Re: [gmx-users] conserved energy

  You should also understand energy at the atomic level, the standard atom-atom inteeractions from general O chem, or chem suck as leonard jones and coulumb...per the standard, non-indexed outputs...they do not follow newtonian based energy systems even though the algorithm is newtonian based in m

Re: [gmx-users] Editconf error

On 5/22/15 4:57 PM, Jorge Dagnino wrote: As this is my first time with this kind of error, i don't know which part of the coordinate file is relevant, :( If you can tell me which part do you need, i can paste it Email me the files off-list. -Justin -- =

Re: [gmx-users] Editconf error

As this is my first time with this kind of error, i don't know which part of the coordinate file is relevant, :( If you can tell me which part do you need, i can paste it Thanks. 2015-05-22 17:17 GMT-03:00 Justin Lemkul : > > > On 5/22/15 4:07 PM, Jorge Dagnino wrote: > >> Here are the complete

Re: [gmx-users] PMF calculation with constraint distance

On 5/21/15 5:19 PM, leila salimi wrote: Thanks Justin. Yes I have done PMF with Blue moon ensemble with DFT. Now I want to do the same with gromacs to have some knowledge about my FF parameters and compare with my DFT results! You meant I have to do with different configuration and average the

Re: [gmx-users] first residue in chains warning issue

On 5/22/15 3:39 AM, Ming Tang wrote: Dear Justin, Is there any significant difference between the equilibrated states of the protein equilibrated by NPT with all-bonds constrained and without any constraints? If the difference is quite small, then I can choose constraining bonds to increas

Re: [gmx-users] Pull code

On 5/22/15 7:00 AM, Ming Tang wrote: Dear Justin, I want to simulate my triple helix using SMD, Can I use umbrella + distance? Shrug. Depends on what you're doing and trying to observe. I saw many people doing SMD simulation by fixing one end and pull another end in their journal. Besides

Re: [gmx-users] H-bond query

On 5/22/15 9:19 AM, soumadwip ghosh wrote: Hello all, I am trying to see what happens to the no. of Watson-Crick hydrogen bonds between two parallel chains of a double stranded DNA on incorporating a flat graphene sheet. The no of interchain H-bonds are supposed to decrease with t

Re: [gmx-users] LINSC WARNING

On 5/22/15 10:46 AM, Ahmet Yıldırım wrote: I haven't tried vsites on GPU. I just used them for the united atom ffs (espically GROMOS ffs) with reaction field method. Actually I didn't get good results about the ligand in the system. Maybe the problem was force field (54A7) I used. Because for G

Re: [gmx-users] conserved energy

On 5/22/15 11:56 AM, Ahmet Yıldırım wrote: Dear users, The total energy obtained from the .edr file is the sum of potential and kinetic energy of system. But there is not any information about conserved energy in manual. Maybe I couldn't find it. I am looking for answers of the following quest

Re: [gmx-users] Editconf error

On 5/22/15 4:07 PM, Jorge Dagnino wrote: Here are the complete files. pdb2gmx input: http://pastebin.com/HBmrR0eF .gro output: http://paste2.org/ahY6MB99 editconf input: http://paste2.org/9fPp6J02 editconf output: http://paste2.org/v1IsPp6O Can you just upload all the relevant coordinate

Re: [gmx-users] Editconf error

Here are the complete files. pdb2gmx input: http://pastebin.com/HBmrR0eF .gro output: http://paste2.org/ahY6MB99 editconf input: http://paste2.org/9fPp6J02 editconf output: http://paste2.org/v1IsPp6O Thanks. 2015-05-22 16:21 GMT-03:00 Barnett, James W : > It'd be more helpful for troubleshoo

Re: [gmx-users] Editconf error

It'd be more helpful for troubleshooting your problem if you post the entire file in each case, not just parts of them. If it's a large file use Pastebin.com or something similar. -- James "Wes" Barnett Ph.D. Candidate Chemical and Biomolecular Engineering Tulane University Boggs Center for Ene

Re: [gmx-users] Editconf error

Here are the coordinates from my pdb file: ATOM 1 N MET G 27 69.331 43.147 76.443 1.00 0.00 N ATOM 2 CA MET G 27 68.996 44.047 75.331 1.00 0.00 C ATOM 3 C MET G 27 67.818 43.550 74.510 1.00 0.00 C ATOM 4 O MET G 27 66.981 44

[gmx-users] conserved energy

Dear users, The total energy obtained from the .edr file is the sum of potential and kinetic energy of system. But there is not any information about conserved energy in manual. Maybe I couldn't find it. I am looking for answers of the following questions: -Which energy contributions/terms does th

Re: [gmx-users] LINSC WARNING

I haven't tried vsites on GPU. I just used them for the united atom ffs (espically GROMOS ffs) with reaction field method. Actually I didn't get good results about the ligand in the system. Maybe the problem was force field (54A7) I used. Because for GROMOS ffs there is another problem that is heli

Re: [gmx-users] 4 Titan X or 2?

