Re: [gmx-users] GPU in Ubuntu

From my experience its fine, the main problems are annoying changes to gedit, other side software and a few bugs that pop up, as the come out with a new release rather quickly...I usually avoid the new releases for at least 6 months now, and havnt really had much problem with larger bugs, such as

[gmx-users] multiple molecules of same type and .top file

Dear All, I am trying to generate .top file for my system. I would be obliged if you could explain following topology file question to me, since it is not very clearly mentioned anywhere: In LAMMPS software that I am used to, user is required to enter details of topology for all the molecules of

[gmx-users] quesion about MIC

Dear All, I am a new user of gromacs, and I want to use gromacs on MIC. Recently I see the gromacs-5.0beta2 published, and in the lists of rebision changes, I see it has been added the SIMD supported for Intel MIC. But when run the gromacs on MIC, it doesn't use the MIC card. On the other

[gmx-users] REMD - step 12005: Water molecule starting at atom 7030 can not be settled

Dear Gmx Users, I am running REMD of a small protein in water. I have 36 temperatures. After minimization I equilibrate each with nvt and npt ensemble. Then I start REMD with -multidir. The mdp: ; Run parameters integrator = md; leap-frog integrator nsteps = 5000 dt =

Re: [gmx-users] MM-GB/SA analysis in Gromacs

Dear Andrea, I've simulated a protein dimer for a long time span and now I need to perform MM-PBSA calculations to get the binding free energy between the two monomers. Could you please send me the script to carry out this calculation. I've read your paper Exploring PHD Fingers and H3K4me0

[gmx-users] problem with NVT equilibration for membrane protein

Dear all, I am working with an homology model of a protein inserted in a POPC membrane. I first ran minimization on the system, which ended up with I think reasonable values for Fmax and Epot: Steepest Descents converged to Fmax 1000 in 1390 steps Potential Energy = -1.2822042e+06 Maximum force

[gmx-users] constraints

Hi everybody, ​​ I am running a simulation of a protein bonded on a metallic structure. In the mdp files of the MD run I have set constraints = none while during the equilibration I had set constraints = all-bond in order to reach the MD step with the structure of my protein still in order.

[gmx-users] gen-pairs, nrexcl and [ pairs ] in itp files

Dear All, I am attempting to make modifications to the Gromos 53A6 forcefield in order to implement the Gromos 56Acarbo forcefield in GROMACS. Most of the modifications are straightforward except for some of the LJ parameters. As well as simple adjustments to most of the 1-4 interaction

[gmx-users] 2D PMF for two ions

Hello, I am trying to carry out a 2D PMF calculations of two ions in a peptidic channel using GROMACS (and Umbrella Sampling). I have several technical questions: -Should I consider pull_ngroups= 3 (two of them ions and the other one the channel)? -Or should I carry out a 1D PMF for one

[gmx-users] I keep receiving messages that I have been unsubscribed from the mailing list.

On April 24, May 5, and May 11, I have received messages with the subject, You have been unsubscribed from the gromacs.org_gmx-users mailing list. These e-mail do not have any text to them at all. I immediately resubscribe myself only to receive another the following week.  I do not believe that I

[gmx-users] Gromacs 5, TNG, and older trajectory formats

Dear Gromacs users, It seems that with the next Gromacs release (version 5) a new trajectory format (TNG) is released

Re: [gmx-users] crystal slab and position restraints: com option

On 5/11/14, 2:01 PM, Chetan Mahajan wrote: Thanks, Justin. I was also under impression that with com option, distance between slab atoms (which are position restrained) remains same, even though coordinates change. So doesn't it mean that TiO2 slab dimensions should remain same? No. Under

Re: [gmx-users] multiple molecules of same type and .top file

On 5/12/14, 2:43 AM, Chetan Mahajan wrote: Dear All, I am trying to generate .top file for my system. I would be obliged if you could explain following topology file question to me, since it is not very clearly mentioned anywhere: In LAMMPS software that I am used to, user is required to

Re: [gmx-users] problem with NVT equilibration for membrane protein

On 5/12/14, 5:32 AM, Floriane Montanari wrote: Dear all, I am working with an homology model of a protein inserted in a POPC membrane. I first ran minimization on the system, which ended up with I think reasonable values for Fmax and Epot: Steepest Descents converged to Fmax 1000 in 1390

Re: [gmx-users] constraints

On 5/12/14, 6:14 AM, Nicola Staffolani wrote: Hi everybody, ​​ I am running a simulation of a protein bonded on a metallic structure. In the mdp files of the MD run I have set constraints = none while during the equilibration I had set constraints = all-bond in order to reach the MD step

