrun -s next.tpr -cpi state.cpt
>
> the following error appeared:
>
>
> *Output file appending has been requested,*
> *but some output files listed in the checkpoint file md_0_1.cpt*
> *are not present or not named as the output files by the current program:*
> *Expect output files present:*
>
> *Expected output files not present or named differently:*
> *  md_0_1.log*
> *  md_0_1.xtc*
> *  md_0_1.edr*
>
> *---*
> *Program: gmx mdrun, version 2016.4*
> *Source file: src/gromacs/mdrunutility/handlerestart.cpp (line 177)*
>
> *Fatal error:*
> *File appending requested, but 3 of the 3 output files are not present or
> are*
> *named differently. For safety reasons, GROMACS-2016 and later only allows
> file*
> *appending to be used when all files have the same names as they had in
> the*
> *original run. Checkpointing is merely intended for plain continuation of
> runs.*
> *For safety reasons you must specify all file names (e.g. with -deffnm),
> and*
> *all these files must match the names used in the run prior to
> checkpointing*
> *since we will append to them by default. If you used -deffnm and the
> files*
> *listed above as not present are in fact present, try explicitly
> specifying*
> *them in respective mdrun options. If the files are not available, you can
> add*
> *the -noappend flag to mdrun and write separate new parts. For mere*
> *concatenation of files, you should use the gmx trjcat tool instead.*
>
>
> I do not understand. the input files are correct.
>
> Em qui, 8 de nov de 2018 às 14:13, <
> gromacs.org_gmx-users-requ...@maillist.sys.kth.se> escreveu:
>
> > Send gromacs.org_gmx-users mailing list submissions to
> > gromacs.org_gmx-users@maillist.sys.kth.se
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or, via email, send a message with subject or body 'help' to
> > gromacs.org_gmx-users-requ...@maillist.sys.kth.se
> >
> > You can reach the person managing the list at
> > gromacs.org_gmx-users-ow...@maillist.sys.kth.se
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of gromacs.org_gmx-users digest..."
> >
> >
> > Today's Topics:
> >
> >1. start the simulation of the last stopping point. (Edjan Silva)
> >2. Re: start the simulation of the last stopping point. (Paul Bauer)
> >3. Re: DispErsion correction (Farial Tavakoli)
> >4. Assigning charge to closely related functional group
> >   (Tushar Ranjan Moharana)
> >5. 4. Re: 5. Re: 3. Re: Strange pullx coordinates (PMF
> >   (CROUZY Serge 119222)
> >
> >
> > --
> >
> > Message: 1
> > Date: Thu, 8 Nov 2018 10:23:13 -0300
> > From: Edjan Silva 
> > To: gromacs.org_gmx-users@maillist.sys.kth.se
> > Subject: [gmx-users] start the simulation of the last stopping point.
> > Message-ID:
> > <
> > capf4pyb-pq8bbtfr3o5sfasl42jgwvu5kusle8l4l8sdi1y...@mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Dear fellow scientists,
> >
> > I'm doing a 40ns simulation between DNA and a small molecule. It occurred
> > that around 30 nanoseconds, the computer hung up.
> >
> > How do I start the simulation from the 30 nanoseconds performed?
> >
> >
> > --
> >
> > Message: 2
> > Date: Thu, 8 Nov 2018 14:22:56 +0100
> > From: Paul Bauer 
> > To: gromacs.org_gmx-users@maillist.sys.kth.se
> > Subject: Re: [gmx-users] start the simulation of the last stopping
> > point.
> > Message-ID: <6edfea12-973e-15e2-4d3d-86f67c1dc...@gmail.com>
> > Content-Type: text/plain; charset=utf-8; format=flowed
> >
> > Hello,
> >
> > you can find information on how to extend simulations here:
> >
> >
> http://manual.gromacs.org/documentation/current/user-guide/managing-simulations.html
> >
> > Cheers
> >
> > Paul
> >
> > On 2018-11-08 14:23, Edjan Silva wrote:
> > > Dear fellow scientists,
> > >
> > > I'm doing a 40ns simulation between DNA and a small molecule. It
> occurred
> > > that around 30 nanoseconds, the computer hung up.
> > >
> > > How do I start the simulation from the 30 nanoseconds performed?
> >
> >
> > --
> >
> > Message: 3
> > Date: Thu, 8 Nov 2018 19:28:01 +0330
> > From: Farial Tavakoli 
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] DispErsion correction
> > Message-ID:
> > <
> > cadmafqhwfx8dpb2e8b1xyb6yyvba93p0jh3eyfq6wn5sxcm...@mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > Dear Justin and Dallas
> >
> > Thank you for your replying
> 

Re: [gmx-users] LINCS warning

[Mark Abraham]

Hi,

I can't tell whether that's a periodicity artefact in your visualization,
or the topology is indeed junk. You will likely need to inspect the output
of the tool that generated it. Rarely do these things "just work."

