Hi Alex , sorry to post my problem too many times.
Coming back to your questions related to my problem 1. angles are 90,90,120 in x,y and z respectively. actually in quantum espresso this structure is little bit easy to handle. 2. without LINCS i haven't tried the simulation, i will do it without LINCS and get back to you. 3. I am basically interested in dynamics of water through porous graphene. if i am not using constraint and all it is getting crumbled and shape of graphene changes. 4. Yes, it is stable. Regards On Thu, Sep 6, 2018 at 5:35 AM < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > > 1. Orthorhombic structure and Lincs warnings (sagar bathla) > 2. Re: Orthorhombic structure and Lincs warnings (Alex) > 3. Re: Orthorhombic structure and Lincs warnings (Alex) > 4. Re: Justin paper 2010 pulling (Justin Lemkul) > 5. Re: i have a question about multiple chain simulation at the > same box (Justin Lemkul) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 6 Sep 2018 01:05:03 +0530 > From: sagar bathla <sagarbath...@gmail.com> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] Orthorhombic structure and Lincs warnings > Message-ID: > < > caexvse4c4pjpun0nsnycsdj33ge6vlfysbbxe8w+hmaky9q...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Dear all, > > Can simulation for orthorhombic structure be done in gromacs? > Actually I am working with 2-D graphene sheets which are like a > parallelogram. > > In my system, there is a graphene sheet (restrained)and water. > After the energy minimization, energy is coming positive (order of 10^8) > On Visualization in vmd, the structure appears to be rectangle and there > comes a warning with it > > 152 inconsistant shifts etc. > > When I am trying to equillibrate the system then so many lines warnings > appears of rotation of bonds more than 90 degrees and simulation crashes > everytime. > > Is there any problem with structure or y else? > Earlier also I posted this but issue hasn't resolved yet. > > Please help me to find this problem. > > Regards > Sagar > > > ------------------------------ > > Message: 2 > Date: Wed, 5 Sep 2018 13:45:34 -0600 > From: Alex <nedoma...@gmail.com> > To: Discussion list for GROMACS users <gmx-us...@gromacs.org> > Cc: Discussion list for GROMACS users > <gromacs.org_gmx-users@maillist.sys.kth.se> > Subject: Re: [gmx-users] Orthorhombic structure and Lincs warnings > Message-ID: > < > camjz6qhx-fnmnqxgeoypz22cq4yrvn8eynddhfqpyfg1kym...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > It's not the first time you're posting this message and there's a reason > noone is replying. > > 1. What are the inter-axis angles of that orthorhombic box? Why not a > rectangular box? > 2. Why are you using LINCS with graphene, which should _not_ be simulated > with constraints? > 3. Why are you restraining your system on top of everything else? > 4. Did you verify that your graphene model (without constraints or > restraints) was stable prior to adding water? > > Alex > > On Wed, Sep 5, 2018 at 1:35 PM sagar bathla <sagarbath...@gmail.com> > wrote: > > > Dear all, > > > > Can simulation for orthorhombic structure be done in gromacs? > > Actually I am working with 2-D graphene sheets which are like a > > parallelogram. > > > > In my system, there is a graphene sheet (restrained)and water. > > After the energy minimization, energy is coming positive (order of 10^8) > > On Visualization in vmd, the structure appears to be rectangle and there > > comes a warning with it > > > > 152 inconsistant shifts etc. > > > > When I am trying to equillibrate the system then so many lines warnings > > appears of rotation of bonds more than 90 degrees and simulation crashes > > everytime. > > > > Is there any problem with structure or y else? > > Earlier also I posted this but issue hasn't resolved yet. > > > > Please help me to find this problem. > > > > Regards > > Sagar > > -- > > 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-requ...@gromacs.org. > > > > > ------------------------------ > > Message: 3 > Date: Wed, 5 Sep 2018 13:45:34 -0600 > From: Alex <nedoma...@gmail.com> > To: Discussion list for GROMACS users <gmx-us...@gromacs.org> > Cc: Discussion list for GROMACS users > <gromacs.org_gmx-users@maillist.sys.kth.se> > Subject: Re: [gmx-users] Orthorhombic structure and Lincs warnings > Message-ID: > < > camjz6qhx-fnmnqxgeoypz22cq4yrvn8eynddhfqpyfg1kym...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > It's not the first time you're posting this message and there's a reason > noone is replying. > > 1. What are the inter-axis angles of that orthorhombic box? Why not a > rectangular box? > 2. Why are you using LINCS with graphene, which should _not_ be simulated > with constraints? > 3. Why are you restraining your system on top of everything else? > 4. Did you verify that your graphene model (without constraints or > restraints) was stable prior to adding water? > > Alex > > On Wed, Sep 5, 2018 at 1:35 PM sagar bathla <sagarbath...@gmail.com> > wrote: > > > Dear all, > > > > Can simulation for orthorhombic structure be done in gromacs? > > Actually I am working with 2-D graphene sheets which are like a > > parallelogram. > > > > In my system, there is a graphene sheet (restrained)and water. > > After the energy minimization, energy is coming positive (order of 10^8) > > On Visualization in vmd, the structure appears to be rectangle and there > > comes a warning with it > > > > 152 inconsistant shifts etc. > > > > When I am trying to equillibrate the system then so many lines warnings > > appears of rotation of bonds more than 90 degrees and simulation crashes > > everytime. > > > > Is there any problem with structure or y else? > > Earlier also I posted this but issue hasn't resolved yet. > > > > Please help me to find this problem. > > > > Regards > > Sagar > > -- > > 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-requ...