Re: [gmx-users] Gromacs 5, TNG, and older trajectory formats

Hi, The new TNG format and library do not affect other formats. So, if you do not write/read TNG everything should work as before. There are some TNG features that are not implemented yet in GROMACS, e.g. writing energy data and/or other custom data. In a future version of GROMACS the TNG

Re: [gmx-users] constraints

Hi Justin, thank you for your clear reply! However, it still comes as surprising to me that a standard N-H bond (entered as a gb_2 one with the same parameters as described in Table 2.5.2.1 of the GROMOS96 Manual and User Guide) enters in conflict with the standard dt value: indeed dt = 0.002 →

Re: [gmx-users] constraints

On 5/12/14, 9:03 AM, Nicola Staffolani wrote: Hi Justin, thank you for your clear reply! However, it still comes as surprising to me that a standard N-H bond (entered as a gb_2 one with the same parameters as described in Table 2.5.2.1 of the GROMOS96 Manual and User Guide) enters in

Re: [gmx-users] gen-pairs, nrexcl and [ pairs ] in itp files

Bogdan, I had found that a little while ago but was unable to find again so thankyou for pointing me to it again and writing it in the first place. Jon, I hadn't found those file previously and they are consistent with what I have come up with independently so I guess that is a good sign. Out

Re: [gmx-users] constraints

OK, got it, thanks a lot Justin! ;) .0005 ps is indeed working... It is not clear to me what I miss - from the Chemistry or Physics point of view - when I constraint the X-H bonds... I mean, will the rest of the dynamics (for example, the oscillations of the other couples of bonded atoms) be

Re: [gmx-users] constraints

On 5/12/14, 9:50 AM, Nicola Staffolani wrote: OK, got it, thanks a lot Justin! ;) .0005 ps is indeed working... It is not clear to me what I miss - from the Chemistry or Physics point of view - when I constraint the X-H bonds... I mean, will the rest of the dynamics (for example, the

[gmx-users] confirm please

Dear All, I am using amber2gromacs tool acpype for converting input files for AMBER into those for GROMACS. There are some differences in these files (.gro and .top) compared to the information given in gromacs manual 4.6.5 abotu these kind of files. First, while listing charges and vander waals

Re: [gmx-users] confirm please

gromacs is not giving error, but just wanted to confirm, especially the first question. In absence of column for at.num, how would gromacs reading my file know that second column is for mass? It's ofcourse commented as to mass, but comments are not read anyways. Thanks Chetan On Mon, May 12,

Re: [gmx-users] REMD - step 12005: Water molecule starting at atom 7030 can not be settled

What would you recommend then? Equilibrate with Berendsen barostat and v-rescale thermostat? On Mon, May 12, 2014 at 2:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/12/14, 3:58 AM, Steven Neumann wrote: Dear Gmx Users, I am running REMD of a small protein in water. I have 36

Re: [gmx-users] REMD - step 12005: Water molecule starting at atom 7030 can not be settled

I would generally encourage the use of NVT REMD. However, note that P-R does exhibit unstable oscillatory behaviour when not close to equilibrium. REMD is supposed to stay in equilibrium by design, but this gets double crossed if the exchange period is too short with respect to the autocorrelation

Re: [gmx-users] Why in g_mindist the default 'distace for contacts' -d is .6

It was probably just a convenient number for whoever wrote the tool originally. Mark On May 12, 2014 10:41 PM, Lalit upmu...@gmail.com wrote: Hi All, In the g_mindist calculations, the default distance for contacts is taken as 0.6 nm. Is there a physical significance to this number? Why it

Re: [gmx-users] REMD - step 12005: Water molecule starting at atom 7030 can not be settled

Thanks a lot! So which combination of thermostat/barostat would provide a proper ensemble without crashes? I am looking in the literature but did not find anything. On Tue, May 13, 2014 at 6:34 AM, Mark Abraham mark.j.abra...@gmail.comwrote: I would generally encourage the use of NVT REMD.

Re: [gmx-users] refcoord-scaling

Thanks, Mark. With timestep to be 1 fs (instead of 2 fs) in production run, job is running fine without blowing up. (equilibration run also contains timestep to be 1 fs and refcoord-scaling option is set to com). However, time step to 1 fs in production run does not affect water and its

[gmx-users] Citing gromacs tools

Hi All, In many papers, the authors cite the main gromacs paper and simply declare in the methods section that they used the gromacs analysis suite. Is that a good practice or should each tool be cited separately? Eg: g_sas says: PLEASE READ AND CITE THE FOLLOWING REFERENCE Frank