Re: [gmx-users] AVX related compiler error during build with P100 RHEL7

Any ideas on this one? Thanks! On Mon, Jul 3, 2017 at 9:33 PM, Guyen Gn wrote: > Still did not work. change xMIC to xCore and log is below (if it was other > way around, then originally it must have not worked). > Script file is all oneline. > > -- Performing Test

Re: [gmx-users] NPT problem

No, I mean that: 1. Graphene dimensions cannot be exactly 9 x 9. It is a crystal and its in-plane dimensions are _precisely_ determined by the unit cell counts in the corresponding directions. 2. The box size needs to be adjusted in accordance with basic geometry of the crystal and its lattice

Re: [gmx-users] Scd or -Scd?

That should have read |Scd| and not [Scd] in the last sentence. On 14/07/17 18:40, Thomas Piggot wrote: As far as I'm aware (and happy to be corrected if someone knows better) it is simply a convention that stems from the fact that the signs of the order parameters were not originally

Re: [gmx-users] Scd or -Scd?

As far as I'm aware (and happy to be corrected if someone knows better) it is simply a convention that stems from the fact that the signs of the order parameters were not originally determined from experiments and so were reported in these works as |Scd|. Given that the order parameters of the

[gmx-users] Scd or -Scd?

Dear Justine,Why are the order parameter data reported in articles as -S_CD (minus S_CD)?  Thanks,Ganj -- 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

[gmx-users] (no subject)

jivesh.mad...@gmail.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

[gmx-users] 'fudgeQQ' parameter in the topology file

Dear Gromacs user, I read from the Gromacs Manual (version 5.1.2) that, while fudgeLJ is used only when generate pairs is set to ‘yes’, fudgeQQ is always used. 1. If I set fudgeQQ = 0.0, will gromacs annulate the 1-4 interactions ? 2. If I explicitly insert a (Coulomb 1-4) scaling factor in my

[gmx-users] equilibration

Hi justin  Thank you for reply and sorry for sending in another email, because when i wanted to reply, it was rejected.Actually, since i am a new gromacs user, i used all .mdp files ( em.mdp, nvt.mdp,...) in protein-ligand complex ( lysosym 4 ) tuturial in gromacs. And did all the steps and

Re: [gmx-users] Equilibration

blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Hi justin  Thank you for replyActually, since i am a new gromacs user, i used all .mdp files ( em.mdp, nvt.mdp,...) in

Re: [gmx-users] Equilibration

blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; }Hi justin  Thank you for replyActually, since i am a new gromacs user, i used all .mdp files ( em.mdp, nvt.mdp,...) in

Re: [gmx-users] Ramping down the restraint on molecules

Thanks Justin Regards, Lakshman On Thu, Jul 13, 2017 at 8:27 PM, Justin Lemkul wrote: > > > On 7/13/17 10:37 AM, Lakshman Ji Verma wrote: > >> Dear all, >> >> I want to ramp down the restraint on the two molecules from 1000k to 0 on >> some time interval so that restraint is

[gmx-users] 'fudgeQQ' parameter in the topology file

Dear Gromacs user, I read from the Gromacs Manual (version 5.1.2) that, while fudgeLJ is used only when generate pairs is set to ‘yes’, fudgeQQ is always used. 1. If I set fudgeQQ = 0.0, will gromacs annulate the 1-4 interactions ? 2. If I explicitly insert a (Coulomb 1-4) scaling factor in my

Re: [gmx-users] Concrete pull code explanation needed

On 7/13/17 8:11 PM, Du, Yu wrote: -Original Messages- From: "Justin Lemkul" Sent Time: Thursday, July 13, 2017 To: gmx-us...@gromacs.org Cc: Subject: Re: [gmx-users] Concrete pull code explanation needed On 7/11/17 8:23 PM, Du, Yu wrote: On 7/10/17 11:19 PM,

Re: [gmx-users] Non-periodic COM Pulling

On 7/13/17 1:56 PM, Daniel Kozuch wrote: Justin, It was my understanding that direction-periodic would not allow for the NPT ensemble (which I would like to use if possible, and why I did not use it in the first place). Is there a way around this? Not that I'm aware of. -Justin --

Re: [gmx-users] Equilibration

On 7/13/17 11:21 AM, ‪farial tavakoli‬ ‪ wrote: Hi Justin Thank you so much for your reply about minimize ligand in vacuoaccording to :http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System I minimized my protein and ligand alone to fix the problem (

Re: [gmx-users] frozen ligand for free energy calculations

On 7/13/17 11:51 AM, Ahmet Yildirim wrote: OK, thanks. Which of the following option do you suggest me under intermolecular interactions? 1) function type 6, 1 and 1 for [ bonds ], [ angles ] and [ dihedrals ] respectively 2) function type 6, 1 and 1 for [ bonds ], [ angle_restraints ] and[

Re: [gmx-users] LINCS warning during constrained md

Dear Mark, I understand your point, but I've used the Martini-backmapping protocol written in the initram.sh wrapper found in Martini documentation (https://github.com/Tsjerk/MartiniTools/blob/master/initram.sh), so it seems to me quite weird that it was not working in the proper manner. an

Re: [gmx-users] NPT problem

The graphene is 9*9 nm, and I proposed the box to be 11*11 nm. Do you mean that the box dimensions are small and thats the problem? Thanks,Mohammad From: Alex To: Discussion list for GROMACS users ; Discussion list for GROMACS users

Re: [gmx-users] NPT problem

I used "gmx x2top -f gr.gro -o topol1.top -ff cnt_oplsaa -name CNT -noparam -pbc" for generating the topology. then I used "gmx editconf -f grvmdn.pdb -o gr.gro -box 11 11 11 -angles 90 90 90" for creating the box And where did "-box 11 11 11" come from? For pbc to work the box in your

Re: [gmx-users] Periodic Molecule's Free Energy Calculation Error

Hi Jason, I didn't have time to look at all of those papers, but look for instance at eq. (2) in Hilder et al's paper and the definition of the f_dmp function on the right -- this tapers off short-range interactions for close neighbors. I am not sure if this particular function results in

Re: [gmx-users] NPT problem

Hi Alex, Thank you for your reply. By the term "results were good or not" I meant that whether the temperature, pressure, and density have converged to the preferred values or not (I mentioned it in the parenthesis, too). I used "gmx x2top -f gr.gro -o topol1.top -ff cnt_oplsaa -name CNT

Re: [gmx-users] xtc trajectory only

Hi, What does gmx check or dump tell you about what is in the files you're writing? Mark On Fri, 14 Jul 2017 08:30 Atila Petrosian wrote: > Dear Mark, > Thanks for your answer. > > I deleted (nstxout = 5000) in mdp file. But still both of xtc and > trr trajectory

[gmx-users] xtc trajectory only

Dear Mark, Thanks for your answer. I deleted (nstxout = 5000) in mdp file. But still both of xtc and trr trajectory files were created. Best, Atila -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't