> On 22 May 2015, at 16:08, Albert wrote: > > how about the following: > > > 2 x Intel Xeon E5­2680V3,12 cores, 2.5­3.3 GHz My guess is that two TITAN X will be more than enough to balance the CPU compute power. To save some money, you could also start with two GTX 980 instead of the TITANs

Re: [gmx-users] LINSC WARNING

Hi, On Fri, May 22, 2015 at 3:57 PM Albert wrote: > that's interesting. > > How about the ligand in the system? The hydrogen should also be treated > in virtual site? Is it possible treat the binding pocket as explicit > atoms, and all the rest in virtual hydrogen? > You're probably thinking of

Re: [gmx-users] 4 Titan X or 2?

how about the following: 2 x Intel Xeon E5­2680V3,12 cores, 2.5­3.3 GHz Cool & Silent Features Supermicro dual Xeon motherboard 64GB ECC DDR4 RAM 4­channel 2133 MHz, 8 x 8 GB 256GB Samsung SSD 850 PRO 2 x 6000 GB WD Red hard drive, 7200 rpm Asus GTX TITAN X, 12 GB GDDR5 Asus GTX TITAN X, 12 GB G

Re: [gmx-users] 4 Titan X or 2?

> On 22 May 2015, at 15:51, Albert wrote: > > Hello: > > I am going to perform MD simulation for a typical biological system with > 60,000-80,000 atoms in all. Amber FF would be used for the whole system. > > I am just wondering will a 4x Titan X much faster than 2xTitan X? That depends on w

Re: [gmx-users] LINSC WARNING

that's interesting. How about the ligand in the system? The hydrogen should also be treated in virtual site? Is it possible treat the binding pocket as explicit atoms, and all the rest in virtual hydrogen? Does it support GPU? thx a lot Albert On 05/22/2015 03:51 PM, Ahmet Yıldırım wrote:

Re: [gmx-users] LINSC WARNING

Hi Phan, If you want to use the time step of 4 fs, you can try to use "virtual sites" (gmx pdb2gmx -f ... -vsite hydrogens). Please look at the following web site. https://www.wenmr.eu/wenmr/md-simulations-using-gromacs-web-server Virtual sites:The use of virtual sites offers another possibility

[gmx-users] 4 Titan X or 2?

Hello: I am going to perform MD simulation for a typical biological system with 60,000-80,000 atoms in all. Amber FF would be used for the whole system. I am just wondering will a 4x Titan X much faster than 2xTitan X? thanks a lot Albert -- Gromacs Users mailing list * Please search the a

Re: [gmx-users] do_dssp

Thanks Mark. On Fri, May 22, 2015 at 3:17 PM, Mark Abraham wrote: > Yes > > On Fri, May 22, 2015 at 2:59 PM MUSYOKA THOMMAS < > mutemibiochemis...@gmail.com> wrote: > > > Hi Gromacs users, > > I did my simulations using an older version of GROMACS (ie 4.5.7) and > after > > reading through vario

Re: [gmx-users] LINSC WARNING

Thank a lot for your suggestion. Tuong VY 2015-05-22 20:21 GMT+09:00 Mark Abraham : > Hi, > > Start by learning what makes a time step stable, e.g. manual 6.8 > > Mark > > On Fri, May 22, 2015 at 10:51 AM Vy Phan wrote: > > > Dear Gromacs Users, > > When I run npt equilibrium, I set the step s

[gmx-users] H-bond query

Hello all, I am trying to see what happens to the no. of Watson-Crick hydrogen bonds between two parallel chains of a double stranded DNA on incorporating a flat graphene sheet. The no of interchain H-bonds are supposed to decrease with time. But I am not sure how to use g_hbond in ord

Re: [gmx-users] do_dssp

Yes On Fri, May 22, 2015 at 2:59 PM MUSYOKA THOMMAS < mutemibiochemis...@gmail.com> wrote: > Hi Gromacs users, > I did my simulations using an older version of GROMACS (ie 4.5.7) and after > reading through various posts, it seems I have to do the dssp analysis > using a newer version. Can I use

[gmx-users] do_dssp

Hi Gromacs users, I did my simulations using an older version of GROMACS (ie 4.5.7) and after reading through various posts, it seems I have to do the dssp analysis using a newer version. Can I use the trajectories I got from the previous older version of GROMACS to perform dssp analysis on Gromacs