Mark

On Sun, Nov 11, 2018 at 3:01 AM Farial Tavakoli 
wrote:

> Dear Mark
>
> Thank you for your reply
> I got dt=0.5 ps and run EM and NVT on the ligand in vacuo and got this
> results:
> EM results:
>
> Steepest Descents converged to machine precision in 80 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  = -3.4145945e+03
> Maximum force =  6.6494578e+04 on atom 81
> Norm of force =  1.0602226e+04
>
> and NVT results:
>
> starting mdrun 'mig'
> 20 steps, 10.0 ps.
> step 199900, remaining wall clock time: 0 s
> Writing final coordinates.
> step 20, remaining wall clock time: 0 s
>Core t (s)   Wall t (s)(%)
>Time:  349.726   87.431  400.0
>  (ns/day)(hour/ns)
> Performance:9.8822.429
> I checked ligand.gro (generated using acpype script) and nvt.gro (generated
> by dt = 0.5) files by VMD and noticed the phosphate groups were not
> bound to tyrosine residues in ligand.gro and there was bad contacts in them
> in nvt.gro . Is it because of VMD software or there is a problem in
> converting files?
> If it is needed I will send you my files to you.
>
> Thanks in advance
> Farial
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Re: [gmx-users] Error: Cannot set thread affinities on the current platform

[Mark Abraham]

Hi,

Unfortunately Cygwin isn't a supported platform for GROMACS. Setting such
affinities is very important for performance, but doing so on cygwin
requires doing things outside of Cygwin, I believe. There are some blog
posts around that might help.

Mark

On Sun, Nov 11, 2018 at 6:45 PM Neena Susan Eappen <
neena.susaneap...@mail.utoronto.ca> wrote:

> Hello GROMACS users,
>
>
> I am running GROMACS version 5.1.1 on windows using cygwin (latest
> version).After the following command: gmx mdrun -deffnm nvt
>
> Error message: Compiled SIMD instructions: SSE4.1, GROMACS could use
> AVX2_256 on this machine, which is better
>
> Reading file nvt.tpr, VERSION 5.1.1 (single precision)
> Changing nstlist from 10 to 20, rlist from 1 to 1.029
>
> Using 1 MPI thread
> Using 4 OpenMP threads
>
> NOTE: Cannot set thread affinities on the current platform.
> starting mdrun 'Protein in water'
> 5 steps,100.0 ps.
>
> Could there be anything incompatible between Cygwin and Gromacs here? Any
> insight would be appreciated, Many thanks,
>
>
> Neena Eappen
> Graduate Student
> Jockusch Lab, U of T
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Re: [gmx-users] Insert Molecules Settings

[Mark Abraham]

Hi,

The tools look first in the working directory for such files, so copy it
there and modify however suits you.

Mark

On Mon, Nov 12, 2018 at 2:42 PM tca1  wrote:

> I sent this message on Friday, but I didn't see it show up in my
> digest, so I'm trying again. Here's the previous text:
>
>
> Thanks all for your suggestions so far. I believe I've got things more
> or less functional but I want to refine how I'm constructing my
> initial simulation box.
>
> In particular, I'm using a custom coarse-grained system, so I'd like
> to be able to tailor the effective vdW radii for use with
> insert-molecules and solvate commands to accommodate the typically
> larger sizes of the CG sites. However, many of my simulations are on
> clusters or other resources where I can't edit the vdwradii.dat file
> and not all CG particles in my simulation have the same radii, so just
> updating the default radius using the -radius option isn't completely
> satisfactory either.
>
>   Is there a way to tailor these values for each type of CG particle
> without editing the database file, or some other similar workaround to
> this issue?
>
> Thanks,
> Tom
>
>
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Re: [gmx-users] Global minimum

[Mark Abraham]

Hi,

That's not a relevant thing. In statistical mechanics you have an ensemble
of configurations.

