Re: [gmx-users] -inter command

On 1/18/18 7:02 AM, za...@tezu.ernet.in 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

Re: [gmx-users] six member ring won't stay flat

On 1/18/18 7:51 AM, MD wrote: On Thu, Jan 18, 2018 at 7:43 AM, Justin Lemkul wrote: On 1/17/18 6:11 PM, Mark Abraham wrote: Hi, If you poke your finger into something, it isn't going to stay flat. :-) And to add on to this, in the CHARMM parametrization protocol, the

Re: [gmx-users] six member ring won't stay flat

whoops, Thank you :)) On Thu, Jan 18, 2018 at 9:05 AM, Justin Lemkul wrote: > > > On 1/18/18 9:04 AM, MD wrote: > >> On Thu, Jan 18, 2018 at 8:48 AM, Justin Lemkul wrote: >> >> >>> On 1/18/18 8:46 AM, MD wrote: >>> >>> I have a question related to charmm. Does

Re: [gmx-users] six member ring won't stay flat

On Thu, Jan 18, 2018 at 7:43 AM, Justin Lemkul wrote: > > > On 1/17/18 6:11 PM, Mark Abraham wrote: > >> Hi, >> >> If you poke your finger into something, it isn't going to stay flat. :-) >> > > And to add on to this, in the CHARMM parametrization protocol, the first > step is

Re: [gmx-users] SDS initial setup

On 1/18/18 7:28 AM, za...@tezu.ernet.in wrote: Dear Gromacs Users I am trying to simulate a protein with 200 SDS molecules. After inserting 200 molecules inside the box with the protein at the center (size of the cubic box is 324 nm3), few of the SDS molecules are outside the box from each

Re: [gmx-users] regarding pbc issue

On 1/17/18 12:06 PM, Rose wrote: Thank you so much,I've got it now. we know that for example 2 molecule can not stick to each other they just close enough till repulse each other. Now, imagine pulling, if I can not see "really broken" structures in classicalMD , so what would be my

Re: [gmx-users] six member ring won't stay flat

On 1/17/18 6:11 PM, Mark Abraham wrote: Hi, If you poke your finger into something, it isn't going to stay flat. :-) And to add on to this, in the CHARMM parametrization protocol, the first step is always an in vacuo geometry optimization (QM vs. MM comparison) to make sure the topology

Re: [gmx-users] tilt angle for POPC

On 1/18/18 12:24 AM, Mohsen Ramezanpour wrote: Dear Gromacs users, I am interested in calculation of tilt angle for the POPC headgroup (angle distribution between the P-N vector and Z axis). I am not sure if my approach is correct as my angle distribution does not seem reasonable. Given a

Re: [gmx-users] six member ring won't stay flat

On 1/18/18 8:46 AM, MD wrote: I have a question related to charmm. Does charmm have a name/structure chart for all the parametrized molecules? I want to borrow some parameters info from those molecules but often I can't quickly figure out what they are. Not in one places, but every CHARMM

Re: [gmx-users] gmx enenrgy

On 1/18/18 12:38 AM, kordza...@aut.ac.ir wrote: Hi all when we use gmx energy what is the difference between LJ-(SR), LJ-14, Coulomb-14, Coulomb(SR)? those mentioned energies, give us energy interaction of total system. right? Not necessarily, because there may be long-range terms from

Re: [gmx-users] six member ring won't stay flat

I have a question related to charmm. Does charmm have a name/structure chart for all the parametrized molecules? I want to borrow some parameters info from those molecules but often I can't quickly figure out what they are. Ming On Jan 18, 2018 8:18 AM, "MD" wrote: >

Re: [gmx-users] six member ring won't stay flat

On 1/18/18 9:04 AM, MD wrote: On Thu, Jan 18, 2018 at 8:48 AM, Justin Lemkul wrote: On 1/18/18 8:46 AM, MD wrote: I have a question related to charmm. Does charmm have a name/structure chart for all the parametrized molecules? I want to borrow some parameters info from

Re: [gmx-users] gmx enenrgy

Hello Dr.Lemkul Thank you very much for your answer I try to do it. Regards Azadeh -- This email was Anti Virus checked by Security Gateway. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

[gmx-users] Recentering a protein

Hi I am new to gromacs (using v. 2016.4) and need to check the following steps for my system. 01. I have prepared the system with Amber 14, minimized, heated to 300K, equilibrated 02. Then I used Acpype to convert the amber top and equilibrated  rst file to gromacs .top and .gro files03.

