[gmx-users] trjconv -pbc nojump

Hi, I want to use trjconv -pbc nojump to create a trajectory without box jumping of molecules. The molecules (lipids) also start to diffuse out of the box like they should, but in some a part of the molecule still jumps (as I could observe in xy direction), while the rest doesn't, leading to

Re: [gmx-users] about g_wham command of gromacs

On 01/09/15 23:09, 凌未风 wrote: Hello: I have a strange problem when I use g_wham to generate free energy profiles based on umbrella sampling (US) results. I have about ~30 windows of US simulations, 3 microseconds for each window, saved every 10 ps in the pullf.xvg files. When I try to

[gmx-users] Inconsistent shifts after switching form 4.5.7 to 5.0.4 version

Dear Gromacs users, Good someone give me a hit about the following issue. I am running a system which contains few periodic molecules (graphene sheets). Everything was running fine when the simulations were performed using group cut-off scheme and GROMACS 4.5.7. However, when I tried to

Re: [gmx-users] Re : Unusual Blow up

Nima Soltani writes: > I really appreciate your time that you spend helping me Justin > the starting structure looks like this: > https://www.dropbox.com/l/qGSSN0MRJKUtJronECThnn > and the topology of the *metal* is: > https://www.dropbox.com/l/c0Cp7RUeuaoDGS7aSuk1Sn In fact

[gmx-users] No default Ryckaert-Bell. types

Dear users. I'm trying to build the file .top for a molecule with opls FF. To do this I used MKTOP but when I run grompp I get this error: "ERROR 23 [file nor.top, line 227]: No default Ryckaert-Bell. types" This is my file .top: [ moleculetype ] ; Namenrexcl MOL 3

Re: [gmx-users] No default Ryckaert-Bell. types

Thank you for your answer. how can I put these parameters in the .top file? Best regard. 2015-09-02 17:34 GMT+02:00 Naga Rajesh Tummala : > The parameters for the RB dihedral in line 227 are not described in the > opls forcefield. Either you can provide the parameters

Re: [gmx-users] No default Ryckaert-Bell. types

The parameters for the RB dihedral in line 227 are not described in the opls forcefield. Either you can provide the parameters in your top file or include the dihedral paramters in the opls forcefield files tht comes with gromacs. On Wed, Sep 2, 2015 at 11:28 AM, Daniele Veclani

Re: [gmx-users] Re : Unusual Blow up

Justin Lemkul writes: > > > On 9/1/15 10:29 PM, Nima Soltani wrote: > > Nima Soltani ...> writes: > > > >> > >> Thank you for your kind help dear Justin > >> this is link of one of the pdb files that has been generated after Blow up > >> by Gromacs: > >>

Re: [gmx-users] No default Ryckaert-Bell. types

In the dihedrals section, similar to the bonds and angles section, the parameters are followed after the dihedral type.. 2 1 3 4 3 v0 v1 v2 v3 v4 v5 for RB type On Wed, Sep 2, 2015 at 11:48 AM, Daniele Veclani wrote: > Thank you for your answer. > > how can I put

Re: [gmx-users] extend a simulation just with xtc file

trjconv -dump $last_frame -o conf.gro grompp -c conf.gro This will allow you to restart the simulation, if you do not care about an exact continuation of the phase space trajectory that you probably do not. On Wed, Sep 2, 2015 at 10:51 AM, Adriana Garro wrote: >

Re: [gmx-users] Re : Unusual Blow up

On 9/2/15 11:59 AM, Nima Soltani wrote: Justin Lemkul writes: On 9/1/15 10:29 PM, Nima Soltani wrote: Nima Soltani ...> writes: Thank you for your kind help dear Justin this is link of one of the pdb files that has been generated after Blow up by Gromacs:

Re: [gmx-users] OPLS/AA parameters for 2-propanol

Normally, this sort of things is done via mechanical combining of the known groups -- CH3, -CH, OH -- from the force field. If your goal is to increase accuracy for pure 2-propanol per se, then play with the distribution of electronic density between OH and CH. If 2-propanol is to be used as a

Re: [gmx-users] Re : Unusual Blow up

Justin Lemkul writes: > > > On 9/2/15 11:59 AM, Nima Soltani wrote: > > Justin Lemkul ...> writes: > > > >> > >> > >> On 9/1/15 10:29 PM, Nima Soltani wrote: > >>> Nima Soltani ...> writes: > >>> > > Thank you for your kind help dear Justin > this is link of one