Mark

On Mon, Nov 12, 2018 at 12:11 AM Shan Jayasinghe <
shanjayasinghe2...@gmail.com> wrote:

> Dear Gromacs Users,
>
> How do we get the global minimum from a MD simulation? Is there any method
> available in Gromacs to reach global minimum structure rather than local
> minimum structures?
>
> Thank you.
> --
> Best Regards
> Shan Jayasinghe
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Re: [gmx-users] Building Gromacs

[Mark Abraham]

Hi,

On Mon, Nov 12, 2018 at 3:46 PM Jasper Jordan  wrote:

> I was sure that a month ago when I started down the path of building and
> making Gromacs available for our user community, that I read a statement
> that whenever there is a hardware change, you need to rebuild Gromacs. I
> took this quite literally. So I assume that if hardware isn't identical
> (make, model, etc) a rebuild is required.
>

That's not a statement you'd find in the GROMACS docs, so I presume you've
followed some blog post or similar. Buyer beware, in such cases.

Well, now I can't find the statement, and we're attempting to deploy to AWS
> where we might have 1 core, or 8, and we may have no GPUs, or 1, 8, or 16
> per instance. So people are asking why I need to rebuild, and I can't give
> them an answer because I can't find the statement any more.
>

As Justin said, the hardware generation matters, not the hardware count.

Mark


> Can somebody tell me if it is required? Was it required? Or is it just a
> misremembery that I need to just discard?
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Re: [gmx-users] Running GPU issue

[Mark Abraham]

Hi,

It can share.

Mark

On Mon, Nov 12, 2018 at 10:19 PM Kovalskyy, Dmytro 
wrote:

> Hi,
>
>
>
> To perform GPU with Gromacs does it require exclusive  GPU card or Gromacs
> can share the video card with X-server?
>
>
> Thank you
>
>
> Dmytro
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Re: [gmx-users] Unable to generate .rtp file from gro and pdb file.

[Mark Abraham]

Hi,

Your topology had 5 GEL and 2 PE, which means you have 7 things that could
be a problem. Start with 1 so you find out where the problem is.

Mark

On Mon, Nov 12, 2018 at 10:40 PM Karpurmanjari Kakati <
ch18resch01...@iith.ac.in> wrote:

