[gmx-users] gromacs.org_gmx-users Digest, Vol 158, Issue 181

Thu Jun 29 11:50:15 CEST 2017

Hi, 
Thanks Alex. 
I have now solved the problem.
I assumed ³gen - pairs = yes² within [ Defaults ] of the topology was
generating automatically a list of pairs of 1-4 interactions as well as
modifying the LJ and QQ parameters for those interactions.
I have now listed the 1-4 pairs within [ Pairs ] and it has led to the
correct equilibrium bond length.
Cheers, 
Amanda

On 28/06/2017, 19:22, "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: Atom types comparison between CGenFF and Charm36FF
>      (Justin Lemkul)
>   2. Re: Atom types comparison between CGenFF and Charm36FF
>      (Mohsen Ramezanpour)
>   3. Re: Using SLLOD to find Viscosity (nishi kashyap)
>   4. Deform a liquid (nishi kashyap)
>   5. Anybody using Silica InterfaceFF on Gromacs?
>      (Diez Fernandez, Amanda)
>   6. Re: Anybody using Silica InterfaceFF on Gromacs? (Alex)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Wed, 28 Jun 2017 10:21:32 -0600
>From: Justin Lemkul <jalemkul at vt.edu>
>To: gmx-users at gromacs.org
>Subject: Re: [gmx-users] Atom types comparison between CGenFF and
>	Charm36FF
>Message-ID: <350dd743-bdfa-76ee-a401-039cadaf1d8a at vt.edu>
>Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
>On 6/28/17 9:10 AM, Mohsen Ramezanpour wrote:
>> Thanks Justin for your comment.
>> 
>> I have a bit of difficulty for the finding the analog parts to these two
>> parts.
>> 
>> Is there any database (preferably with shapes) for the molecules
>>available
>> in charmmFF?
>> 
>
>The CHARMM topology files have full residue names and chemical structure
>drawings.  Within the toppar directory (download the tarball from our
>site), 
>just grep -r "RESI" *
>
>If you have additional questions about this or CHARMM parametrization,
>contact 
>me off list as this is not really a GROMACS issue.
>
>-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
>
>jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>http://mackerell.umaryland.edu/~jalemkul
>
>==================================================
>
>
>------------------------------
>
>Message: 2
>Date: Wed, 28 Jun 2017 10:38:13 -0600
>From: Mohsen Ramezanpour <ramezanpour.mohsen at gmail.com>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] Atom types comparison between CGenFF and
>	Charm36FF
>Message-ID:
>	<CAERzrhskVqO0FhgWg0JiE2AyY-M9C6aGPNnM=YmEezEp5Hzsxw at mail.gmail.com>
>Content-Type: text/plain; charset="UTF-8"
>
>Thanks, Justin.
>
>Sure.
>
>On Wed, Jun 28, 2017 at 10:21 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 6/28/17 9:10 AM, Mohsen Ramezanpour wrote:
>>
>>> Thanks Justin for your comment.
>>>
>>> I have a bit of difficulty for the finding the analog parts to these
>>>two
>>> parts.
>>>
>>> Is there any database (preferably with shapes) for the molecules
>>>available
>>> in charmmFF?
>>>
>>>
>> The CHARMM topology files have full residue names and chemical structure
>> drawings.  Within the toppar directory (download the tarball from our
>> site), just grep -r "RESI" *
>>
>> If you have additional questions about this or CHARMM parametrization,
>> contact me off list as this is not really a GROMACS issue.
>>
>>
>> -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
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
>> --
>> 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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>> send a mail to gmx-users-request at gromacs.org.
>>
>
>
>
>-- 
>*Rewards work better than punishment ...*
>
>
>------------------------------
>
>Message: 3
>Date: Wed, 28 Jun 2017 12:56:47 -0400
>From: nishi kashyap <nishikashyap18 at gmail.com>
>To: gmx-users at gromacs.org
>Subject: Re: [gmx-users] Using SLLOD to find Viscosity
>Message-ID:
>	<CAFYO1favztsnfGt1i5RY2EqHRK_MXYmSuYJwUA-9jopR__WNfw at mail.gmail.com>
>Content-Type: text/plain; charset="UTF-8"
>
>I have read both things thoroughly. I am new to this and so having a hard
>time gathering basic concepts.
>So, correct me if I am wrong:
>
>To calculate shear viscosity in a PEG system:
>1. Created a stable system and given cos_acceleration =0.05
>2. Since I would know A(amplitude of acceleration),rho and k(wave index
>number), I can find out the viscosity
>
>Still, how do I find shear rate from that? Ideally, I should be changing
>shear rate and finding viscosity. How can I do that ?
>
>I might be asking very basic things but please help me here.
>
>
>On Sat, Jun 3, 2017 at 3:25 AM, David van der Spoel <spoel at xray.bmc.uu.se>
>wrote:
>
>> On 02/06/17 22:12, nishi kashyap wrote:
>>
>>> Thanks for replying.
>>> I have also tried that before. If we give the whole system the same
>>> acceleration, then it wouldn't experience any shear. That was what I
>>>was
>>> observing also.
