Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 118, Issue 10

Hi William, If you want to file a bug report you can do that at redmine.gromacs.org. It seems that you are already registered, maybe twice: wrww Will Welch wwelch...@gmail.com 02/03/2014 11:33 PM

[gmx-users] [SOLVED] Problem with radius of gyration calculation

Hi! Following Joao's suggestion I went to check all the commands I used, I realized it was a typo. Namely, I was tellgin g_gyrate to use the wrong index file with the right trajectory. Thanks to everyone for helping out. Jernej On Fri, Feb 7, 2014 at 4:54 AM, wrote: > VMD is an alternative,

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 118, Issue 10

I'm not sure if I'm replying correctly, but I just wanted to mention that I would love to file a report to the redmine list, but I have not been approved to do so. Is there another place I can report this problem? Will On Mon, Feb 3, 2014 at 2:35 PM, < gromacs.org_gmx-users-requ...@maillist.sys.

Re: [gmx-users] Dynamic selections

On Feb 6, 2014 3:31 PM, "Андрей Гончар" wrote: > > Hello. > I'm trying to make a dynamic selection in protein-water complex for further > analysis. It looks like there's no support for dynamic selections in the > GROMACS tools Correct. Teemu has worked hard to build the framework in which they co

Re: [gmx-users] Simulations with Nitroxide Spin Label

On Feb 6, 2014 4:41 PM, "akk5r" wrote: > > Hi, > > Does anyone know if there is a way to incorporate a nitroxide spin labels > into a gromacs simulation of proteins in water. With NMR and EPR it is > possible to obtain distance restraints between labels, and I am interested > to incorporate these

Re: [gmx-users] Different "optimal pme grid ... coulomb cutoff" values from identical input files

On Feb 6, 2014 8:42 AM, "yunshi11 ." wrote: > > On Wed, Feb 5, 2014 at 9:43 AM, Mark Abraham wrote: > > > What's the network? If it's some kind of switched Infiniband shared with > > other user's jobs, then getting hit by the traffic does happen. You can see > > > > > It indeed use an InfiniBand 4

Re: [gmx-users] Forcefield conversion script for POPC lipids

Hi Tom, Yes. that sounds like a good starting point. Please send. Erik On 6 Feb 2014, at 19:39, Thomas Piggot wrote: > Hi Erik, > > It's not a very smart approach, but I have a very basic script that can > convert CHARMM36 (and probably Slipids as I think they are named and ordered > the sa

Re: [gmx-users] Forcefield conversion script for POPC lipids

Hi Erik, It's not a very smart approach, but I have a very basic script that can convert CHARMM36 (and probably Slipids as I think they are named and ordered the same) into some united-atom force fields (43A1-S3, Berger, 53A6L and CKP). I can dig it out and send it to you off list, if you are

Re: [gmx-users] Shifting in Verlet cut-off schemes?

On Mon, Mar 4, 2013 at 3:22 PM, Mark Abraham wrote: > On Sat, Mar 2, 2013 at 6:40 PM, Yun Shi wrote: > > > Hi all, > > > > I have read http://www.gromacs.org/Documentation/Cut-off_schemes, but > > still unsure about how Verlet works. > > > > "The group cut-off scheme can be combined with a buffer

Re: [gmx-users] Problem with radius of gyration calculation

VMD is an alternative, it was my suggestion. I know my similar was similar to ignoring the original questions. Besides, he can calculate end to end distance if he wants. Anyway, you are right:). On Thu, Feb 6, 2014 at 4:32 AM, Ali Alizadeh wrote: > Dear Jernej, > > Why don't try using VMD for c

[gmx-users] Simulations with Nitroxide Spin Label

Hi, Does anyone know if there is a way to incorporate a nitroxide spin labels into a gromacs simulation of proteins in water. With NMR and EPR it is possible to obtain distance restraints between labels, and I am interested to incorporate these restraints into my simulation. If there is a way to i

[gmx-users] Forcefield conversion script for POPC lipids

Hi users, I've searched the web for tools that convert atom names in pdb files from e.g. gromos nomenclature to amber or stockholm lipid nomenclature, but with no luck. Manually mapping the atom names is obviously error prone, so if anyone know of a script or a smart approach for this, do tell.

