Re: [gmx-users] Restarting crashed simmulation.

On 5/11/18 2:11 PM, neelam wafa wrote: Hi! does this means that i should not have used -deffnm md_0_1 in the run command? Actually I am a student and new to gromacs and have no experties in it. I think I need to read more about md run command options. Use -deffnm, it saves you typing and

Re: [gmx-users] Restarting crashed simmulation.

Hi! does this means that i should not have used -deffnm md_0_1 in the run command? Actually I am a student and new to gromacs and have no experties in it. I think I need to read more about md run command options. Regards On Fri, 11 May 2018 10:57 pm Mark Abraham,

Re: [gmx-users] Restarting crashed simmulation.

Hi, Behaviour has changed since 5.1 to make it harder for this happen, but if you do not call mdrun exactly the same way, older implementations of checkpointing would try to be helpful and sometimes actually not be helpful. This only happens if you try to over manage mdrun. It's best to leave it

Re: [gmx-users] Restarting crashed simmulation.

okay, Thanks On Fri, May 11, 2018 at 5:19 PM, Justin Lemkul wrote: > > > On 5/11/18 1:18 PM, neelam wafa wrote: > >> *This is the message of gmx check for both the trajectories. I*t means >> that >> trajectory is not continuous. Am I right? >> > > They are continuous

Re: [gmx-users] Restarting crashed simmulation.

On 5/11/18 1:18 PM, neelam wafa wrote: *This is the message of gmx check for both the trajectories. I*t means that trajectory is not continuous. Am I right? They are continuous (md_0_1.xtc ends at t=2720 ps and traj_comp.xtc starts at the same time) and can be concatenated together. It

Re: [gmx-users] Restarting crashed simmulation.

*This is the message of gmx check for both the trajectories. I*t means that trajectory is not continuous. Am I right? *gmx check -f md_0_1.xtc* Checking file md_0_1.xtc Reading frame 0 time0.000 # Atoms 67864 Precision 0.001 (nm) Reading frame 200 time 2000.000 Item

Re: [gmx-users] Restarting crashed simmulation.

On 5/11/18 1:12 PM, neelam wafa wrote: The previous command was : gmx mdrun -deffnm md_0_1 I didn't ust -cpi falg . Then the only explanation I can think of for what you are observing is that somehow md_0_1.cpt was not accessible, causing mdrun to start over from t = 0 and write a new

Re: [gmx-users] Restarting crashed simmulation.

The previous command was : gmx mdrun -deffnm md_0_1 I didn't ust -cpi falg . On Fri, May 11, 2018 at 5:01 PM, Justin Lemkul wrote: > > > On 5/11/18 12:52 PM, neelam wafa wrote: > >> I used this command: >> gmx mdrun -s md_0_1.tpr -cpi md_0_1.cpt >> >> But I think its not

Re: [gmx-users] Restarting crashed simmulation.

On 5/11/18 12:52 PM, neelam wafa wrote: I used this command: gmx mdrun -s md_0_1.tpr -cpi md_0_1.cpt But I think its not appending as new files are being generated with names state.cpt, state_prev.cpt and traj_comp.xtc while the previous files were md_0_1.cpt, md_0_1_prev.cpt and md_0_1.xtc.

Re: [gmx-users] Restarting crashed simmulation.

I used this command: gmx mdrun -s md_0_1.tpr -cpi md_0_1.cpt But I think its not appending as new files are being generated with names state.cpt, state_prev.cpt and traj_comp.xtc while the previous files were md_0_1.cpt, md_0_1_prev.cpt and md_0_1.xtc. Why has it happened ? I have checked log

Re: [gmx-users] Distribution of water polarization

On Fri, 11 May 2018, 20:04 Justin Lemkul, wrote: > > > On 5/11/18 11:29 AM, rose rahmani wrote: > > On Fri, 11 May 2018, 19:38 Justin Lemkul, wrote: > > > >> > >> On 5/11/18 11:06 AM, rose rahmani wrote: > >>> Hi, > >>> > >>> How can i calculate the

Re: [gmx-users] Distribution of water polarization

On 5/11/18 11:29 AM, rose rahmani wrote: On Fri, 11 May 2018, 19:38 Justin Lemkul, wrote: On 5/11/18 11:06 AM, rose rahmani wrote: Hi, How can i calculate the distribution of water polarization for example for the first two layers of water at the solid surface? How

Re: [gmx-users] Distribution of water polarization

On Fri, 11 May 2018, 19:38 Justin Lemkul, wrote: > > > On 5/11/18 11:06 AM, rose rahmani wrote: > > Hi, > > > > How can i calculate the distribution of water polarization for example > for > > the first two layers of water at the solid surface? > > > > How about the number of

Re: [gmx-users] Distribution of water polarization

On 5/11/18 11:06 AM, rose rahmani wrote: Hi, How can i calculate the distribution of water polarization for example for the first two layers of water at the solid surface? How about the number of water molecules with a given polarization? I mean exactly figure2 of this article. Can gmx

[gmx-users] Distribution of water polarization

Hi, How can i calculate the distribution of water polarization for example for the first two layers of water at the solid surface? How about the number of water molecules with a given polarization? I mean exactly figure2 of this article. Can gmx dipoles do it? Best regards -Rose -- Gromacs

Re: [gmx-users] Restarting crashed simmulation.