Re: [gmx-users] Generate the water box

Use "gmx editconf" first to create the box then "gmx solvate" to fill it with water (omitting -box directive this time). -- James "Wes" Barnett Ph.D. Candidate Chemical and Biomolecular Engineering Tulane University Boggs Center for Energy and Biotechnology, Room 341-B New Orleans, Louisiana 701

[gmx-users] distance constrain of two groups

Dear all, After energy minimization, I want to equilibrate my triple helix using NPT, but need to keep its general shape, as I want to study the load-deformation relationship including the triple helix unfolding stage. During the equilibration, I want to fix the distance between the centre of m

Re: [gmx-users] Lincs all-bonds causing instability in otherwise stable system

Hi, After further thought, the base problem is that there must be at least one rigid triangle, and LINCS can't do this because it couples constraints too much. The water models use [settles] to solve the particular case of a single triangle, and TIP4P and TIP5P water models are implemented with vi

Re: [gmx-users] build nuance in gmx5 (avoiding "file INSTALL cannot find gmx")

Hi, On Thu, May 21, 2015 at 5:50 PM Christopher Neale < chris.ne...@alum.utoronto.ca> wrote: > Dear Szilárd: > > I report it only because it is allowed in gmx4 builds (or at least it > works, I am not sure whether or not is it "allowed"). > Along with the transition to the wrapper binary in 5.0,

Re: [gmx-users] How can i install DSSP for gromacs on centos6?

Hi, Searching google would have been faster for you ;-) There's a few hundred posts about how to get DSSP working with do_dssp. If you want to use such an old version of GROMACS, you'll need to use an old version of DSSP, because DSSP 2 changed how it accepts input and won't accept the old version

Re: [gmx-users] How to connect different parts of a polymer?

Hi, Given .rtp entries for the repeat units, pdb2gmx can use the specbond.dat mechanism to generate cross-links, as it does e.g. for disulfide links in proteins. See manual. Mark On Fri, May 22, 2015 at 12:12 PM faride badalkhani < farideh.kham...@gmail.com> wrote: > Dear GMX users > > I am try

Re: [gmx-users] LINSC WARNING

Hi, Start by learning what makes a time step stable, e.g. manual 6.8 Mark On Fri, May 22, 2015 at 10:51 AM Vy Phan wrote: > Dear Gromacs Users, > When I run npt equilibrium, I set the step size is 4fs. I go many LINCS > WARNING > "bonds that rotate more than 30 degrees" > > > When I reduce th

Re: [gmx-users] water box moves during MD simulation

Hi, You can follow the advice here for making the visual representation whatever you want. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Mark On Fri, May 22, 2015 at 10:16 AM Ming Tang wrote: > Dear Mark, > > Thanks a lot. > Is it possible to get the water box f

Re: [gmx-users] Pull code

Dear Justin, I want to simulate my triple helix using SMD, Can I use umbrella + distance? I saw many people doing SMD simulation by fixing one end and pull another end in their journal. Besides, my triple helix deviates a bit from Z axis, but I do not know the angle. I checked both dim for dis

[gmx-users] How to connect different parts of a polymer?

Dear GMX users I am trying to parametrize GROMOS FF for PAMAM dendrimers. I have paramerized core of the dendrimer, its repeat units, and terminal groups separately. but I dont know how to connect them to build a complete dendrimer so that GROMACS can recognize dendrimer structure exactly. Could y

[gmx-users] LINSC WARNING

Dear Gromacs Users, When I run npt equilibrium, I set the step size is 4fs. I go many LINCS WARNING "bonds that rotate more than 30 degrees" When I reduce the step size to 2fs. All thing is fine. Could someone here explain to me? Finally, I want to use step size is 4fs. Any suggestions for me?

Re: [gmx-users] water box moves during MD simulation

Dear Mark, Thanks a lot. Is it possible to get the water box fixed through command in .mdp, or using a specific option to fix the water box, like -nojump for g_traj? -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillis

[gmx-users] How can i install DSSP for gromacs on centos6?

Hi there I tried to execute dssp for gromacs 4.5.7 by following this instruction: #sudo wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64 -O /usr/local/bin

Re: [gmx-users] first residue in chains warning issue

Dear Justin, Is there any significant difference between the equilibrated states of the protein equilibrated by NPT with all-bonds constrained and without any constraints? If the difference is quite small, then I can choose constraining bonds to increase time step. Thanks a lot. -Origina

[gmx-users] H-bonding

Hello all, I am trying to see what happens to the no. of Watson-Crick hydrogen bonds between two parallel chains of a double stranded DNA on incorporating a flat graphene sheet. The no of interchain H-bonds are supposed to decrease with time. But I am not sure how to use g_hbond in ord