Re: [gmx-users] g_hbond

On Wed, Aug 31, 2011 at 5:54 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > >> One question for Glycine it is easy to assess 3 possible hbonds which >> can create as hydrogen is only one atom as a side chain. >> How about other amino acids and their maximum hbonds they can create?

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

Hi Tsjerk, Thanks for the help, it actually worked. When nstpcouple is set to 1m the system can be equilibrated (NPT) without LINCS error. I hadn't thought about it as I never use NVT (unless doing FE calculations). Is this mean the 4.5.4 is more sensitive the 4.0.7? Is this effect the data c

Re: [gmx-users] g_hbond

On 1/09/2011 6:14 PM, Steven Neumann wrote: On Wed, Aug 31, 2011 at 5:54 PM, Justin A. Lemkul > wrote: Steven Neumann wrote: One question for Glycine it is easy to assess 3 possible hbonds which can create as hydrogen is only one atom as a si

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

Hi Itamar, Yes, it appears that the 4.5.x series is more sensitive, due to the pressure coupling at intervals rather than at every step. Unfortunately the way it is now tied in with calculations of energies and neighbour searching indeed means that having nstpcouple set at 1 results in low simulat

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

On 1/09/2011 6:32 PM, Itamar Kass wrote: Hi Tsjerk, Thanks for the help, it actually worked. When nstpcouple is set to 1m the system can be equilibrated (NPT) without LINCS error. I hadn't thought about it as I never use NVT (unless doing FE calculations). Equilibrating with NVT before NPT c

[gmx-users] Re: cannot inactivate fitting in g_rmsf - incomplete coordinates are written

> Surprisingly I could get complete coordinates from g_covar v4.5.4 without > fitting, without being prompted to choose a group for the least squares fit. > However, g_covar is much slower than g_rmsf and I would avoid using it for > the whole trajectory if I could. > I don't expect o get an answer

[gmx-users] GROMACS 4.5.4 keep crashing all the time

I am glad that the pressure coupling intervals have been identified as a source of instability for poorly equilibrated systems as I was unaware of that. Still, the fact that the SD integrator also solves the problem also suggests that this is simply a poorly equilibrated system. I am not su

[gmx-users] Non-zero total charge

Hi, My system had a no zero total charge: System has non-zero total charge: 6.30e+01 I used genion to neutralize the system by adding 6 CL ions. After updating the topology file, the system still seems to have the same problem. It still has a non-zero total charge: System has non-zero t

Re: [gmx-users] Non-zero total charge

Munishika Kalia wrote: Hi, My system had a no zero total charge: System has non-zero total charge: 6.30e+01 I used genion to neutralize the system by adding 6 CL ions. After updating the topology file, the system still seems to have the same problem. It still has a non-zero total charg

[gmx-users] Non-zero total charge

-zero total charge: System has non-zero total charge: 5.70e+01 Please let me how i can rectify the situation. Many thanks, Munishika -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110901/58ff645a

[gmx-users] Problem building a polymer using pdb2gmx ....

Hi All I'm building a polymer (heterodimer) using pdb2gmx tool. I have included in ffG53a6 the 4 building block I need (aminoacids.rtp in my own dir: ../my_ffG53a6..): X ... A-B-A-B-A-B-A-B-A-B-A ... Y X: starting CAP residue A: a monomer B: the other monomer Y: terminal CAP residue I hav

Re: [gmx-users] Problem building a polymer using pdb2gmx ....

Alberto Sergio Garay wrote: Hi All I'm building a polymer (heterodimer) using pdb2gmx tool. I have included in ffG53a6 the 4 building block I need (aminoacids.rtp in my own dir: ../my_ffG53a6..): X ... A-B-A-B-A-B-A-B-A-B-A ... Y X: starting CAP residue A: a monomer B: the other monomer Y

[gmx-users] Re: Non-zero total charge

> Hi, > > > My system had a no zero total charge: > System has non-zero total charge: 6.30e+01 > I used genion to neutralize the system by adding 6 CL ions. > > After updating the topology file, the system still seems to have the same > problem. > > It still has a non-zero total charge: > Syst

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

Hi Chris, I can imagine that the pressure scaling has a more profound effect on the 'visible' surroundings if a cut-off is used, while this will not be the case when using PME. So the shock for an atom when the coordinates are adjusted can be expected to be greater with cut-off based methods, rend

[gmx-users] half double pair list method in GROMACS

Dear All, I try to apply the half double pair list method for a system containing a glycolipid surfactant and a peptide modeled with the GLYCAM and AMBER99SB force field. Briefly what I did : 1- I have changed the forcefield.itp like this [ defaults ] ; gen_pairs set explicitly ---

[gmx-users] GROMACS 4.5.4 keep crashing all the time

That all makes sense Tsjerk. I wonder if mdrun terminations based on LINCS warnings should come with an additional message to explain that one may try running for a while with nstpcouple=1. Also, I'm still a little curious about a question that Itamar asked a few posts ago: "If this is

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

On 2/09/2011 12:59 AM, chris.ne...@utoronto.ca wrote: That all makes sense Tsjerk. I wonder if mdrun terminations based on LINCS warnings should come with an additional message to explain that one may try running for a while with nstpcouple=1. That tip might be a good thing for the wiki page

[gmx-users] half double pair list method in GROMACS

Dear Stephane: We discussed this in April: http://lists.gromacs.org/pipermail/gmx-users/2011-April/060839.html At that time I also provided a method for you to verify your files (and the method in general). It is possible for you to answer your gen-pairs question by looking into the manua