> Hi,
> I didn't understand, what you exactly meant. Could you be more elaborate?
>
> Karpurmanjari
>
> On Sun, Nov 11, 2018 at 12:37 PM Karpurmanjari Kakati <
> ch18resch01...@iith.ac.in> wrote:
>
> > Hi
> > I tried doing the same, like you said.
> > 1. Copied the OPLS AA force field files to the directory, where my pdb
> > files were present.
> > 2. Modified the rtp file. but the error comes up in the pdb2gmx "no
> > residjue type in the residue database. "
> > Alternatively, what I tired doing is the following:
> >
> > 1. I constructed the polymer in Avogrado software.
> > 2. Used OBGMX to make the itp file. But the charge column genereated by
> > OBGMX is .
> > 3. To include charge, I went back to Avogrado, and took the charges from
> > each atom and included it in the itp file by replacing the   against
> > each atom.
> > 4. Now my topology file looks something like this:
> >
> >
> >
> > #include "oplsaa.ff/forcefield.itp"
> >
> >
> >
> > [ atomtypes ]
> > ; name1 name2   mass charge  ptype   sigma   epsilon
> > N_3  N_314.0067  0.227A  0.3261   0.2889
> > C_3  C_312.0107  0.050   A  0.3431   0.4396
> > C_2  C_212.0107  0.261  A  0.3431   0.4396
> > O_2  O_215.9994  -0.013   A  0.3118   0.2512
> > N_2  N_214.0067  -0.302   A  0.3261   0.2889
> > N_R  N_R14.0067  -0.289   A  0.3261   0.2889
> > O_3  O_315.9994  -0.390A  0.3118   0.2512
> > H_   H_  1.0079  0.200  A  0.2571   0.1842
> > NE  NE14.0067  0.227   A  0.3261   0.2889
> > NH1  NH114.0067  0.227   A  0.3261   0.2889
> > NH2  NH214.0067  0.227   A  0.3261   0.2889
> >
> > CA  CA12.0107  0.050   A  0.3431   0.4396
> > C  C12.0107  0.050  A  0.3431   0.4396
> > CB  CB12.0107  0.261   A  0.3431   0.4396
> > CG  CG12.0107  0.261   A  0.3431   0.4396
> > CD  CD12.0107 0.261   A  0.3431   0.4396
> > CZ  CZ12.0107  0.261   A  0.3431   0.4396
> > N   N14.0067  0.227A  0.3261   0.2889
> > H1   H1  1.0079  0.200   A  0.2571   0.1842
> > H2   H2  1.0079  0.200   A  0.2571   0.1842
> > HA   HA  1.0079 0.200   A  0.2571   0.1842
> > HB1   HB1  1.0079  0.200   A  0.2571   0.1842
> > HB2   HB2  1.0079  0.200   A  0.2571   0.1842
> > HB3   HB3  1.0079  0.200   A  0.2571   0.1842
> > H   H  1.0079  0.200   A  0.2571   0.1842
> > HA1   HA1  1.0079  0.200   A  0.2571   0.1842
> > HA2   HA2  1.0079  0.200   A  0.2571   0.1842
> > HG1   HG1  1.0079  0.200   A  0.2571   0.1842
> > HG2   HG2  1.0079  0.200   A  0.2571   0.1842
> > HD1   HD1  1.0079  0.200   A  0.2571   0.1842
> > HD2   HD2  1.0079  0.200   A  0.2571   0.1842
> > HE   HE  1.0079  0.200   A  0.2571   0.1842
> > HH21   HH21  1.0079  0.200   A  0.2571   0.1842
> > HH22   HH22  1.0079  0.200   A  0.2571   0.1842
> > HH11   HH11  1.0079  0.200   A  0.2571   0.1842
> > HH12   HH12  1.0079  0.200   A  0.2571   0.1842
> > HG   HG  1.0079  0.200   A  0.2571   0.1842
> > HD   HD  1.0079  0.200   A  0.2571   0.1842
> > HW1   HW1  1.0079 0.200   A  0.2571   0.1842
> > HW2  HW2  1.0079  0.200   A  0.2571   0.1842
> > O  O15.9994 -0.390   A  0.3118   0.2512
> >
> >
> >
> > #include 
> >
> > ; Include Position restraint file
> > #ifdef POSRES
> > #include "posre-gel.itp"
> > #endif
> >
> > #include 
> >
> > ; Include Position restraint file
> > #ifdef POSRES
> > #include "posre-pe.itp"
> > #endif
> >
> > [ system ]
> > GEL and PE
> >
> > [ molecules ]
> > GEL  5
> > PE   2
> >
> >
> >
> > And now I am performing EM in vacuum for the system. The error comes to
> be
> > it stops Energy minimization before the desired energy is reached.
> > Like I read from other error mails, it says the topology or the itp file
> > had defects.
> >
> >
> > My query is, I just added charges to the itp file generated from OBGMX.
> > Is that the reason why my energy minimization is stopping at the 

Re: [gmx-users] dssp excutable-error

[Mark Abraham]

Hi,

Have you followed the advice in gmx help do_dssp about setting the
environment variables? Did you install the correct version of dssp?

Mark

On Mon, Nov 12, 2018 at 11:43 PM marzieh dehghan 
wrote:

> Dear all
> I installed dssp software on ubuntu version 12.04 in the /usr/local/bin,
> when I run the following command "*sudo find / -name dssp*" it showed the
> mentioned pathway, but when I apply the following comand "*gmx do_dssp -f
> xtc -s tpr -o xpm -sc xvg -tu ns*"
>
> I confronted to this error:
> *"failed to execute command: try specifying your dssp version with the -ver
> option" *
>
> please let me know how to solve this problem.
>
> Thanks in advances.
> Best wishes.
> Marzieh
> --
>
>
>
>
> *Marzieh DehghanPhD of BiochemistryInstitute of biochemistry and Biophysics
> (IBB)University of Tehran, Tehran- Iran.*
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Re: [gmx-users] Subject: Re: Group WAT referenced in the .mdp file was not found in the index file

[Mark Abraham]

Hi,

If you want to engage in discussion, please don't subscribe to the digest,
because you can no longer reply to your own discussion in a way that means
people understand the context.

