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.co...@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-----
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<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> On Behalf Of
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Sent: jueves, 30 de enero de 2020 23:31
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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...@yahoo.com>
To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org>
Subject: [gmx-users] 3D monitors
Message-ID: <2141569556.1500215.1580394239...@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" <sli...@g.uky.edu>
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Analysis with .sh file
Message-ID:
<CAC+hMcAQhU+J0mCudNCiydYM2EnK4_ttx+7EX+v-uFS12KUn=q...@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 <ashmakhan...@gmail.com>
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Regarding rdf and number of molecules in the FSS
of tetramer
Message-ID:
<cag89cr68btyevasakxz+-npaibco8fa9k6sm+qrdlf4eafx...@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.rm...@gmail.com>
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Customize gromac FF for lipid parameters
Message-ID:
<CACWq+6_7TSkH4ajiYLOYOMwGjxBxG6J=wwxbp5y9cbg7cfz...@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
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