[gmx-users] Non zero total charge

Hi, The genion command i used is genion -s genion.tpr -o ago_water_ions.gro -nn 6 I used this to add 6 CL ions and i got the following error:   System has non-zero total charge: 5.70e+01 So i should add another 5 CL ions to neutralize the system? Many thanks, Munishika -- gmx-users maili

Re: [gmx-users] Non zero total charge

Not 5. 57. Look at the exponent. On Thu, Sep 1, 2011 at 11:46 AM, Munishika Kalia wrote: > Hi, > The genion command i used is > genion -s genion.tpr -o ago_water_ions.gro -nn 6 > I used this to add 6 CL ions and i got the following error: >   System has non-zero total charge: 5.70e+01 > > S

RE: [gmx-users] order parameter

Hi, Thanks lot for replying. I am doing all-atom simulation. I am doing the PBC before finding the angle. also I normalise the vectors before finding the angle. Yes I have checked that the formula I am using for the order parameter is correct. I am doing the averaging correctly. 1. I take

Re: [gmx-users] Non zero total charge

I believe your problem is that you do not understand scientific notation. 5.70e+01 = 57. Cl- has a charge of -1. Need I say more. On Thu, Sep 1, 2011 at 11:46 AM, Munishika Kalia wrote: > Hi, > > The genion command i used is > genion -s genion.tpr -o ago_water_ions.gro -nn 6 > > I used this t

[gmx-users] Half double pair list method in GROMACS

Hi Chris, Sorry to repost the same question, but I have really tested your method the last few weeks. My question about the gen-pairs directive come from the fact that I have read a message from you http://lists.gromacs.org/pipermail/gmx-users/2006-September/023761.html Where you detailed how

Re: [gmx-users] order parameter

Parthasarathi, Ramya wrote: Hi, Thanks lot for replying. I am doing all-atom simulation. I am doing the PBC before finding the angle. also I normalise the vectors before finding the angle. Yes I have checked that the formula I am using for the order parameter is correct. I am doing the av

[gmx-users] order parameter

In addition to Justin's comment about g_order being incorrect for unsaturated carbons, you won't ever get numerical agreement with g_order, even for saturated carbons, because g_order does not use your explicit hydrogens. g_order uses the positions of the carbons to rebuild the hydrogen pos

[gmx-users] Half double pair list method in GROMACS

It's a typo, but it's in the discussion and not in the "do this" part of the method so I decided not to mention it. I don't see another question in this post, so I hope that you have figured things out. Note that I have never tested the exact implementation that I suggested in that April em

[gmx-users] GROMACS 4.5.4 keep crashing all the time

That seems possible Mark. I had actually assumed that Itamar extracted a .gro from the 4.0.7 simulations and created a new .tpr with 4.5.4 grompp. If that was the case, then I would still be surprised that it had instability problems. One sees a lot of charmm papers where people do slow hea

RE: [gmx-users] order parameter

[X] Hi Justin, Thanks for the reply, and this is the graph, the red curve is what GROMACS gives, the blue curve is what I get.. yes I am considering the unsaturated carbons in to account. I have to see which is closer to the experimental result. Hi Chris, Thanks for the information , I will s

Re: [gmx-users] order parameter

Parthasarathi, Ramya wrote: Hi Justin, Thanks for the reply, and this is the graph, the red curve is what GROMACS gives, the blue curve is what I get.. yes I am considering the unsaturated carbons in to account. I have to see which is closer to the experimental result. I can't see any

[gmx-users] pdb2gmx response time

Hi All, when I pdb2gmx on a very small (~20 atoms) peptide, it seemingly got stuck in the middle, showing Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.rtp Opening library file /share/apps/gromacs407/share/gromacs/top/aminoacids.dat Opening library

[gmx-users] Half double pair list method in GROMACS

Chris, Thank you for your confirmation. I did the changes. I am currently doing some tests, I will send you a feedback about the results off-list (if you want) shortly. A bientôt Stéphane Message: 1 Date: Thu, 01 Sep 2011 14:38:53 -0400 From: chris.

Re: [gmx-users] pdb2gmx response time

Yao Yao wrote: Hi All, when I pdb2gmx on a very small (~20 atoms) peptide, it seemingly got stuck in the middle, showing Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.rtp Opening library file /share/apps/gromacs407/share/gromacs/top/aminoacids.d

Re: [gmx-users] order parameter

Parthasarathi, Ramya wrote: I am sorry I pasted the picture do not know whether it got posted or not so I am attching the figure in JPEG format. Your code is producing completely unreasonable values, so I would suspect some error in whatever you've done. In this case, Gromacs is providing

[gmx-users] anisotripic polarization in water model

Dear GMX users, I am using GMX 4.5.3 I wnat to implement the anisotropic polarization of water, i.e. the polarizability is different in each direction. Is is possible with GROMACS? Can anybody help me how to do it? Thank you in advanced for all your helps/comments. Best, Jae H. Park ==

[gmx-users] atom type not in rtp entry

Hi, I get the following error message when i try to pdb2gmx my protein file: Fatal error: Atom D21 in residue LEU 1 was not found in rtp entry LEU with 11 atoms while sorting atoms. I wonder which of these need to be changed! Thank you for your time. ___

Re: [gmx-users] atom type not in rtp entry

On 2/09/2011 11:47 AM, Sweta Iyer wrote: Hi, I get the following error message when i try to pdb2gmx my protein file: Fatal error: Atom D21 in residue LEU 1 was not found in rtp entry LEU with 11 atoms while sorting atoms. I wonder which of these need to be changed! Please describe your over