Re: [gmx-users] pdb2gmx yielding (a couple of) -nan values for coordinates of built hydrogen atoms

Well, it is building hydrogen atoms, and that could go astray if the coordinates from which they are built are badly behaved (e.g. co-linear). Mark On Fri, Apr 18, 2014 at 4:47 AM, Christopher Neale < chris.ne...@alum.utoronto.ca> wrote: > In most cases, I get what I expect when I execute the f

[gmx-users] pdb2gmx yielding (a couple of) -nan values for coordinates of built hydrogen atoms

In most cases, I get what I expect when I execute the following command: echo -e "6\n1\n" | pdb2gmx -f ${b}e.gro -o ${b}et.gro -p tmp.top -i ${b}_posre.itp -ter -ignh However, I have one input .gro file for which the output .gro file has -nan for all coordinates for HB1 and HB2 atoms. I built t

Re: [gmx-users] Using GPU to do simulations

On Thu, Apr 17, 2014 at 8:45 PM, wrote: > Hi everyone, > > I am trying to do some pulling simulations by gromacs (i.e., pull a ligand > from its binding site), as the system is large I want to accelerate the > simulations by GPU. I want to confirm that, Does GPU simulation support the > pulling c

Re: [gmx-users] Using GPU to do simulations

On 4/17/14, 2:45 PM, mirc...@sjtu.edu.cn wrote: Hi everyone, I am trying to do some pulling simulations by gromacs (i.e., pull a ligand from its binding site), as the system is large I want to accelerate the simulations by GPU. I want to confirm that, Does GPU simulation support the pulling co

[gmx-users] Using GPU to do simulations

Hi everyone, I am trying to do some pulling simulations by gromacs (i.e., pull a ligand from its binding site), as the system is large I want to accelerate the simulations by GPU. I want to confirm that, Does GPU simulation support the pulling code of GROMACS? Can I use GPU acceleration to do

Re: [gmx-users] Conserved Energy in csvr NVT runs

Dear Mark, Dear Users, Thank you for the detailed and prompt answer! I'm sorry I probably wasn't clear enough, and I didn't attach the full input. So I'll attach to avoid confusion. >IIRC there is a conserved quantity written, but as you can see in Bussi's >original paper, it has a t dependence.

Re: [gmx-users] negative HB lifetime

Thanks Erik; You're alright, The problem is in the ACF; it falls dramatically to zero. In this case, what's the solution? should I extend my simulation to more time? Thanks Djamila -- View this message in context: http://gromacs.5086.x6.nabble.com/negative-HB-lifetime-tp5015830p5015900.html Sent

[gmx-users] H-bond analysis

hi, I try to analyze H-bonds in an MD trajectory. when i look at the definition of an H-bond used by g_hbond it appears that only three atoms (acceptor, donor, hydrogen, ADH) are used in the analysis performed by this program ... however, i would assume that in fact 4 (or up to 6) atoms should be

Re: [gmx-users] Potential for Frozen atoms

Hi, As Vitaly said, you are mixing the methods. If you want to find out the potential between 2 atoms, why don't you just go into the FF, pick out relevant parameters from there and plot it. So for 2 non-bonded atoms the contribution would be VdW and Coulomb. Putting things further than cut-off

Re: [gmx-users] genconf of box of a few types of molecules

Thank you, this makes perfect sense! -- View this message in context: http://gromacs.5086.x6.nabble.com/genconf-of-box-of-a-few-types-of-molecules-tp5015876p5015897.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archi

Re: [gmx-users] segmentation fault

Hi, Probably the Fedora package has broken dependencies. IIRC Jussi Letoha maintains that, but you should report the problem through the Fedora channels. Otherwise, you need to build GROMACS yourself following the usual installation instructions. Mark On Apr 17, 2014 9:20 AM, "Meenakshi Rajput"

Re: [gmx-users] Potential for Frozen atoms

Hi Sukriti Gupta - Your setup is great. The only scientific problem is that all those divalent cations in the force fields are being parametrized, to a larger or a smaller extent, with condensed systems in mind. That is, if you use them in the liquid phase and for temperature-driven dynamics, the

[gmx-users] Fuse Protein and non Protein Part of Ligand

Hi, I have a small problem, I have a relatively big ligand (ca 1200Da) and I want to fuse him (the fragments exist as rtp). And I thought that the online servers to calculate could be not good enough for that ligand. For that reason I have chosen the specbond.dat wa. Now I am able to fuse the par

Re: [gmx-users] Potential for Frozen atoms

On Thu, Apr 17, 2014 at 5:54 AM, sukriti002 wrote: > Actually I just want to find out potential between two Cu2+ ions, but as > gromacs doesn't allow total charge to be a non zero value, No. This is allowed. Whether you'd want to is another matter. I had to add two > sulphate ions. So I kept 2

[gmx-users] segmentation fault

dear gromacs users I tried mdrun in gromacs on fedora20 but *it stopped in between and showing the fallowing error * *:-**Segmentation fault (Core dumped) * *Can any one please tell what is the problem and how to solve it? * -- Gromacs Users mailing list * Please search the archive at http://ww

[gmx-users] segmentation fault

dear gromacs users I tried mdrun in gromacs but *it stopped in between and showing the fallowing error * *:-**Segmentation fault (Core dumped) * *Can any one please tell what is the problem and how to solve it? * -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.or

Re: [gmx-users] Is there a tool for calculating mechanical properties of materials using GROMACS

Not as such, but so long as there is a common trajectory format, there's usually no great barrier to doing a simulation with one tool and analyzing it with any other. Mark On Thu, Apr 17, 2014 at 3:33 AM, xiaowu759 wrote: > Dear GMXers, > I try to calculate mechanical properties of materials us