[gmx-users] user defined potential(repulsive) for atoms falling with in three residues
Hi all, I am using a user defined potential to describe non-bonded interactions, which describes attractive potential for residues separated by four or more bonds . Now I want to describe a user defined potential(repulsive) for atoms falling with in three residues and which are not determined to be attractive, as I tried to elaborate below: condition 1: if the two atoms are separated by four or more bonds i use attractive LJ potential. condition 2: if two atoms are not determined to be attractive or fall with in three bonds of each other(i, i+3) then their interaction is defined by repulsive term: E(rep)= epsilon (sigma/rij)^12 Please let me know how I can implement this in Gromacs. Thanks and Regards, Mohan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] User defined potential
On 14/05/2012 2:24 PM, mohan maruthi sena wrote: Hi all, I want to define a potential form and give it as input for which i have seen manual ,thought gromacs table option is fine, i have an example of generating 9-6 potential form , My question is how to generate table.xvg, what is the command to generate table.xvg from code table.c. There's no general way to generate new tables from within GROMACS. Some already exist in the $GMXLIB/share folder. mdrun -debug will write out the tables it is using. Otherwise, working out how to take a suitable spreadsheet you have created and export to a text file is often the most straightforward procedure. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] User defined potential
Hi all, I want to define a potential form and give it as input for which i have seen manual ,thought gromacs table option is fine, i have an example of generating 9-6 potential form , My question is how to generate table.xvg, what is the command to generate table.xvg from code table.c. with regards, Mohan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] user defined potential
Dear GROMACS users,if I want to use table defined potential for nonbonded interactions I have to do so for all pairs between different grops or is there a possibility to specify just one kind lets say BH potential by tables and to use wdvtype=cut-off for LJ interactions. It seems to me that this is not possible. Could you be so kind and confirm my opinion that if I want to mix BH and LJ potential I have to define all interactions by tables. Zuzana Benkova -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] user defined potential function for 1-4 interaction
Hi Berk:
Thanks for your eply. I guess I would supply two column in the table for the
bond type 9 [r(nm) and W(kJ/mol) ]. In that case (according to the user manual)
what is the significance of k? how k will come into the calculation? If I
select "constraints = all bond" will that affect bond type 9?
Thanks,
M. H. Rahman
- Original Message -
From: Berk Hess
To: Discussion list for GROMACS users
Sent: Friday, October 09, 2009 10:02 AM
Subject: RE: [gmx-users] user defined potential function for 1-4 interaction
Hi,
Unfortunately this is not possible.
If you do not have to many pairs, you can change all (or all minus one type)
from pairs to tabulated bonds (bonds type 9) in your topology.
Then you can supply as many different bond tables as you like.
Note that this will supply a single potential though,
not separate Coulomb, dispersion and repulsion tables.
Berk
--
From: mhrah...@dal.ca
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] user defined potential function for 1-4 interaction
Date: Fri, 9 Oct 2009 09:48:19 -0300
I think there must be a way in gromacs to pass tabulated potenttial for 1-4
interaction for two groups as interaction between different pairs can be
significantly different and can change the structure of an indiviual molecule.
I would request: Please let me know if it is possible to pass tabulated
potential for pair inteaction for two groups. if my method, which you will see
below, is wrong please let me know the correct way. I searched previous
communications regarding tabulated potential but could not get my answer. I
hope I am not wasing your time.
Thanks.
- Original Message -
From: LuLanyuan
To: gmx-users@gromacs.org
Sent: Thursday, October 08, 2009 8:04 PM
Subject: RE: [gmx-users] user defined potential function for 1-4 interaction
Hi,
As I remember, you can only use one table for 1-4 interactions. Don't know
if it's changed
in the latest version.
Lanyuan
> From: mhrah...@dal.ca
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] user defined potential function for 1-4
interaction
> Date: Thu, 8 Oct 2009 19:10:39 -0300
>
> Hi all:
> I posted this earlier but did not get any help I really need to slove
this
> issue.
>
> What should be the way to pass a formatted table for the 1-4 interaction
> for two or more different groups? Reading page 150 and 180 of manual 4.0,
> I
> understand user defined potential functions can be passed for many groups
> using energygrp_table in .mdp file but nothing is clearly mentioned
> regarding pair interaction
>
> I have two grps for 1-4 interactions MTN and SFT.
> mdrun command includes:
> -table table.xvg -tablep pair.xvg
> ; .mdp file contains,
> energygrps = MTN SFT
> energygrp_table: MTN MTN MTN SFT
>
> I passed three tables for pair interaction in the
> name pair.xvg, pair_MTN_MTN.xvg and pair_MTN_SFT.xvg.
> I see the later two tabels are not recognized. If pair_MTN_MTN.xvg and
> pair_MTN_SFT.xvg are not supplied GROMACS donot issue any warning.
> I am afraid that I failed to submit separate table for pair interaction
> properly in this way.
