[gmx-users] Anybody using Silica InterfaceFF on Gromacs?

[Diez Fernandez, Amanda]

Hi Mark, 

*So, for the record, the actual issue is that GROMACS does not implement
*some kind of tapering of non-bonded interactions that would apply between
*particle pairs at short range?

This is the extract from the supporting information of the paper I refer
to that explains the issue
(³http://irep.ntu.ac.uk/id/eprint/4652/7/4652__Perry_SI.pdf²):
"Full inclusion of attractive nonbond interactions between 1,4 bonded
atoms in most force fields (CHARMM, CVFF, PCFF, COMPASS) requires a 4%
increase in r (the equilibrium bond length parameter of the forcefield)
Partial inclusion of attractive nonbond interactions between 1,4 bonded
atoms (50% of Lennard-Jones interactions and 5/6 of Coulomb interactions
in AMBER) requires only a 2.5% increase, and 12-6 LJ parameters identical
to these in CVFF and CHARMM can then be used."

My particular issue was that I assumed gen-pairs=yes in the [ default ]
section of the topology file meant that Gromacs automatically generated a
list of atoms undergoing 1-4 interactions (as well as automatically
generating the modified LJ and Coulomb parameters for those interactions).
When I proceeded to manually specify the list of atoms undergoing 1-4
interactions within the [pairs] section of the topology, the silica system
compressed during the simulation to produce the correct equilibrium bond
length observed experimentally.

Thanks, 
Amanda  





On 03/07/2017, 06:34, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se
on behalf of gromacs.org_gmx-users-request 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> wrote:

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>Today's Topics:
>
>   1. Re: Anybody using Silica InterfaceFF on Gromacs? (Mark Abraham)
>   2. Re: Can not open file: run.trr (Mark Abraham)
>   3. Re: Can not open file: run.trr (Mark Abraham)
>   4. Re: Anybody using Silica InterfaceFF on Gromacs? (Alex)
>   5. Multiple output log. xtc .edr files generated using	mpirun
>      (Abhishek Acharya)
>   6. Grid Spacing (Apramita Chand)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Mon, 03 Jul 2017 00:03:52 +0000
>From: Mark Abraham <mark.j.abraham at gmail.com>
>To: gmx-users at gromacs.org
>Subject: Re: [gmx-users] Anybody using Silica InterfaceFF on Gromacs?
>Message-ID:
>	<CAMNuMAS5yoMY5Nd7ewgixXc+BQop5eHt1E5wEJZoY-0BMjvhSQ at mail.gmail.com>
>Content-Type: text/plain; charset="UTF-8"
>
>Hi,
>
>On Fri, Jun 30, 2017 at 2:46 AM Alex <nedomacho at gmail.com> wrote:
>
>> >
>> >
>> >>
>> >> He he, childish :)
>> >
>> > David, no offense intended. I just think that when applied to solids,
>>the
>> entire concept of what works so well for biomolecular systems becomes a
>>bit
>> of a joke. And vice versa, to be fair. Spoken from experience, really
>>-- we
>> here used Gromacs to simulate things that I keep telling people not to
>> simulate with Gromacs, and it got published!. :)
>>
>
>Sure - one should use a tool capable of doing the job, and use its
>optional
>capabilities accordingly. Choosing non-bonded exclusions based on bonds,
>in
>a way that does not implement the intended model physics, is indeed wrong,
>but that doesn't make the use of modified 1-4 pair interactions "childish"
>in general ;-)
>
>
>> In any case, I second what was said above re: # of exclusions.
>>Solid-state
>> potentials use smooth drop-offs to exclude long-range interactions
>>between
>> close neighbor sharing elements, so looking into David's suggestion may
>>in
>> fact fix the issues immediately.
>>
>
>So, for the record, the actual issue is that GROMACS does not implement
>some kind of tapering of non-bonded interactions that would apply between
>particle pairs at short range?
>
>Mark
>
>
>> Alex
>> --
>> 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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>> send a mail to gmx-users-request at gromacs.org.
>>
>
>
>------------------------------
>
>Message: 2
>Date: Mon, 03 Jul 2017 00:06:16 +0000
>From: Mark Abraham <mark.j.abraham at gmail.com>
>To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
>Subject: Re: [gmx-users] Can not open file: run.trr
>Message-ID:
>	<CAMNuMARRYPPQNhjvaG0452Bor4jDRZM08Ekj1-zF7QJKFpX=Hg at mail.gmail.com>
>Content-Type: text/plain; charset="UTF-8"
>
>Hi,
>
>Use tools like rsync to do your file copies and preserve suitable
>permissions automatically. And try to avoid copying files > 2GB to
>partitions formatted in Windows-friendly fashion to e.g. FAT32 file
>sytems,
>as external hard drives might be formatted.
>
>Mark
>
>On Sun, Jul 2, 2017 at 10:59 PM Samith Rathnayake <samithzzz1 at gmail.com>
>wrote:
>
>> Hi everyone,
>>
>> Recently I was run a 30ns gromacs simulation.And for the analysis part,
>>i
>> was copied down the entire file directory of the simulation into an
>> external hard disk and shift it into another computer with same OS and
>>same
>> version of gromacs (ubuntu 14.04 and gromacs 4.6.5). After copied down
>>to
>> another computer, I was work with the file permission scenario by using
>>the
>> command: chmod 777 for every and each file .Then  I was run the g_rms
>> command for the  RMSD analysis.But i was got the :
>>
>> 
>>.........................................................................
>>...............................................
>> Program g_rms, VERSION 4.6.5
>> Source code file: /build/buildd/gromacs-4.6.5/src/gmxlib/gmxfio.c, line:
>> 524
>>
>> Can not open file:
>> run70.trr
>> For more information and tips for troubleshooting, please check the
>>GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>>
>> 
>>.........................................................................
>>..............................................
>> The command worked with the same files when those files were in the
>> previous (original location) computer.Even i arranged the file
>>permission
>> on the new computer (new space) the trr files cant open.
>> How to overcome this situation?
>>
>>
>> thank you in advance.
>> --
>> 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-request at gromacs.org.
>>
>
>
>------------------------------
>
>Message: 3
>Date: Mon, 03 Jul 2017 00:06:16 +0000
>From: Mark Abraham <mark.j.abraham at gmail.com>
>To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
>Subject: Re: [gmx-users] Can not open file: run.trr
>Message-ID:
>	<CAMNuMARRYPPQNhjvaG0452Bor4jDRZM08Ekj1-zF7QJKFpX=Hg at mail.gmail.com>
>Content-Type: text/plain; charset="UTF-8"
>
>Hi,
>
>Use tools like rsync to do your file copies and preserve suitable
>permissions automatically. And try to avoid copying files > 2GB to
>partitions formatted in Windows-friendly fashion to e.g. FAT32 file
>sytems,
>as external hard drives might be formatted.
>
>Mark
>
>On Sun, Jul 2, 2017 at 10:59 PM Samith Rathnayake <samithzzz1 at gmail.com>
>wrote:
>
>> Hi everyone,
>>
>> Recently I was run a 30ns gromacs simulation.And for the analysis part,
>>i
>> was copied down the entire file directory of the simulation into an
>> external hard disk and shift it into another computer with same OS and
>>same
>> version of gromacs (ubuntu 14.04 and gromacs 4.6.5). After copied down
>>to
>> another computer, I was work with the file permission scenario by using
>>the
>> command: chmod 777 for every and each file .Then  I was run the g_rms
>> command for the  RMSD analysis.But i was got the :
>>
>> 
>>.........................................................................
>>...............................................
>> Program g_rms, VERSION 4.6.5
>> Source code file: /build/buildd/gromacs-4.6.5/src/gmxlib/gmxfio.c, line:
>> 524
>>
>> Can not open file:
>> run70.trr