Re: [gmx-users] OPLS/AA parameters for 2-propanol

Thanks for the answer again. So I saw that for self-diffusion and viscosity I can just use gmx tcaf and gmx msd. As an experimental setup, would a squared box with 500 molecules of 2-propanol in NPT equilibration for a 10ns be a good system to use tcaf and msd? For the heat of vaporization I

Re: [gmx-users] OPLS/AA parameters for 2-propanol

On 9/2/15 9:47 PM, Ebert Maximilian wrote: Thanks for the answer again. So I saw that for self-diffusion and viscosity I can just use gmx tcaf and gmx msd. As an experimental setup, would a squared box with 500 molecules of 2-propanol in NPT equilibration for a 10ns be a good system to use

Re: [gmx-users] OPLS/AA parameters for 2-propanol

Hi justin, thank you for the answer. From your experience to calculate the shear viscosity with gmx tcaf for the correction term your mentioned (2.837297kBT/(6πηL)) would a trajectory with coordinates and velocities every 1 ps enough? Thanks On Sep 2, 2015, at 9:55 PM, Justin Lemkul

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 137, Issue 14

I want to see the change in secondary structure of the protein in vacuum as well as in specific solvent. On Wed, Sep 2, 2015 at 4:05 PM, < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to >

[gmx-users] Unwrapping of ssDNA

Hi all, I am a little bit confused about the unwrapping dynamics of a single stranded nucleic acid from the surface of a carbon nanotube. Say I have a NA-CNT hybrid and I think in presence of excess salt the adsorbed DNA will adopt a partially collapsed state thus breaking the initial

Re: [gmx-users] HREX simulation

Dear all, I have a very basic question regarding the demux.pl

[gmx-users] Adding urea molecules to lysozyme simulation

Hello Everyone, I have completed the very nice tutorial for lyzosyme available here: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html As I am working with unfolding, I would like to try simulate the unfolding by adding urea. I have made a urea.gro

Re: [gmx-users] Testing gromacs on IBM POWER8

On 27-08-2015 04:17, Mark Abraham wrote: Hi, I have no idea what you're trying to show with these graphs. Your vertical axis of time makes it looks like a 2.5 year old AMD chip is walking all over POWER8? Other points 1) GROMACS doesn't use configure or fortran, so don't mention that This is

Re: [gmx-users] OPLS/AA parameters for 2-propanol

It is difficult to get a very wrong density, especially for relatively rigid compounds. In the meantime, deviations of density within 2% of the experimental value should be admitted acceptable. A better criterion is to compare self-diffusion or viscosity to the experiment. Another famous property

Re: [gmx-users] Adding urea molecules to lysozyme simulation

On 9/2/15 4:04 PM, Martin Nors Pedersen wrote: Hello Everyone, I have completed the very nice tutorial for lyzosyme available here: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html As I am working with unfolding, I would like to try simulate the

Re: [gmx-users] Free energy calculation using inter-molecular bonded interaction

On 9/2/15 10:21 AM, Atsutoshi Okabe wrote: I mean that the entire [intermolecular_interaction] directive were commented out below; ;[ intermolecular-interactions ] ;[ bonds ] ;411 3173 6 0.55 2090 ;[ angles ] ;411 3173 3152 1 164.5 20.9 ;409 411 3173 1 122.3 20.9 ;[ dihedrals ]

Re: [gmx-users] trjconv -pbc nojump

On 9/2/15 9:36 AM, Reisser, Sabine (IPC) wrote: Well, in the end I would like to have an average value for the P atoms of each leaflet. I know which lipids belong to which leaflet, but I need to avoid box jumps along z, otherwise I will obviously get a wrong average. Using first trjconv -pbc

Re: [gmx-users] NVE Vacuum Fluctuation of Energy

The major source is rounded numbers -- in all functions, not only in the motion propagation algorithm. On Tue, Sep 1, 2015 at 11:20 PM, Johnny Lu wrote: > Dear Users, > > I was trying to run NVE simulation of alanine peptide in vacuum with double > precision gromacs

Re: [gmx-users] OPLS/AA parameters for 2-propanol

Thanks for the reply. I think I found relatively good atom types for iso propanol and derived the partial charges using antechamber and red server. I next check the density of pure iso propanol and used the closest definition to the real value. Iso propanol is used as co-solvent with water with