Mark

On Tue, Nov 13, 2018 at 1:13 AM Rahma Dahmani 
wrote:

> Hi Justin,
> Thanks for your response,
> I am using a topology file constructed from amber tools ...
>
>
> --
>
>
>
>
>
>
> *Rahma Dahmani Doctorante en CHIMIE Unité de Recherche: Physico-Chimie des
> Matériaux à l'état condensé, Laboratoire de Chimie Théorique et
> Spectroscopie MoléculaireUniversité de Tunis El Manar, Faculté des Sciences
> de Tunis Campus Universitaire Farhat Hached - BP n ° 94 - Rommana 1068,
> Tunisie Tél: (+216) 28151042 <+216%2028%20151%20042>*
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Re: [gmx-users] Do need to recompile GROMACS with hardware changes

[Mark Abraham]

Hi,

On Tue, Nov 13, 2018 at 8:15 AM Darin Lory-External <
darin.l...@regeneron.com> wrote:

> To Distribution:
>
> Do you need to recompile GROMACS with any hardware changes, i.e. 1 GPU to
> 8 GPU or 16 GPUs.
>

No. You might require a recompilation if the generation of the hardware
changes, or the available libraries or drivers are of a different version
or in a different place.

My coworker says he saw this requirement in the documentation.  But with
> the new release 2018.4, it's not there.
>

There's no requirement to do so. But doing so ensures no problems and
maximum performance. Depends what you know about your execution environment.

Mark
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Re: [gmx-users] Setting rcon according to system

[Mark Abraham]

Hi,

Possibly. It would be simpler to use fewer processors, such that the
domains can be larger.

What does mdrun think it needs for -rcon?

Mark

On Tue, Nov 13, 2018 at 7:06 AM Sergio Perez  wrote:

> Dear gmx comunity,
>
> I have been running my system without any problems with 100 processors. But
> I decided to make some of the bonds of my main molecule constrains. My
> molecule is not an extended chain, it is a molecular hydrated ion, in
> particular the uranyl cation with 5 water molecules forming a pentagonal by
> bipyramid. At this point I get a domain decomposition error and I would
> like to reduce rcon in order to run with 100 processors. Since I know that
> by the shape of my molecule, two atoms connected by several constraints
> will never be further appart than 0.6nm, can I use this safely for -rcon?
>
> Thank you very much!
> Best regards,
> Sergio Pérez-Conesa
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Re: [gmx-users] ali.mof...@mail.utoronto.ca

[Mark Abraham]

Hi,

It looks like the configure that is part of the FFTW build that you
requested from GROMACS does not like your build location. Perhaps that's
because your username has a space in it and configure can't handle that.
Unfortunately GROMACS can't fix that, so I suggest you try to build from
some other location, like /tmp.

Mark

On Tue, Nov 13, 2018 at 9:06 PM Ali Kaazempur-Mofrad <
ali.mof...@mail.utoronto.ca> wrote:

> Hello. I am trying to install GROMACS and when I enter 'make'', I get this
> response. What can I do to fix this?
>
>
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether build environment is sane... configure: error: unsafe
> srcdir value: '/mnt/c/Users/Ali
> Mofrad/Downloads/gromacs-2018.4/build/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild'
> src/contrib/fftw/CMakeFiles/fftwBuild.dir/build.make:109: recipe for
> target
> 'src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/fftwBuild-configure'
> failed
> make[3]: ***
> [src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/fftwBuild-configure]
> Error 1
> CMakeFiles/Makefile2:1435: recipe for target
> 'src/contrib/fftw/CMakeFiles/fftwBuild.dir/all' failed
> make[2]: *** [src/contrib/fftw/CMakeFiles/fftwBuild.dir/all] Error 2
> CMakeFiles/Makefile2:1165: recipe for target 'CMakeFiles/check.dir/rule'
> failed
> make[1]: *** [CMakeFiles/check.dir/rule] Error 2
> Makefile:626: recipe for target 'check' failed
> make: *** [check] Error 2
>
> --
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[gmx-users] ali.mof...@mail.utoronto.ca

[Ali Kaazempur-Mofrad]

Hello. I am trying to install GROMACS and when I enter 'make'', I get this 
response. What can I do to fix this?


checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... configure: error: unsafe srcdir 
value: '/mnt/c/Users/Ali 
Mofrad/Downloads/gromacs-2018.4/build/src/contrib/fftw/fftwBuild-prefix/src/fftwBuild'
src/contrib/fftw/CMakeFiles/fftwBuild.dir/build.make:109: recipe for target 
'src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/fftwBuild-configure' 
failed
make[3]: *** 
[src/contrib/fftw/fftwBuild-prefix/src/fftwBuild-stamp/fftwBuild-configure] 
Error 1
CMakeFiles/Makefile2:1435: recipe for target 
'src/contrib/fftw/CMakeFiles/fftwBuild.dir/all' failed
make[2]: *** [src/contrib/fftw/CMakeFiles/fftwBuild.dir/all] Error 2
CMakeFiles/Makefile2:1165: recipe for target 'CMakeFiles/check.dir/rule' failed
make[1]: *** [CMakeFiles/check.dir/rule] Error 2
Makefile:626: recipe for target 'check' failed
make: *** [check] Error 2

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Re: [gmx-users] pdb generator

[Victor Rosas Garcia]

Hello Momin

The best tool I have found for dealing with cif files, including exporting
to pdb, is Mercury.  You can download it for free from:
https://www.ccdc.cam.ac.uk/Community/csd-community/freemercury/

Hope this helps

Victor

El mar., 13 nov. 2018 a las 8:04, Momin Ahmad ()
escribió:

> Hi,
>
> is there a tool where i can use for example a .cif file (or .xyz) file
> to generate a .pdb file with correct classification? For example
> Avogadro classifies all atoms as LIG and i cannot change it. Is there
> also another tool which can be used to generate large scale crystal
> structures with building blocks as input?
>
>
> Cheers
>
> Momin
>
> --
> Momin Ahmad
>
> Karlsruhe Institute of Technology (KIT)
> Steinbuch Centre for Computing (SCC)
> Hermann-von-Helmholtz-Platz 1
> 76344 Eggenstein-Leopoldshafen
> Phone: +49 721 608-24286
> E-Mail: momin.ah...@kit.edu
>
> --
> Gromacs Users mailing list
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> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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Re: [gmx-users] pdb generator

[Ali Ahmed]

You should know how many atoms in each residue then how many residues of
XXX you have then you can see.
Suggestion, if possible use sperate pdb files then use solvation option to
produce your system .gro  or pdb. This will help you in editing each pdb
then get your correct gromacs input files.
Best

On Tue, Nov 13, 2018 at 9:35 AM Momin Ahmad  wrote:

> Hi Ali,
>
> thanks for you help. How can you distinguish between a C atom from
> residue XXX and another C atom from residue YYY when there are about
> 2000 atoms in the file. Did you write a script for that? If there doesnt
> exist a tool with a GUI to solve this then i will have to write my own
> builder.
>
> Cheers
>
> Momin
>
> Am 13.11.18 um 16:31 schrieb Ali Ahmed:
> > well if you use Linux then you can use GVim to do highlight and do simple
> > changes on one type only then use find and replace option. That what I do
> > when I have more than one type. It needs one hour practice then you will
> be
> > ok. Or you can write a script for such things.
> > Best
> >
> > On Tue, Nov 13, 2018 at 9:15 AM Momin Ahmad  wrote:
> >
> >> Hi Ali,
> >>
> >> my problem is that there is not only one molecule but two different
> >> molecules which build up a crystaline structure. For example i have 10
> >> XXX and 100 YYY in the .pdb file.
> >>
> >> Cheers
> >>
> >> Momin
> >>
> >> Am 13.11.18 um 16:12 schrieb Ali Ahmed:
> >>> Hi,
> >>> I use Avogadro and it is easy to change LIG to anything you want. I
> just
> >>> use find and replace option which takes less than a minute.
> >>> Best
> >>> Ali
> >>>
> >>> On Tue, Nov 13, 2018 at 8:04 AM Momin Ahmad 
> wrote:
> >>>
>  Hi,
> 
>  is there a tool where i can use for example a .cif file (or .xyz) file
>  to generate a .pdb file with correct classification? For example
>  Avogadro classifies all atoms as LIG and i cannot change it. Is there
>  also another tool which can be used to generate large scale crystal
>  structures with building blocks as input?
> 
> 
>  Cheers
> 
>  Momin
> 
>  --
>  Momin Ahmad
> 
>  Karlsruhe Institute of Technology (KIT)
>  Steinbuch Centre for Computing (SCC)
>  Hermann-von-Helmholtz-Platz 1
>  76344 Eggenstein-Leopoldshafen
>  Phone: +49 721 608-24286
>  E-Mail: momin.ah...@kit.edu
> 
>  --
>  Gromacs Users mailing list
> 
>  * Please search the archive at
>  http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>  posting!
> 
>  * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
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>  https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>  send a mail to gmx-users-requ...@gromacs.org.
> 
> >> --
> >> Momin Ahmad
> >>
> >> Karlsruhe Institute of Technology (KIT)
> >> Steinbuch Centre for Computing (SCC)
> >> Hermann-von-Helmholtz-Platz 1
> >> 76344 Eggenstein-Leopoldshafen
> >> Phone: +49 721 608-24286
> >> E-Mail: momin.ah...@kit.edu
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
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> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> --
> Momin Ahmad
>
> Karlsruhe Institute of Technology (KIT)
> Steinbuch Centre for Computing (SCC)
> Hermann-von-Helmholtz-Platz 1
> 76344 Eggenstein-Leopoldshafen
> Phone: +49 721 608-24286
> E-Mail: momin.ah...@kit.edu
>
> --
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Re: [gmx-users] pdb generator