Re: [gmx-users] tilt angle for POPC

Looking at index file made in the above mentioned way, as way as the following way: gmx make_ndx -f SYSTEM.gro -o index.ndx keep 0 r 1-100 name 1 upperleaflet 1 & a P N name 2 vector q gave the same results. Interestingly, even if I make the index file like: gmx make_ndx -f SYSTEM.gro -o

Re: [gmx-users] tilt angle for POPC

And, I used Charmm36 FF for simulations in Gromacs v. 2016.3 Cheers, Mohsen On Thu, Jan 18, 2018 at 11:28 AM, Mohsen Ramezanpour < ramezanpour.moh...@gmail.com> wrote: > Hi Justin, > > On Thu, Jan 18, 2018 at 5:42 AM, Justin Lemkul wrote: > >> >> >> On 1/18/18 12:24 AM, Mohsen

Re: [gmx-users] tilt angle for POPC

Hi Justin, On Thu, Jan 18, 2018 at 5:42 AM, Justin Lemkul wrote: > > > On 1/18/18 12:24 AM, Mohsen Ramezanpour wrote: > >> Dear Gromacs users, >> >> I am interested in calculation of tilt angle for the POPC headgroup (angle >> distribution between the P-N vector and Z axis). >>

Re: [gmx-users] tilt angle for POPC

I did more tests and here are the conclusions for the pick mentioned earlier. The pick appears when the -binw gets smaller and smaller. For the default value of gangle (which is 1), one cannot detect such a pick and you will get a normal distribution. Even for a -binw of 0.1 everything looks

[gmx-users] SDS initial setup

Dear Gromacs Users I am trying to simulate a protein with 200 SDS molecules. After inserting 200 molecules inside the box with the protein at the center (size of the cubic box is 324 nm3), few of the SDS molecules are outside the box from each side of the box. I have used the following command

Re: [gmx-users] Umbrella Sampling

On 1/18/18 12:37 AM, Moradzadeh, Alireza wrote: Hi! I am trying to do umbrella sampling between two 2D-sheets. I did it according bevan lab tutorial the problem I encounter is that after pulling steps. I perform umbrella sampling with rate of 0.0 however, two sheets get back together and

Re: [gmx-users] six member ring won't stay flat

I know what you mean, but I didn't see any other molecules getting too close to the ring :) On Wed, Jan 17, 2018 at 6:11 PM, Mark Abraham wrote: > Hi, > > If you poke your finger into something, it isn't going to stay flat. :-) > > Mark > > On Wed, Jan 17, 2018 at 9:44

[gmx-users] Three different diffusivities by "gmx msd" /

Dear GROMACS community, evaluating the diffusivity of as single dodecyl sulfate (DS) anion, I use a small trajectory chunk "md_1.trr" 5 ps (500 frames) long for testing purposes. The .trr has been stripped of any atoms except the 42 ones forming the DS chain (12H25SO4). What is more, I

Re: [gmx-users] six member ring won't stay flat

Coolbeans! Thank you Justin :) Ming On Jan 18, 2018 7:54 AM, "Justin Lemkul" wrote: > > > On 1/18/18 7:51 AM, MD wrote: > >> On Thu, Jan 18, 2018 at 7:43 AM, Justin Lemkul wrote: >> >> >>> On 1/17/18 6:11 PM, Mark Abraham wrote: >>> >>> Hi, If you

Re: [gmx-users] six member ring won't stay flat

On Thu, Jan 18, 2018 at 8:48 AM, Justin Lemkul wrote: > > > On 1/18/18 8:46 AM, MD wrote: > >> I have a question related to charmm. Does charmm have a name/structure >> chart for all the parametrized molecules? I want to borrow some parameters >> info from those molecules but

Re: [gmx-users] SDS initial setup

Besides the fact that there cannot be molecules outside a periodic box, are you sure that you want such a high SDS concentration? You are nearly 15 times over the cmc, in the real world you would most likely end up with a hydrated SDS crystals (Mol. Cryst. Liq. Cryst., Vol. 549:pp. 160–165, 2011)

[gmx-users] An conda package for installing gromacs 4.5.5 on 64-bit linux system

Hi gromacs users: I just wrote this to share that I write a conda package let you to install gromacs 4.5.5 on 64-bit linux system: https://anaconda.org/hsiaoyi0504/gromacs The objective of this package is to let people build applications based on gromacs more easier, such as prediction system

Re: [gmx-users] An conda package for installing gromacs 4.5.5 on 64-bit linux system

Why 4.5.5? On Thu, Jan 18, 2018 at 11:26 PM, 蕭毅 wrote: > Hi gromacs users: > > I just wrote this to share that I write a conda package let you to install > gromacs 4.5.5 on 64-bit linux system: > https://anaconda.org/hsiaoyi0504/gromacs > > The objective of this package

Re: [gmx-users] Rupture force definition

Dear Justin Thanks for your explanation . Yes I am agree that it will depend on the k value and path direction. Let suppose we map the experimental spring constant and rate then it will be some how relevant for my study. My another query is the same from umbrella sampling of puling code. If I

[gmx-users] -inter command

> 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