Re: [gmx-users] Testing gromacs on IBM POWER8

On 27-08-2015 10:03, Szilárd Páll wrote: A few more things to add: - we don't have CPU SIMD kernels for Power8, so comparing the plain C kernels against AVX kernels on AMD is not exactly fair; That was our hypothesis after seeing the results. One of our goals was to assess the readiness of

Re: [gmx-users] demux.pl input file

On 9/2/15 9:21 AM, Nawel Mele wrote: 2015-09-02 14:09 GMT+01:00 Justin Lemkul : On 9/2/15 8:48 AM, Nawel Mele wrote: 2015-09-02 13:38 GMT+01:00 Justin Lemkul : On 9/2/15 8:33 AM, Nawel Mele wrote: Dear Justin, Thank you for your answer, So from

Re: [gmx-users] trjconv -pbc nojump

Thanks for the reply, but I don't want the lipids to jump from one edge of the box to the other, which they do with this option, even though they remain complete. Cheers Sabine -- Dr. Sabine Reißer Theoretical Chemical Biology Institute of Physical Chemistry Karlsruhe Institute of Technology

Re: [gmx-users] extend a simulation just with xtc file

Hi No, I don't have a cpt file, I mean I have one but it is the final cpt because the simulation finished (in a wrong way). The problem came up in the last 15 ns, I had checked before and it was going fine. I already reran the simulation but this time using subtrajectories. Thanks! Adriana

[gmx-users] Unwrapping of ssNA

Hi all, I am a little bit confused about the unwrapping dynamics of a single stranded nucleic acid from the surface of a carbon nanotube. Say I have a NA-CNT hybrid and I think in presence of excess salt the adsorbed DNA will adopt a partially collapsed state thus breaking the initial

Re: [gmx-users] trjconv -pbc nojump

Well, in the end I would like to have an average value for the P atoms of each leaflet. I know which lipids belong to which leaflet, but I need to avoid box jumps along z, otherwise I will obviously get a wrong average. Using first trjconv -pbc whole and then -pbc nojump actually seems to work

Re: [gmx-users] demux.pl input file

Dear Nawel, You need to concatenate the log files of replica "0". Regards, Andrea 2015-09-02 12:16 GMT+02:00 Nawel Mele : > Dear Users, > > I have performed a REMD simulation on a protein with 48 replicas. I have > 400ns of REMD simulation and by consequence several

Re: [gmx-users] demux.pl input file

Dear Andrea, Thank you very much for your quick answer. I would like to ask you another quick question. Like I said I am interested on a particular temperature , so I wanted to use the demux.pl file to follow the trajectory of my temperature of interest through the temperature space. But, if I

[gmx-users] vacuum simulations

Dear gromacs users I have performed the vacuum simulation of protein. The structure was minimized after generating the box using the following mdp parameters. ; ;User spoel (236) ;Wed Nov 3 17:12:44 1993 ;Input file ; cpp = /usr/bin/cpp define =

[gmx-users] demux.pl input file

Dear Users, I have performed a REMD simulation on a protein with 48 replicas. I have 400ns of REMD simulation and by consequence several restart simulation and so several .log files: run1_0.log , run1_0.log run1_47.log run2_0.log , run2_0.log run2_47.log . . . runx_0.log , runx_0.log

Re: [gmx-users] vacuum simulations

Dear Tasneem, Like on previous replies to your last email, people need to understand what is the purpose of your simulation(s), otherwise it is difficult to help. "Cooking" and "simulating" are two completely different things, there is no recipe for the latter. One needs to understand what one

Re: [gmx-users] trjconv -pbc nojump

Hi Reisser, Instead of using -pbc nojump, use -pbc whole. On Wed, Sep 2, 2015 at 2:47 PM, Reisser, Sabine (IPC) < sabine.reis...@kit.edu> wrote: > Hi, > > > I want to use trjconv -pbc nojump to create a trajectory without box > jumping of molecules. The molecules (lipids) also start to diffuse

Re: [gmx-users] Green Kubo viscocity calculation

Try 5-20fs. On Wed, Sep 2, 2015 at 12:06 AM, Aishwary Shivgan wrote: > Currently I saving the energies after every 50 fs. Should I decrease more? > On Sep 2, 2015 3:23 AM, "Vitaly V. Chaban" wrote: > >> Sure, viscosity is overestimated,

Re: [gmx-users] demux.pl input file

On 9/2/15 8:33 AM, Nawel Mele wrote: Dear Justin, Thank you for your answer, So from the REMD simulation we get different output files: - .trr : trajectory file - .edr : energy file - .cpt: checkpoint used in case of crash - .log I am not use to perform REMD with gromacs so I am not sure