[Momin Ahmad]

Hi Ali,

thanks for you help. How can you distinguish between a C atom from 
residue XXX and another C atom from residue YYY when there are about 
2000 atoms in the file. Did you write a script for that? If there doesnt 
exist a tool with a GUI to solve this then i will have to write my own 
builder.


Cheers

Momin

Am 13.11.18 um 16:31 schrieb Ali Ahmed:

well if you use Linux then you can use GVim to do highlight and do simple
changes on one type only then use find and replace option. That what I do
when I have more than one type. It needs one hour practice then you will be
ok. Or you can write a script for such things.
Best

On Tue, Nov 13, 2018 at 9:15 AM Momin Ahmad  wrote:


Hi Ali,

my problem is that there is not only one molecule but two different
molecules which build up a crystaline structure. For example i have 10
XXX and 100 YYY in the .pdb file.

Cheers

Momin

Am 13.11.18 um 16:12 schrieb Ali Ahmed:

Hi,
I use Avogadro and it is easy to change LIG to anything you want. I just
use find and replace option which takes less than a minute.
Best
Ali

On Tue, Nov 13, 2018 at 8:04 AM Momin Ahmad  wrote:


Hi,

is there a tool where i can use for example a .cif file (or .xyz) file
to generate a .pdb file with correct classification? For example
Avogadro classifies all atoms as LIG and i cannot change it. Is there
also another tool which can be used to generate large scale crystal
structures with building blocks as input?


Cheers

Momin

--
Momin Ahmad

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

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send a mail to gmx-users-requ...@gromacs.org.


--
Momin Ahmad

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

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send a mail to gmx-users-requ...@gromacs.org.


--
Momin Ahmad

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

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Re: [gmx-users] pdb generator

[Ali Ahmed]

well if you use Linux then you can use GVim to do highlight and do simple
changes on one type only then use find and replace option. That what I do
when I have more than one type. It needs one hour practice then you will be
ok. Or you can write a script for such things.
Best

On Tue, Nov 13, 2018 at 9:15 AM Momin Ahmad  wrote:

> Hi Ali,
>
> my problem is that there is not only one molecule but two different
> molecules which build up a crystaline structure. For example i have 10
> XXX and 100 YYY in the .pdb file.
>
> Cheers
>
> Momin
>
> Am 13.11.18 um 16:12 schrieb Ali Ahmed:
> > Hi,
> > I use Avogadro and it is easy to change LIG to anything you want. I just
> > use find and replace option which takes less than a minute.
> > Best
> > Ali
> >
> > On Tue, Nov 13, 2018 at 8:04 AM Momin Ahmad  wrote:
> >
> >> Hi,
> >>
> >> is there a tool where i can use for example a .cif file (or .xyz) file
> >> to generate a .pdb file with correct classification? For example
> >> Avogadro classifies all atoms as LIG and i cannot change it. Is there
> >> also another tool which can be used to generate large scale crystal
> >> structures with building blocks as input?
> >>
> >>
> >> Cheers
> >>
> >> Momin
> >>
> >> --
> >> Momin Ahmad
> >>
> >> Karlsruhe Institute of Technology (KIT)
> >> Steinbuch Centre for Computing (SCC)
> >> Hermann-von-Helmholtz-Platz 1
> >> 76344 Eggenstein-Leopoldshafen
> >> Phone: +49 721 608-24286
> >> E-Mail: momin.ah...@kit.edu
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> --
> Momin Ahmad
>
> Karlsruhe Institute of Technology (KIT)
> Steinbuch Centre for Computing (SCC)
> Hermann-von-Helmholtz-Platz 1
> 76344 Eggenstein-Leopoldshafen
> Phone: +49 721 608-24286
> E-Mail: momin.ah...@kit.edu
>
> --
> Gromacs Users mailing list
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> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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Re: [gmx-users] pdb generator

[Momin Ahmad]

Hi Ali,

my problem is that there is not only one molecule but two different 
molecules which build up a crystaline structure. For example i have 10 
XXX and 100 YYY in the .pdb file.


