[gmx-users] gromacs.org_gmx-users Digest, Vol 189, Issue 80, 2. Re: Analysis with .sh file (Li, Shi)

[Christian Blau]

HI Riccardo,


in this case, it's the piping that does not work, so gromacs does not get the right "return". An alternative is

printf "10\n12\n"


Best,

Christian

On 2020-01-31 09:22, ric.concu at gmail.com wrote:
> Dear all,
>
> This is an example of a line I have been using on Gromacs 5.0.4:" echo
>      "10" "12" | gmx rdf -f box_tot -s box-npt -n box -o Mol1 &" and this is
>      the error message I'm receiving from Gromacs: "Error in user input:
>      Invalid selection '10 12 '
>       B  Near '12'
>       B B B  syntax error "
> Regards,
> Riccardo
>
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of
> gromacs.org_gmx-users-request at maillist.sys.kth.se
> Sent: jueves, 30 de enero de 2020 23:31
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: gromacs.org_gmx-users Digest, Vol 189, Issue 80
>
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> Today's Topics:
>
>     1. 3D monitors (tarzan p)
>     2. Re: Analysis with .sh file (Li, Shi)
>     3. Regarding rdf and number of molecules in the FSS of	tetramer
>        (Ashma Khan)
>     4. Customize gromac FF for lipid parameters (Yogesh Sharma)
>     5. Re: Customize gromac FF for lipid parameters (Justin Lemkul)
>     6. Re: gromacs-2020 build gcc/nvcc error (Ryan Woltz)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 30 Jan 2020 14:23:59 +0000 (UTC)
> From: tarzan p <tarzan11_11 at yahoo.com>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: [gmx-users] 3D monitors
> Message-ID: <2141569556.1500215.1580394239642 at mail.yahoo.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi all..Am looking for some good 3D monitors (either passive or active)Need
> suggestions for some good 3D monitors for protein structure and interactions
> visualization...
> with best wishes
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 30 Jan 2020 09:50:09 -0500
> From: "Li, Shi" <sli259 at g.uky.edu>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] Analysis with .sh file
> Message-ID:
> 	<CAC+hMcAQhU+J0mCudNCiydYM2EnK4_ttx+7EX+v-uFS12KUn=Q at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
>>
>> Dear all,
>>
>> I have recently upgrade my Gromacs to the 2019 version from the 5.0.4
>> and I found out that now that while I'm trying to use a .sh, as I was
>> doing in the version 5.0.4, now I'm receiving back an error since the
>> syntax is wrong. I'm wondering if someone could please help me.
>>
>>
> What is the script in your .sh file? There is not enough information to find
> out what goes wrong.
>
>
>
>> Regards,
>>
>> Riccardo
>>
>>
>>
>> ------------------------------
>>
>>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 30 Jan 2020 20:29:56 +0530
> From: Ashma Khan <ashmakhan200 at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Regarding rdf and number of molecules in the FSS
> 	of	tetramer
> Message-ID:
> 	<CAG89CR68btyevasAkXz+-npAiBCo8fa9k6sm+QRDLF4EafXF4Q at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear user's
> I have calculated the rdf of urea molecules around the peptides for
> different concentration of urea and obtained that peak height of first
> solvation shell (FSS) decreases with increase in concentration of urea.
> After that I have calculated the number of urea molecules in FSS and found
> that urea molecules in the FSS increases with concentration of urea. There
> is no correlation between the peak height of FSS and number of urea
> molecules. Can anybody suggest me ? what is the reason The command I have
> used is gmx rdf -f md.xtc -s md.tpr -o rdf.xvg -selrpos whole_res_com
> -seltype whole_res_com gmx select -f md.xtc -s md.tpr -os number.xvg -select
> "resname URE and within 0.5 of group protein" -selrpos whole_res_com
> -seltype whole_res_com
>
>
> --
> Ashma Khan
> Research Scholar
> Department of Chemistry
> AMU, Aligarh
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 31 Jan 2020 01:32:43 +0530
> From: Yogesh Sharma <yogesh.rma13 at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Customize gromac FF for lipid parameters
> Message-ID:
> 	<CACWq+6_7TSkH4ajiYLOYOMwGjxBxG6J=wwXbP5y9CBG7cfzP4w at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hey everyone,
> I have a membrane patch generated by charmm gui. I want to customize my
> gromac forcefield in accordance with it. I want some suggestion in
> extracting information from charmmff. I guess i need information to add in
> ffbonded and ffnonbonded files. Can someone help me with it
>
> I don't want to run simulations in charmmff
>
>