Re: [gmx-users] trjconv -pbc nojump

On 9/2/15 9:04 AM, Reisser, Sabine (IPC) wrote: Thanks, I made them whole and tried to cluster the lipids with -pbc cluster. However, I keep getting a Fatal error: Molecule 1 marked for clustering but not atom 1 in it - check your index! This happens no matter which index group I use. Do you

Re: [gmx-users] demux.pl input file

On 9/2/15 6:35 AM, Nawel Mele wrote: Dear Andrea, Thank you very much for your quick answer. I would like to ask you another quick question. Like I said I am interested on a particular temperature , so I wanted to use the demux.pl file to follow the trajectory of my temperature of interest

Re: [gmx-users] trjconv -pbc nojump

On 9/2/15 7:17 AM, Reisser, Sabine (IPC) wrote: Thanks for the reply, but I don't want the lipids to jump from one edge of the box to the other, which they do with this option, even though they remain complete. Making molecules whole should be the first step, followed by removing jumps.

Re: [gmx-users] Re : Unusual Blow up

On 9/1/15 10:29 PM, Nima Soltani wrote: Nima Soltani writes: Thank you for your kind help dear Justin this is link of one of the pdb files that has been generated after Blow up by Gromacs: https://www.dropbox.com/s/e3h05hohwp1va7p/step2170066b.pdb?dl=0 What other types of

Re: [gmx-users] demux.pl input file

Dear Justin, Thank you for your answer, So from the REMD simulation we get different output files: - .trr : trajectory file - .edr : energy file - .cpt: checkpoint used in case of crash - .log I am not use to perform REMD with gromacs so I am not sure which files do I need to concatenated to

Re: [gmx-users] demux.pl input file

2015-09-02 13:38 GMT+01:00 Justin Lemkul : > > > On 9/2/15 8:33 AM, Nawel Mele wrote: > >> Dear Justin, >> >> Thank you for your answer, >> >> So from the REMD simulation we get different output files: >> - .trr : trajectory file >> - .edr : energy file >> - .cpt: checkpoint used

Re: [gmx-users] trjconv -pbc nojump

Thanks, I made them whole and tried to cluster the lipids with -pbc cluster. However, I keep getting a Fatal error: Molecule 1 marked for clustering but not atom 1 in it - check your index! This happens no matter which index group I use. Do you have any ideas what's the reason? Cheers Sabine

Re: [gmx-users] demux.pl input file

On 9/2/15 8:48 AM, Nawel Mele wrote: 2015-09-02 13:38 GMT+01:00 Justin Lemkul : On 9/2/15 8:33 AM, Nawel Mele wrote: Dear Justin, Thank you for your answer, So from the REMD simulation we get different output files: - .trr : trajectory file - .edr : energy file - .cpt:

Re: [gmx-users] demux.pl input file

2015-09-02 14:09 GMT+01:00 Justin Lemkul : > > > On 9/2/15 8:48 AM, Nawel Mele wrote: > >> 2015-09-02 13:38 GMT+01:00 Justin Lemkul : >> >> >>> >>> On 9/2/15 8:33 AM, Nawel Mele wrote: >>> >>> Dear Justin, Thank you for your answer, So from

Re: [gmx-users] OPLS/AA parameters for 2-propanol

I saw the papers you mentioned but one is a not clear how they parameterized, one is missing the supporting material and the last is not showing the parameters they used. I will check with the initial paper of Jorgensen again but if I recall it correctly he mentioned some problems with

Re: [gmx-users] Free energy calculation using inter-molecular bonded interaction

I mean that the entire [intermolecular_interaction] directive were commented out below; ;[ intermolecular-interactions ] ;[ bonds ] ;411 3173 6 0.55 2090 ;[ angles ] ;411 3173 3152 1 164.5 20.9 ;409 411 3173 1 122.3 20.9 ;[ dihedrals ] ;409 411 3173 3152 2 12.0 20.9 ;407 409 411

[gmx-users] Fwd: Tcaf for viscosity calculation

-- Forwarded message -- From: "Sunil Ghimire" Date: 2 Sep 2015 08:16 Subject: Tcaf for viscosity calculation? To: Cc: Dear sir , Can we use g_tcaf for calculation of viscosity of noble gases? -- Gromacs Users mailing list *