>> For more information and tips for troubleshooting, please check the
>>GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>>
>> 
>>.........................................................................
>>..............................................
>> The command worked with the same files when those files were in the
>> previous (original location) computer.Even i arranged the file
>>permission
>> on the new computer (new space) the trr files cant open.
>> How to overcome this situation?
>>
>>
>> thank you in advance.
>> --
>> 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-request at gromacs.org.
>>
>
>
>------------------------------
>
>Message: 4
>Date: Sun, 2 Jul 2017 18:27:05 -0600
>From: Alex <nedomacho at gmail.com>
>To: gmx-users at gromacs.org
>Subject: Re: [gmx-users] Anybody using Silica InterfaceFF on Gromacs?
>Message-ID: <15f6281f-d32c-4f72-4014-f592f24b1bcf at gmail.com>
>Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>> Sure - one should use a tool capable of doing the job, and use its
>>optional
>> capabilities accordingly. Choosing non-bonded exclusions based on
>>bonds, in
>> a way that does not implement the intended model physics, is indeed
>>wrong,
>> but that doesn't make the use of modified 1-4 pair interactions
>>"childish"
>> in general ;-)
>>
>You are correct. My point only holds in a situation where people indeed
>are doing that: using an inappropriate tool. And you see how many people
>on this list ask questions about doing solid-state simulations with
>Gromacs. I have a dual background and could give many examples where the
>use of what works for proteins/lipids in water is, well, childish, for
>lack of a better word in solid-state systems. I hope noone takes
>offense. :) The "problem" is that, thanks to your hard work, Gromacs is
>delightful to use, much more so than LAMMPS, and my hope is that one day
>you guys will just implement things like REBO and ReaxFF and MEAM, and
>Weber-Stillinger and what-not. If you do that, I will fly to your
>location, give you a hug, and personally buy you a steak dinner. In
>other words, my hope is that one day Gromacs will be an appropriate tool
>for all of classical MD, solid or liquid state.
>> So, for the record, the actual issue is that GROMACS does not implement
>> some kind of tapering of non-bonded interactions that would apply
>>between
>> particle pairs at short range?
>>
>Within the question initially posed (about silica), Gromacs is fairly
>capable of everything necessary, it is just a matter of carefully
>reading the documentation on the original solid-state potential and then
>setting up the adopted forcefield, including the nrexl, etc. The much
>bigger issue (with solid-state things in general) is the springs for
>bonds, angles, etc, and use permanent molecular topologies. Wrong phonon
>spectra, wrong elastic properties away from 0K, wrong rippling spectra
>of graphene and likely all atomically thin membranes, inability to do
>covalent bond breaking/formation, etc, etc. That is, things Gromacs was
>never intended for. But then again, see what I said above.
>
>Alex
>
>
>------------------------------
>
>Message: 5
>Date: Mon, 3 Jul 2017 10:58:47 +0530
>From: Abhishek Acharya <abhi117acharya at gmail.com>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: [gmx-users] Multiple output log. xtc .edr files generated
>	using	mpirun
>Message-ID:
>	<CAB1aw3w3ooNi1BJMUw5HwcRYzoR9xFP1+1eCY-XBcnPDB7iOeA at mail.gmail.com>
>Content-Type: text/plain; charset="UTF-8"
>
>Hello GROMACS users,
>
>I am trying to run a simulation on a university cluster; I am using
>gromacs-5.1.2. The problem is while running mdrun, using the following
>command:
>
>mpirun -np 32 gmx mdrun -s prod.tpr -deffnm prod_out -pin on   ### I
>expected gmx mdrun_mpi here but it was not available.
>
>I am getting multiple log files, xtc, edr files as the output and all the
>log files say the following:
>
>
>Running on 1 node with total 16 cores, 16 logical cores
>Hardware detected:
>  CPU info:
>    Vendor: GenuineIntel
>    Brand:  Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz
>    Family:  6  model: 45  stepping:  7
>    CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr
>nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1
>sse4.2 ssse3 tdt x2apic
>    SIMD instructions most likely to fit this hardware: AVX_256
>    SIMD instructions selected at GROMACS compile time: AVX_256
>
>This in itself is pretty weird. I am guessing that the package is not
>properly installed by the admin. My question is what is the exact problem
>with the setup and what is the solution; i need to communicate this to the
>admin. Although, I reported the issue previously, but it seems he doesn't
>understand where the problem seems to be.
>
>
>Thanks in advance.
>
>Sincerely,
>Abhishek Acharya
>Research Associate,
>Department of Molecular Nutrition
>CSIR-Central Food Technological Research Institute,
>Mysuru-570020
>
>
>------------------------------
>
>Message: 6
>Date: Mon, 3 Jul 2017 11:04:56 +0530
>From: Apramita Chand <apramita.chand at gmail.com>
>To: gromacs.org_gmx-users at maillist.sys.kth.se
>Subject: [gmx-users] Grid Spacing
>Message-ID:
>	<CA+gTzoZ5xCZudtXPsZkOoZxkvGdMy=dFW4zniZKNA25K6UFOTg at mail.gmail.com>
>Content-Type: text/plain; charset="UTF-8"
>
>Dear All,
>Which is more appropriate fourier grid spacing for gromos53a6 ff with
>cutoffs being 0.9 and 1.4nm?
>0.16 or 0.12??
>I've not seen too many papers with 0.16 being used for this forcefield and
>that too with cutoffs like 1.0 for rcoulomb and rvdw.
>
>Is there any problem if I use fourier spacing of 0.16 with these
>cutoffs(0.9,1.4)?
>
>Also,should the grid spacing be same for equilibration and production
>runs??
>
>Yours sincerely,
>Apramita
>
>
>------------------------------
>
>-- 
>Gromacs Users mailing list
>
>* Please search the archive at
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>posting!
>
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>
>End of gromacs.org_gmx-users Digest, Vol 159, Issue 8
>*****************************************************