Re: [gmx-users] calcium parameters

Hey, > What makes you think that the chemical behaviour of divalent Ca ion > resembles Ca bound to oxygen? Probably because there's quite a body of literature about charge-transfer, polarization and partial bond character of calcium ions with oxygens. But there's not a conclusive answer on how to

[gmx-users] Residence time and trjorder

Dear gmx-users, I used trjorder in order to study the water molecules that are closer than 5 A from my protein. trjorder -s structure.tpr -f traj.xtc -n prot_water.ndx -o ordered.pdb -nshell nshell_.xvg -r 0.5 -b 0 -e 5000 But now I need to analyse the residence time of a water molecule, I mean

Re: [gmx-users] Residence time and trjorder

HI Carla, I wrote a similar code, see attached. But it is written for my condition. You should modify it accordingly. regards, Baofu Qiao On 07/12/2011 02:04 PM, Carla Jamous wrote: Dear gmx-users, I used trjorder in order to study the water molecules that are closer than 5 A from my prote

[gmx-users] Topology for nBuOH

Hi, I'm trying to include parameters of n-butanol in the topology file (below) (i'm not using opls or other force field for butanol), but when i run the grompp program, I obtain the following message: Fatal error: Atomtype Hb not found How can I fix this problem? Thanks Topology file: ; Inc

[gmx-users] R:Re: R: Re: g_mindist on rhombic dodecahedron system

I hope this will be the last message on this subject...sorry to bother you, but I'd need another hint about analysis. All OK about the new reference file that I created following Justin's suggestions. The problem now is that my protein is a homodimeric protein, and when I do: g_rmsf -f prot_boxdodf

[gmx-users] Micelle Modeling

Users, I'm trying to start a micelle modeling project & have tried countless approaches to making a DPC micelle. My problems include: -DPC not being recognized when I try to imput it into the [molecules] seciton of the topology file to account for the DPC molecules in the water topology. Otherwise,

Re: [gmx-users] Topology for nBuOH

Juliana Angeiras wrote: Hi, I'm trying to include parameters of n-butanol in the topology file (below) (i'm not using opls or other force field for butanol), but when i run the grompp program, I obtain the following message: Fatal error: Atomtype Hb not found How can I fix this problem

Re: [gmx-users] R:Re: R: Re: g_mindist on rhombic dodecahedron system

Anna Marabotti wrote: I hope this will be the last message on this subject...sorry to bother you, but I'd need another hint about analysis. All OK about the new reference file that I created following Justin's suggestions. The problem now is that my protein is a homodimeric protein, and when I

Re: [gmx-users] Micelle Modeling

Janowicz, Adrianna C. wrote: Users, I'm trying to start a micelle modeling project & have tried countless approaches to making a DPC micelle. My problems include: -DPC not being recognized when I try to imput it into the [molecules] seciton of the topology file to account for the DPC molecules

Re: [gmx-users] Residence time and trjorder

Dear Boafu, This sounds like a great tool! Carla, note that once you've ordered the water molecules you loose the continuity of their trajectories ... that is because you order them in function of their distance to the protein. I am not sure the definition you give will give you the answer

[gmx-users] Gromacs on IBM clusters

Dear users, I was trying to run gromacs-4.5.3 in IBMcluster using mpich-1.2.7 rather than openmpi. But I was getting some error. Sorry I donot remember the error. But Is it possible to run gromacs-4.5.3 using mpich implementation? Thank you With Regards M. Kavyashree -- gmx-users mailing list

Re: [gmx-users] Gromacs on IBM clusters

Kavyashree M wrote: Dear users, I was trying to run gromacs-4.5.3 in IBMcluster using mpich-1.2.7 rather than openmpi. But I was getting some error. Sorry I donot remember the error. But Is it possible to run gromacs-4.5.3 using mpich implementation? Probably, but without an actual error me

[gmx-users] Re: [gmx-developers] GPU

Hi, As this is not a development-related question I'm moving the discussion to the user's list. Future replies should be sent *only* to gmx-users@gromacs.org. As Axel pointed out, the list of CUDA-compatible devices is much broader than the list of cards we label compatible. The compatibility che

Re: [gmx-users] Gromacs on IBM clusters

On Wed, Jul 13, 2011 at 12:21 AM, Justin A. Lemkul wrote: > > > Kavyashree M wrote: >> >> Dear users, >> >> I was trying to run gromacs-4.5.3 in IBMcluster using mpich-1.2.7 >> rather than openmpi. But I was getting some error. Sorry I donot >> remember the error. But Is it possible to run gromacs

Re: [gmx-users] Gromacs on IBM clusters

Thank you lina, I have been using 4.5.3 in other systems without any problems using openmpi. But this cluster had MPICH which is an implementation of MPI just like openmpi. Even I am new to these terminologies. I will try installing gromacs 4.5.4. Thanks! Thank you With Regards M. Kavyashree On