>
> Thanks,
> M.H.Rahman
>
> ___
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RE: [gmx-users] user defined potential function for 1-4 interaction
Hi, Unfortunately this is not possible. If you do not have to many pairs, you can change all (or all minus one type) from pairs to tabulated bonds (bonds type 9) in your topology. Then you can supply as many different bond tables as you like. Note that this will supply a single potential though, not separate Coulomb, dispersion and repulsion tables. Berk From: mhrah...@dal.ca To: gmx-users@gromacs.org Subject: Re: [gmx-users] user defined potential function for 1-4 interaction Date: Fri, 9 Oct 2009 09:48:19 -0300 I think there must be a way in gromacs to pass tabulated potenttial for 1-4 interaction for two groups as interaction between different pairs can be significantly different and can change the structure of an indiviual molecule. I would request: Please let me know if it is possible to pass tabulated potential for pair inteaction for two groups. if my method, which you will see below, is wrong please let me know the correct way. I searched previous communications regarding tabulated potential but could not get my answer. I hope I am not wasing your time. Thanks. - Original Message - From: LuLanyuan To: gmx-users@gromacs.org Sent: Thursday, October 08, 2009 8:04 PM Subject: RE: [gmx-users] user defined potential function for 1-4 interaction Hi, As I remember, you can only use one table for 1-4 interactions. Don't know if it's changed in the latest version. Lanyuan > From: mhrah...@dal.ca > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] user defined potential function for 1-4 interaction > Date: Thu, 8 Oct 2009 19:10:39 -0300 > > Hi all: > I posted this earlier but did not get any help I really need to slove this > issue. > > What should be the way to pass a formatted table for the 1-4 interaction > for two or more different groups? Reading page 150 and 180 of manual 4.0, > I > understand user defined potential functions can be passed for many groups > using energygrp_table in .mdp file but nothing is clearly mentioned > regarding pair interaction > > I have two grps for 1-4 interactions MTN and SFT. > mdrun command includes: > -table table.xvg -tablep pair.xvg > ; .mdp file contains, > energygrps = MTN SFT > energygrp_table: MTN MTN MTN SFT > > I passed three tables for pair interaction in the > name pair.xvg, pair_MTN_MTN.xvg and pair_MTN_SFT.xvg. > I see the later two tabels are not recognized. If pair_MTN_MTN.xvg and > pair_MTN_SFT.xvg are not supplied GROMACS donot issue any warning. > I am afraid that I failed to submit separate table for pair interaction > properly in this way. > > Thanks, > M.H.Rahman > > ___ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/ma iling_lists/users.php 搜索本应是快乐的，不是么? 快乐搜索，有问必应！微软隆重推出! 立即查看！ ___ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] user defined potential function for 1-4 interaction
I think there must be a way in gromacs to pass tabulated potenttial for 1-4 interaction for two groups as interaction between different pairs can be significantly different and can change the structure of an indiviual molecule. I would request: Please let me know if it is possible to pass tabulated potential for pair inteaction for two groups. if my method, which you will see below, is wrong please let me know the correct way. I searched previous communications regarding tabulated potential but could not get my answer. I hope I am not wasing your time. Thanks. - Original Message - From: LuLanyuan To: gmx-users@gromacs.org Sent: Thursday, October 08, 2009 8:04 PM Subject: RE: [gmx-users] user defined potential function for 1-4 interaction Hi, As I remember, you can only use one table for 1-4 interactions. Don't know if it's changed in the latest version. Lanyuan > From: mhrah...@dal.ca > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] user defined potential function for 1-4 interaction > Date: Thu, 8 Oct 2009 19:10:39 -0300 > > Hi all: > I posted this earlier but did not get any help I really need to slove this > issue. > > What should be the way to pass a formatted table for the 1-4 interaction > for two or more different groups? Reading page 150 and 180 of manual 4.0, > I > understand user defined potential functions can be passed for many groups > using energygrp_table in .mdp file but nothing is clearly mentioned > regarding pair interaction > > I have two grps for 1-4 interactions MTN and SFT. > mdrun command includes: > -table table.xvg -tablep pair.xvg > ; .mdp file contains, > energygrps = MTN SFT > energygrp_table: MTN MTN MTN SFT > > I passed three tables for pair interaction in the > name pair.xvg, pair_MTN_MTN.xvg and pair_MTN_SFT.xvg. > I see the later two tabels are not recognized. If pair_MTN_MTN.xvg and > pair_MTN_SFT.xvg are not supplied GROMACS donot issue any warning. > I am afraid that I failed to submit separate table for pair interaction > properly in this way. > > Thanks, > M.H.Rahman > > ___ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/ma iling_lists/users.php -- 搜索本应是快乐的，不是么? 快乐搜索，有问必应！微软隆重推出! 立即查看！ -- ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] user defined potential function for 1-4 interaction