On 5/11/18 10:42 AM, neelam wafa wrote: Dear Sir Justin! I have restarted the simmulation but its producing a separate log file starting from the step where restarted. Is it normal response or there is some problem with my restart? That shouldn't happen; everything should be appended unless

Re: [gmx-users] V2018.1 building issues

Ok, got it, thanks! On Fri, May 11, 2018 at 10:23 AM, Mark Abraham wrote: > Hi, > > I'm surprised that was able to work in 2016, but nevertheless it was never > designed to work and should not be relied upon. Build a separate binary for > each hardware flavor and have

Re: [gmx-users] Restarting crashed simmulation.

Dear Sir Justin! I have restarted the simmulation but its producing a separate log file starting from the step where restarted. Is it normal response or there is some problem with my restart? Thanks in advance. On Fri, May 11, 2018 at 12:06 PM, neelam wafa wrote: >

Re: [gmx-users] Bias potential during umbrella sampling

Hi Meena, No, they are not generally the same. The reaction coordinate using 'distance' is the norm of the COM distance vector (>=0). Using direction, it's the projection onto the given vector (possibly negative). -- Viveca On Fri, May 11, 2018 at 11:33 AM, Meena Singh

Re: [gmx-users] Non integer charge value

On 5/11/18 6:20 AM, Hemalatha Jayabal wrote: I apologize for the previous formatting. Well it's no better here but it's immediately clear you're still doing something wrong: [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 202 HYP rtp HYP q +1.2 1 NH3

Re: [gmx-users] KCl forms crystals at c=0.15M with amber99sb-ildn

On 5/11/18 11:19 AM, Mark Abraham wrote: Hi, On Fri, May 11, 2018 at 12:07 PM Daniel Bauer wrote: Hi, thanks for the response! Now i know what I have to do :) So did I understand you right that the ion parameters that are currently used in amber99sb by GROMACS

Re: [gmx-users] V2018.1 building issues

Hi, I'm surprised that was able to work in 2016, but nevertheless it was never designed to work and should not be relied upon. Build a separate binary for each hardware flavor and have the module system choose the correct one to load, per our installation guide

Re: [gmx-users] KCl forms crystals at c=0.15M with amber99sb-ildn

Hi, On Fri, May 11, 2018 at 12:07 PM Daniel Bauer wrote: > Hi, > > thanks for the response! Now i know what I have to do :) > > So did I understand you right that the ion parameters that are currently > used in amber99sb by GROMACS are not identical with the ones

Re: [gmx-users] KCl forms crystals at c=0.15M with amber99sb-ildn

Hi, thanks for the response! Now i know what I have to do :) So did I understand you right that the ion parameters that are currently used in amber99sb by GROMACS are not identical with the ones implemented in the current version of amber99sb used by AMBER? If yes, whats the reason for this

Re: [gmx-users] Restarting crashed simmulation.

Thanks Sir Justin! I have continued the simmulation from the last step. Regards On Thu, May 10, 2018 at 12:08 PM, Justin Lemkul wrote: > > > On 5/10/18 7:08 AM, neelam wafa wrote: > >> Hi gmx users! >> >> I am running a 5ns md simmulation of a protein with 250 steps. It >>

Re: [gmx-users] Non integer charge value

I apologize for the previous formatting. [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 202 HYP rtp HYP q +1.2 1 NH3 202 HYP N 1 -0.3 14.007 ; qtot -0.3 2 HC 202 HYP H1 2 0.33 1.008 ; qtot 0.03 3 HC 202 HYP H2 3 0.33 1.008 ; qtot 0.36 4 HC 202 HYP H3 4 0.33

[gmx-users] Bias potential during umbrella sampling

Dear GROMACS users, Currently I am doing umbrella sampling for adsorption of molecule on solid surface. I have frozen the coordinates for solid surface and pulling the molecule towards the surface. I would like to know that while using options pull-geometry = distance and pull-dim = N N Y is

Re: [gmx-users] Non integer charge value

I applied the said terminus as well but I ended up getting the same error. [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 202 HYP rtp HYP q +1.2 1 NH3 202 HYP N 1 -0.3 14.007 ; qtot -0.3 2 HC 202 HYP H1 2 0.33 1.008 ; qtot 0.03 3 HC 202 HYP H2 3 0.33 1.008