[gmx-users] Re:isotropic force constant

Thank you for your advice,I have find define=-DPOSRE in my pr.mdp file, but I don't know which parameter indicate isotropic force constant of 100kjmol-1A-1. Though I use ref_t=300 for my simulation. > > > Dear users: > > > I have a position restrain .mdp file need to set,I use 300K > >

RE: [gmx-users] Restarting a gromacs calcluation

>> Dear Users, >> >> Thank for your help. I started a 10 ns simulation, but it dies because of >> an error in the cluster PBS system, so I want to continue the simulation >> from the last (r,v) point. May I still use tpbconv to restart from that >> last point and continue the simulation. >> Che

[gmx-users] POPC membrane simulation (popc.itp)

Hi all: I ´m working on membrane peptides simulation under lipid (POPC, from Peter Tieleman group site) and i want to do a popc.itp file using ffG53a5 force field. Some days ago i was working with dppc membranes and i took one lipid and run it through pdb2gmx, using my favourite force field and

Re: [gmx-users] problem regarding "mdrun" and "g_hbond"

Hi David, Of course, it's not a dogma... But in your case, it will be well thought over. That makes the difference. (From another point of view, if the simulation system is small, often you'll still want temperature coupling anyway...). Anyway, as with all gromacs warnings, they should just make

Re: Re: [gmx-users] Appropriate tool to get the number of solvent molecules within a cutoff distance around protein molecule

Thank you very much for your attention! Best regards, Ozge Engin -Original Message- From: Yang Ye <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Date: Sun, 18 Mar 2007 00:35:13 +0800 Subject: Re: [gmx-users] Appropriate tool to get the number of solvent molecules within a cu

Re: [gmx-users] Fatal error when using Hbond restraints

Robert Johnson wrote: Hello everyone, I'm performing a simulation that includes a 2D infinite SiO2 substrate. I'm not interested in the high frequency motion of the substrate bonds, so I'm applying position restraints to all the SiO2 atoms. I have other molecules in the system such as water and D

Re: [gmx-users] Fatal error when using Hbond restraints

Robert Johnson wrote: Hello everyone, I'm performing a simulation that includes a 2D infinite SiO2 substrate. I'm not interested in the high frequency motion of the substrate bonds, so I'm applying position restraints to all the SiO2 atoms. I have other molecules in the system such as water and D

[gmx-users] Fatal error when using Hbond restraints

Hello everyone, I'm performing a simulation that includes a 2D infinite SiO2 substrate. I'm not interested in the high frequency motion of the substrate bonds, so I'm applying position restraints to all the SiO2 atoms. I have other molecules in the system such as water and DNA that require hydroge

Re: [gmx-users] Adding a new force field to Gromacs

Yang Ye wrote: Actually it is about to add a new form of potential energy function. A quick but dirty method is to user User Table for NB interaction. Check it from the manual. Regards, Yang Ye Tandia, Adama wrote: Dear ALL: Is it documented somewhere how can one add a new non-bonded force

Re: [gmx-users] Appropriate tool to get the number of solvent molecules within a cutoff distance around protein molecule

try g_trjorder. Some code modification may be needed. Regards, Yang Ye OZGE ENGIN wrote: Hi, I want to calculate the number of solvent molecules within a cutoff distance around the protein molecule. I could not find the appropriate command for this in manual. Moreover, I could not understand t

Re: [gmx-users] oplsaa with tip4p

Create the top for the protein alone. Then insert #include and add new entries under [ molecules ] section Regards, Yang Ye Christian Seifert wrote: Hi. I want to use the ff oplsaa with tip4p water (as suggested in the manual). Using: genbox_d -cp hpo4_box.pdb -o hpo4_water.pdb -cs tip4p.gr

Re: [gmx-users] Restarting a gromacs calcluation

Milan Melichercik wrote: Dňa Pi 16. Marec 2007 14:19 Triguero, Luciano O napísal: Dear Users, Thank for your help. I started a 10 ns simulation, but it dies because of an error in the cluster PBS system, so I want to continue the simulation from the last (r,v) point. May I still use tpbconv

Re: [gmx-users] Adding a new force field to Gromacs

Actually it is about to add a new form of potential energy function. A quick but dirty method is to user User Table for NB interaction. Check it from the manual. Regards, Yang Ye Tandia, Adama wrote: Dear ALL: Is it documented somewhere how can one add a new non-bonded force field into Groma

Re: [gmx-users] backup files

Thank you, but only for the record, in my system I have to type cp \#conf.gro# good.gro (Note the " \ ") Regards. Pedro. 2007/3/17, Mark Abraham <[EMAIL PROTECTED]>: > Thanks for you reply but, I'm afraid it doesn't work with me! > > In fact, if I write "more \#conf.gro#" I can read from t

Re: [gmx-users] Appropriate tool to get the number of solvent molecules within a cutoff distance around protein molecule

Hi. g_hbond can do that, sort of. You can calculate e.g. the nr of water oxygens within a certain distance from the protein. The limitation lies in that g_hbond operates at a atom basis, not molecule, meaning that there is strictly no way of finding the number of solvent molecules directly.

Re: [gmx-users] freezing/position restraints and minimization

Jeroen van Bemmelen wrote: Hmm, interesting... And what about the -DFLEXIBLE definition in your mdp file during steepest descent minimization? Do you know if that will also deform your (SPC) water molecules? And will that deformation be corrected again during the first equilibration step(s)?

Re: [gmx-users] Gromacs 3.3.1 vs SegFault

Stas Bobritsky wrote: Hi all. I`m trying to make short MD simulation in tRNA+water+ions(Na+) system. But mdrun fails with Segmentaiont Fault. I can`t fix it, please help, if it`s possible. Gromacs version: 3.3.1 Forcefield: ffamber99p. most likely a bad starting structure. try to minimize with

回复： [gmx-users] about PMF calculation

try mdrun_d and g_wham: Can you tell me how to produce pdo file? thank you very much! 黄永棋 <[EMAIL PROTECTED]> 写道： Hi gmx-users I am a gromacs beginner, I want to do the PMF calculation ,I have done as the manual said ,I added the ppa, ndx files and got a pdo file . But I don't know

Re: [gmx-users] freezing/position restraints and minimization

Hmm, interesting... And what about the -DFLEXIBLE definition in your mdp file during steepest descent minimization? Do you know if that will also deform your (SPC) water molecules? And will that deformation be corrected again during the first equilibration step(s)? I ask this, because I read o

[gmx-users] about PMF calculation

Hi gmx-users I am a gromacs beginner, I want to do the PMF calculation ,I have done as the manual said ,I added the ppa, ndx files and got a pdo file . But I don't know what to do with this pdo file. Can anyone tell me what should I do if I want to calculate the PMF? Thanks in advance. Yong

[gmx-users] Gromacs 3.3.1 vs SegFault

Hi all. I`m trying to make short MD simulation in tRNA+water+ions(Na+) system. But mdrun fails with Segmentaiont Fault. I can`t fix it, please help, if it`s possible. Gromacs version: 3.3.1 Forcefield: ffamber99p. Stas Bobritsky, student. ___ gmx-users

[gmx-users] Appropriate tool to get the number of solvent molecules within a cutoff distance around protein molecule

Hi, I want to calculate the number of solvent molecules within a cutoff distance around the protein molecule. I could not find the appropriate command for this in manual. Moreover, I could not understand the information for g_sorient.Could you give me a more detailed explanation for this? Than