Cheers

Momin

Am 13.11.18 um 16:12 schrieb Ali Ahmed:

Hi,
I use Avogadro and it is easy to change LIG to anything you want. I just
use find and replace option which takes less than a minute.
Best
Ali

On Tue, Nov 13, 2018 at 8:04 AM Momin Ahmad  wrote:


Hi,

is there a tool where i can use for example a .cif file (or .xyz) file
to generate a .pdb file with correct classification? For example
Avogadro classifies all atoms as LIG and i cannot change it. Is there
also another tool which can be used to generate large scale crystal
structures with building blocks as input?


Cheers

Momin

--
Momin Ahmad

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

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send a mail to gmx-users-requ...@gromacs.org.


--
Momin Ahmad

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

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Re: [gmx-users] pdb generator

[Ali Ahmed]

Hi,
I use Avogadro and it is easy to change LIG to anything you want. I just
use find and replace option which takes less than a minute.
Best
Ali

On Tue, Nov 13, 2018 at 8:04 AM Momin Ahmad  wrote:

> Hi,
>
> is there a tool where i can use for example a .cif file (or .xyz) file
> to generate a .pdb file with correct classification? For example
> Avogadro classifies all atoms as LIG and i cannot change it. Is there
> also another tool which can be used to generate large scale crystal
> structures with building blocks as input?
>
>
> Cheers
>
> Momin
>
> --
> Momin Ahmad
>
> Karlsruhe Institute of Technology (KIT)
> Steinbuch Centre for Computing (SCC)
> Hermann-von-Helmholtz-Platz 1
> 76344 Eggenstein-Leopoldshafen
> Phone: +49 721 608-24286
> E-Mail: momin.ah...@kit.edu
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] Do need to recompile GROMACS with hardware changes

[Darin Lory-External]

To Distribution:

Do you need to recompile GROMACS with any hardware changes, i.e. 1 GPU to 8 GPU 
or 16 GPUs.

My coworker says he saw this requirement in the documentation.  But with the 
new release 2018.4, it's not there.

Can anyone confirm? Many thanks for any responses.

-Darin

Darin S Lory
Cloud & Data Center Engineering
Email: darin.l...@regeneron.com
Simplify | Innovate | Reuse
 
 


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[gmx-users] pdb generator

[Momin Ahmad]

Hi,

is there a tool where i can use for example a .cif file (or .xyz) file 
to generate a .pdb file with correct classification? For example 
Avogadro classifies all atoms as LIG and i cannot change it. Is there 
also another tool which can be used to generate large scale crystal 
structures with building blocks as input?



Cheers

Momin

--
Momin Ahmad

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

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[gmx-users] Setting rcon according to system

[Sergio Perez]

Dear gmx comunity,

I have been running my system without any problems with 100 processors. But
I decided to make some of the bonds of my main molecule constrains. My
molecule is not an extended chain, it is a molecular hydrated ion, in
particular the uranyl cation with 5 water molecules forming a pentagonal by
bipyramid. At this point I get a domain decomposition error and I would
like to reduce rcon in order to run with 100 processors. Since I know that
by the shape of my molecule, two atoms connected by several constraints
will never be further appart than 0.6nm, can I use this safely for -rcon?

Thank you very much!
Best regards,
Sergio Pérez-Conesa
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[gmx-users] How to use rcon based on my system.

[Sergio Perez]

Dear gmx comunity,

I have been running my system without any problems with 100 processors. But
I decided to make some of the bonds of my main molecule constrains. My
molecule is not an extended chain, it is a molecular hydrated ion, in
particular the uranyl cation with 5 water molecules forming a pentagonal by
bipyramid. At this point I get a domain decomposition error and I would
like to reduce rcon in order to run with 100 processors. Since I know that
by the shape of my molecule, two atoms connected by several constraints
will never be further appart than 0.6nm, can I use this safely for -rcon?

Thank you very much!
Best regards,
Sergio Pérez-Conesa
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