>>> Is there no way/ inbuilt method which use SLLOD , like in LAMMPS ?
>>>
>>
>> Please read my email again carefully, and those references, in
>>particular
>> the Hess paper.
>>
>>
>>
>>> On Fri, Jun 2, 2017 at 4:09 PM, David van der Spoel
>>><spoel at xray.bmc.uu.se
>>> >
>>> wrote:
>>>
>>> On 02/06/17 22:02, nishi kashyap wrote:
>>>>
>>>> Hi
>>>>> I have a system of PEG for which I want to find viscosity. I want to
>>>>>use
>>>>> SLLOD equations to find viscosity for a specific shear rate. I have
>>>>>read
>>>>> allot about different ways , even tried to use 'deform'. But I did
>>>>>not
>>>>> understand what do you mean by "off diagonal elements in a single
>>>>> array".
>>>>> I
>>>>> am not able to understand. And also how do you intend to find shear
>>>>>rate
>>>>> proceeding from that.
>>>>> Could you please give some insight.
>>>>> I would prefer if you just tell me how to use SLLOD equations? I
>>>>>really
>>>>> need it, I have been trying this for so long.
>>>>> Thank You
>>>>>
>>>>> Try using the cos_accel with a few different values.
>>>>>
>>>> See J. Chem. Phys. 119 pp. 7308-7317 (2003) and J. Chem. Phys. 116,
>>>>209
>>>> 2002
>>>>
>>>> --
>>>> David van der Spoel, Ph.D., Professor of Biology
>>>> Head of Department, Cell & Molecular Biology, Uppsala University.
>>>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
>>>> http://www.icm.uu.se
>>>> --
>>>> 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.
>>>>
>>>>
>>>
>>>
>>>
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Head of Department, Cell & Molecular Biology, Uppsala University.
>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
>> http://www.icm.uu.se
>> --
>> 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
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>> send a mail to gmx-users-request at gromacs.org.
>>
>
>
>
>-- 
>Nishi Kashyap
>Undergraduate
>Chemical Engineering
>IIT Delhi
>
>
>------------------------------
>
>Message: 4
>Date: Wed, 28 Jun 2017 13:06:10 -0400
>From: nishi kashyap <nishikashyap18 at gmail.com>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] Deform a liquid
>Message-ID:
>	<CAFYO1fb0HaZXNPgVPLD9GJrJ88+Pfpt8n5MUiFyC==N1UeELmQ at mail.gmail.com>
>Content-Type: text/plain; charset="UTF-8"
>
>Hi
>I am new to gromacs and so a basic doubt.
>How do we use 'deform' as specified in non equilibrium section of mdp
>file?
>Considering I have a box of polymer to be given some shear only in x
>direction, what should be the arguments?
>
>
>-- 
>Nishi Kashyap
>Undergraduate
>Chemical Engineering
>IIT Delhi
>
>
>------------------------------
>
>Message: 5
>Date: Wed, 28 Jun 2017 17:49:04 +0000
>From: "Diez Fernandez, Amanda" <amanda.diez10 at imperial.ac.uk>
>To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
>Subject: [gmx-users] Anybody using Silica InterfaceFF on Gromacs?
>Message-ID: <D579AA9D.F44E%amanda.diez10 at imperial.ac.uk>
>Content-Type: text/plain; charset="us-ascii"
>
>Hi,
>I converted the InterfaceFF silica parameters to use in Gromacs (and to
>be compatible with the AMBER forcefield) and have gotten some problems,
>namely I am getting a slightly bigger equilibrium bond length than I
>should.
>I was wondering if there were other Gromacs users out there that have
>used InterfaceFF silica parameters in Gromacs.
>
>Many thanks,
>Amanda
>
>
>------------------------------
>
>Message: 6
>Date: Wed, 28 Jun 2017 12:22:46 -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: <925932e6-1a3f-b11a-72fb-b2b1f6c630e0 at gmail.com>
>Content-Type: text/plain; charset=utf-8; format=flowed
>
>This community is mostly focused on other things. If you have solid
>silica under a non-native (to Gromacs) forcefield and all the bonded
>parameters have been copied correctly, there may be issues with your
>partial charges, LJ parameters, and mixing rules. Also make sure your
>original forcefield uses the same approach to neighbor searching as
>Gromacs does. Also to my knowledge, very few solid-state potentials use
>the childish 1-4 pair interaction.
>
>Alex
>
>On 6/28/2017 11:49 AM, Diez Fernandez, Amanda wrote:
>> Hi,
>> I converted the InterfaceFF silica parameters to use in Gromacs (and to
>>be compatible with the AMBER forcefield) and have gotten some problems,
>>namely I am getting a slightly bigger equilibrium bond length than I
>>should.
>> I was wondering if there were other Gromacs users out there that have
>>used InterfaceFF silica parameters in Gromacs.
>>
>> Many thanks,
>> Amanda
>
>
>
>------------------------------
>
>-- 
>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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>send a mail to gmx-users-request at gromacs.org.
>
>End of gromacs.org_gmx-users Digest, Vol 158, Issue 181
>*******************************************************