Hi, As I remember, you can only use one table for 1-4 interactions. Don't know if it's changed in the latest version. Lanyuan > From: mhrah...@dal.ca > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] user defined potential function for 1-4 interaction > Date: Thu, 8 Oct 2009 19:10:39 -0300 > > Hi all: > I posted this earlier but did not get any help I really need to slove this > issue. > > What should be the way to pass a formatted table for the 1-4 interaction > for two or more different groups? Reading page 150 and 180 of manual 4.0, > I > understand user defined potential functions can be passed for many groups > using energygrp_table in .mdp file but nothing is clearly mentioned > regarding pair interaction > > I have two grps for 1-4 interactions MTN and SFT. > mdrun command includes: > -table table.xvg -tablep pair.xvg > .mdp file contains, > energygrps = MTN SFT > energygrp_table: MTN MTN MTN SFT > > I passed three tables for pair interaction in the > name pair.xvg, pair_MTN_MTN.xvg and pair_MTN_SFT.xvg. > I see the later two tabels are not recognized. If pair_MTN_MTN.xvg and > pair_MTN_SFT.xvg are not supplied GROMACS donot issue any warning. > I am afraid that I failed to submit separate table for pair interaction > properly in this way. > > Thanks, > M.H.Rahman > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ 上Windows Live 中国首页，下载最新版 MSN！ http://www.windowslive.cn___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] user defined potential function for 1-4 interaction
Hi all: I posted this earlier but did not get any help I really need to slove this issue. What should be the way to pass a formatted table for the 1-4 interaction for two or more different groups? Reading page 150 and 180 of manual 4.0, I understand user defined potential functions can be passed for many groups using energygrp_table in .mdp file but nothing is clearly mentioned regarding pair interaction I have two grps for 1-4 interactions MTN and SFT. mdrun command includes: -table table.xvg -tablep pair.xvg .mdp file contains, energygrps = MTN SFT energygrp_table: MTN MTN MTN SFT I passed three tables for pair interaction in the name pair.xvg, pair_MTN_MTN.xvg and pair_MTN_SFT.xvg. I see the later two tabels are not recognized. If pair_MTN_MTN.xvg and pair_MTN_SFT.xvg are not supplied GROMACS donot issue any warning. I am afraid that I failed to submit separate table for pair interaction properly in this way. Thanks, M.H.Rahman ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] user defined potential function for 1-4 interaction
Hi All: I have two separate problems for this subject. 1) What should be the way to pass a formatted table for the 1-4 interaction for two different groups? Reading page 150 and 180 of manual 4.0, I understand user defined potential functions can be passed for many groups using energygrp_table in .mdp file but nothing is clearly mentioned regarding pair interaction I have two grps for 1-4 interactions MTN and SFT. I would write -tablep pair.xvg in mdrun command and pass three tables in the name pair.xvg, pair_MTN_MTN.xvg and pair_MTN_SFT.xvg. I recognized the later two talbels are not recognized. Then, what should be the correct way. 2) If the same user defined potential function (in a table format) for 1-4 interaction and non-bonded interaction can be used how the potential fuanction can be scaled down for 1-4 interaction. I tried changing parameters in [ pairtypes ] but it appears, I got similar distribution and shape for 0, .5 and 1 scale. Any kind of help will be greatly appreciated. Thanks, M. H. Rahman ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] User defined Potential Table
Hi, Rahul You need an index file for this purpose. Use make_ndx to generate an index file which contains one group including all atoms. Name this group as system. Then, you may take down the atom number for those 3-4 combinations and put them as one group in the index file, while removing them from the [ system ]. Name this new group as [ WCA ]. In your mdp file, put following lines energygrps = system WCA table-extension = 0 energygrp_table = WCA WCA Then you need to generate the parameter file, name them as table_WCA_WCA.xvg. A complete list shall include all combination of the group, WCA v.s. system, system v.s. system. But they shall follow the standard way, so you may just skip the definition. For the meaning of the columns inside the table, check manual as well as check table#-##.xvg inside the top directory. This is not a complete tutorial so you may encounter some error messages. Just follow the instructions given, you shall be able to do it. Yang Ye Rahul Godawat wrote: Hi Berk, Groamcs user forum has really been extremely useful so far to work with gromacs. I want to apply a user defined potential for selected energy groups. Its hard to interpret the information on the gromacs webpage and even going through mailing list archives did not answer many questions I have. All of my energy groups would interact with normal LJ and use PME for coulombtype (if they have charges) except for 3-4 combinations I want to use WCA potential which has a well defined functional form. How would you suggest going about it. Thank you very much Rahul ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] User defined Potential Table
Hi Berk, Groamcs user forum has really been extremely useful so far to work with gromacs. I want to apply a user defined potential for selected energy groups. Its hard to interpret the information on the gromacs webpage and even going through mailing list archives did not answer many questions I have. All of my energy groups would interact with normal LJ and use PME for coulombtype (if they have charges) except for 3-4 combinations I want to use WCA potential which has a well defined functional form. How would you suggest going about it. Thank you very much Rahul ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