[gmx-users] Re: Good method to turn off electrostatics

Hi, Many thanks, Justin, for your time. As a first try, I am going ahead with your proposed option (1): make my own local copy of spce.itp and adjust the call (the #include) in the topology file. I have zeroed the charges in this local copy of spce.itp and tried to prepare for energy minimizatio

Re: [gmx-users] Re: Good method to turn off electrostatics

Andrew DeYoung wrote: Hi, Many thanks, Justin, for your time. As a first try, I am going ahead with your proposed option (1): make my own local copy of spce.itp and adjust the call (the #include) in the topology file. I have zeroed the charges in this local copy of spce.itp and tried to prep

Re: [gmx-users] Micelle Modeling

Also, I forgot to mention that I need to throw a protein into the mix. How would I get both the protein and the DPC into the box? On Tue, July 12, 2011 10:46 am, Justin A. Lemkul wrote: > > > Janowicz, Adrianna C. wrote: >> Users, >> I'm trying to start a micelle modeling project & have tried c

Re: [gmx-users] Micelle Modeling

Janowicz, Adrianna C. wrote: Also, I forgot to mention that I need to throw a protein into the mix. How would I get both the protein and the DPC into the box? Have a look through some of the more advanced tutorials. There is nothing that will walk you through all of it explicitly (and it'

[gmx-users] number of windows in PMF

Hello, I am trying to calculate the binding energy between two monomers in three different dimers, using PMF (Umbrella Sampling method) and following Justin's tutorial. Using 100 windows separated 0.05 nm I get the PMFs represented in "pmf_using_100_points.pdf" (attached), and using 50 windows

Re: [gmx-users] number of windows in PMF

Rebeca García Fandiño wrote: Hello, I am trying to calculate the binding energy between two monomers in three different dimers, using PMF (Umbrella Sampling method) and following Justin's tutorial. Using 100 windows separated 0.05 nm I get the PMFs represented in "pmf_using_100_points.pdf" (

RE: [gmx-users] number of windows in PMF

Thanks a lot for your answer. My system have about 29000 atoms, and the simulation time was 1ns. I have generated the error bars, and indeed you were right, they are too big. The histograms looked good, so I thought they should be well-converged...:S What should I do, extending the simulation

Re: [gmx-users] number of windows in PMF

Rebeca García Fandiño wrote: Thanks a lot for your answer. My system have about 29000 atoms, and the simulation time was 1ns. I have generated the error bars, and indeed you were right, they are too big. The histograms looked good, so I thought they should be well-converged...:S What should

Re: [gmx-users] number of windows in PMF

Justin A. Lemkul wrote: Rebeca García Fandiño wrote: Thanks a lot for your answer. My system have about 29000 atoms, and the simulation time was 1ns. I have generated the error bars, and indeed you were right, they are too big. The histograms looked good, so I thought they should be well-c

RE: [gmx-users] number of windows in PMF

Thanks again for your quick answer! No, I did not prior equilibration, however for the analysis I was considering only the last 0.5 ns. I will try to extend the simulations and see what happens. Is it possible to do it using tpbconv as in a typical simulation? Should I create different files f

Re: [gmx-users] number of windows in PMF

Rebeca García Fandiño wrote: Thanks again for your quick answer! No, I did not prior equilibration, however for the analysis I was considering only the last 0.5 ns. I will try to extend the simulations and see what happens. Is it possible to do it using tpbconv as in a typical simulation? Sho

[gmx-users] residence time calculation

Hi , I am planning to calculate the residence time of a counter-ion near the charged head group of surfactant. I was wondering whether some one can suggest how one can calculate residence time in gromacs? Thanks Sanku-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

Re: [gmx-users] residence time calculation

Sanku M wrote: Hi , I am planning to calculate the residence time of a counter-ion near the charged head group of surfactant. I was wondering whether some one can suggest how one can calculate residence time in gromacs? A similar topic was just discussed a few hours ago. Please check t

Re: [gmx-users] Gromacs on IBM clusters

On 13/07/2011 2:21 AM, Justin A. Lemkul wrote: Kavyashree M wrote: Dear users, I was trying to run gromacs-4.5.3 in IBMcluster using mpich-1.2.7 rather than openmpi. But I was getting some error. Sorry I donot remember the error. But Is it possible to run gromacs-4.5.3 using mpich implementat

Re: [gmx-users] residence time calculation

Hi, I looked into the mailing list and I found that there is a method where one uses g_hbond -contact -ac option to calculate the autocorrelation function of a contact pair and then integrate the autocorrelation function to get the correlation time. I guess the correlation time is the residenc