Re: [gmx-users] Problem with radius of gyration calculation

First of all, Justin is right. Without commands and exact selections we can't help much. Second: "Why don't try using VMD for calculating RG?" - I ask the opposite, ie. why use VMD when you got a native tools to do such? It's like using genuine Nespresso capsules on a white-label machine when you

Re: [gmx-users] about normal mode analysis

On 2/6/14, 9:27 AM, Gmail2 wrote: Double precision result: http://comments.gmane.org/gmane.science.biology.gromacs.user/62746 I assume you mean to say that you're having the same issue as described in that thread? You'll note that Michael mentions the existence of a bug, which has since b

Re: [gmx-users] about normal mode analysis

Double precision result: http://comments.gmane.org/gmane.science.biology.gromacs.user/62746 Ahmet Yıldırım 6 Şub 2014 tarihinde 15:39 saatinde, Justin Lemkul şunları yazdı: > > >> On 2/6/14, 8:25 AM, Ahmet yıldırım wrote: >> Dear users, >> >> I'm trying to do NMA of a structure. When I min

[gmx-users] Dynamic selections

Hello. I'm trying to make a dynamic selection in protein-water complex for further analysis. It looks like there's no support for dynamic selections in the GROMACS tools such as trjconv, g_sas and others. Is there some progress with dynamic selections in the recently announced GROMACS 5? -- Andre

Re: [gmx-users] about normal mode analysis

On 2/6/14, 8:25 AM, Ahmet yıldırım wrote: Dear users, I'm trying to do NMA of a structure. When I minimize a structure: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 3742 steps Potential Energy = -5.2965824e+04 Maximum force = 8.0245171e+00 on atom 3038 Norm of force =

Re: [gmx-users] Problem with radius of gyration calculation

On 2/6/14, 3:26 AM, Jernej Zidar wrote: Hi, I have a polymer system composed of three molecules (I generated it by taking one molecule and 'copied' along the y axis). Now, I'trying to compute the radius of gyration of one of these molecules. When I do the analysis for the smallest system, co

Re: [gmx-users] Since "nstlist has no effect on the accuracy"

Preso appuntamento per sabato mattina...di al papa' che si tenga libero!!! Ivan On 02/06/2014 11:09 AM, Szilárd Páll wrote: PS: The buffer is automatically calculated based on the verlet-buffer-drift set in the mdp file, for more details see the appendix of http://dx.doi.org/10.1016/j.cpc.2013.0

[gmx-users] about normal mode analysis

Dear users, I'm trying to do NMA of a structure. When I minimize a structure: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 3742 steps Potential Energy = -5.2965824e+04 Maximum force = 8.0245171e+00 on atom 3038 Norm of force = 1.3228445e+00 When I try to perform a norma

Re: [gmx-users] Problem with radius of gyration calculation

Dear Jernej, Why don't try using VMD for calculating RG? Jernej wrote: Subject: [gmx-users] Problem with radius of gyration calculation Message-ID: Content-Type: text/plain; charset=UTF-8 Hi, I have a polymer system composed of three molecules (I generated it by

Re: [gmx-users] Different "optimal pme grid ... coulomb cutoff" values from identical input files

Note that your above (CPU) runs had a far from optimal PP-PME balanc (pme mesh/force should be close to one). Performance instability can be caused by a busy network (how many nodes are you running on?) or even incorrect affinity settings. If you post a/some log files, we may be able to tell more

Re: [gmx-users] Since "nstlist has no effect on the accuracy"

PS: The buffer is automatically calculated based on the verlet-buffer-drift set in the mdp file, for more details see the appendix of http://dx.doi.org/10.1016/j.cpc.2013.06.003. -- Szilárd On Thu, Feb 6, 2014 at 11:04 AM, Szilárd Páll wrote: > Exactly. The penalty of large nstlist is large buff

Re: [gmx-users] Since "nstlist has no effect on the accuracy"

Exactly. The penalty of large nstlist is large buffer (rlist), but up to 40-50 with CPUs and up to 100 with GPUs is quite realistic. Hint: in 4.6.x you can use GMX_NSTLIST to override the value set in the mdp. From 5.0 there will be a command line option. Cheers, -- Szilárd On Thu, Feb 6, 2014

Re: [gmx-users] z always small for domain decomposition grid?

More dimensions = more complex communication pattern. See http://pubs.acs.org/doi/abs/10.1021/ct700301q Note that it's not *always* x-y decomposition first, mdrun will look at the dimensions of your system too. One case where manually switching to 3D decomposition can be beneficial is when there i

[gmx-users] Problem with radius of gyration calculation

Hi, I have a polymer system composed of three molecules (I generated it by taking one molecule and 'copied' along the y axis). Now, I'trying to compute the radius of gyration of one of these molecules. When I do the analysis for the smallest system, composed of 483 atoms (i.e. 161 atoms/molecule)