@gromacs.org. > > > > > ------------------------------ > > Message: 4 > Date: Wed, 5 Sep 2018 20:01:06 -0400 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Justin paper 2010 pulling > Message-ID: <44ff90db-f5dc-87d5-71fc-079650414...@vt.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > > > On 9/5/18 1:50 AM, Rakesh Mishra wrote: > > So that means > > > > It is may be due to the difference in the type of interaction. > > > > and I can not understand your this statement "you have to contend with > > forces principally acting perpendicular to the direction of the bias" > > > > Well, what interactions act along the plane perpendicular to the helix > axis of a duplex DNA or RNA? > > -Justin > > > > > On Tue, Sep 4, 2018 at 10:54 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > >> > >> On 9/4/18 11:44 AM, Rakesh Mishra wrote: > >> > >>> Dear Justin, > >>> > >>> Seriously I want to remove my confusion. > >>> I just read your one paper " J.Physical Chemistry B 2010, 114, 1652-60" > >>> Where you have studied stability of Alzheimer. I don't want to ask > about > >>> umbrella sampling used for the calculation of PMF. > >>> > >>> But , before the calculation of PMF , you > >>> have obtained simple dissociation using your pulling protocol of > gromacs > >>> with constant velocity simulation at three different velocities. I am > >>> surprised that you have followed the obvious protocol > >>> of minimization the nvt the npt and then 100ns md production. then you > >>> took > >>> final structure of 100ns and made new box for pulling and followed the > >>> same minimisation and npt for short time. After this you did pulling > along > >>> only one direction (one reaction coordinate) . > >>> > >>> I am surprised that how such a smooth force/time data you have obtained > >>> for > >>> all the velocities (0.01,0.001,0.005) . I am asking because for my > simple > >>> 12bp dsDNA or 22bp siRNA , I also have followed similar protocol and > fixed > >>> one end (say 5') of first strand and pulling opposite end (5') of > second > >>> strand along the helical direction of the system. Here, I am getting > >>> force/time (in the .xvg ) data which is qualitatively similar behaviour > >>> like yours i.e. initially increasing then reach to maximum and then > >>> decreasing almost becomes to zero value. But , In mine case during > initial > >>> time of pulling force is also negative as well large fluctuation of > force > >>> . > >>> But not such a smooth Variation of force/time like your in this paper. > In > >>> your case, force is increasing like linearly in the initial and reaches > >>> the > >>> maximum and then start to decrease. There is no problem to > >>> clarify the peak of force (maximum force) in your pulling (above > mentioned > >>> paper). While in our case its very difficult to clarify the peak force > due > >>> to large fluctuation in value. > >>> Can you please tell me something about the reason. Its smoothness is > now > >>> became headache for my calculation in all the case of pulling. > >>> > >> There is no reason to think that your outcome and mine should look > >> anything alike. Pulling apart two proteins that interact in the way the > >> peptides do in a protofibril is much simpler than the intertwined > nature of > >> a DNA or RNA duplex. If you pull along the helix axis, you have to > contend > >> with forces principally acting perpendicular to the direction of the > bias, > >> as well as the fact that the strands have to slide past one another, > >> requiring major distortion of the helix and/or frictional forces due to > the > >> individual strands unwinding from one another. > >> > >> -Justin > >> > >> -- > >> ================================================== > >> > >> Justin A. Lemkul, Ph.D. > >> Assistant Professor > >> Virginia Tech Department of Biochemistry > >> > >> 303 Engel Hall > >> 340 West Campus Dr. > >> Blacksburg, VA 24061 > >> > >> jalem...@vt.edu | (540) 231-3129 > >> http://www.thelemkullab.com > >> > >> ================================================== > >> > >> -- > >> 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-requ...@gromacs.org. > >> > > > > > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > > > ------------------------------ > > Message: 5 > Date: Wed, 5 Sep 2018 20:01:42 -0400 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] i have a question about multiple chain > simulation at the same box > Message-ID: <b7b5234d-8fdc-1489-94fb-be35d0f9a...@vt.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > > > On 9/5/18 9:25 AM, milad bagheri wrote: > > I'm going to examine the interaction between the two proteins using > > molecular dynamics simulation by gromacs, so I downloaded pdb code 5op1 > > from the rcsb , which has two protein(Complex). I want to create a gap > > between two protein, and then with the same coordinate Put these two > > proteins in a box and run MD 100 nanoseconds, for validation this trick > > compare rmsd x-ray pose and Md pose. > > please help me ... > > Separate the coordinates of the two proteins, translate one of them with > editconf, and concatenate the new coordinates back together. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > > > ------------------------------ > > -- > 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-requ...@gromacs.org. > > End of gromacs.org_gmx-users Digest, Vol 173, Issue 12 > ****************************************************** > -- 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-requ...@gromacs.org.
