Re: [gmx-users] Shift Electrostatic Summation

Shuangxing Dai wrote: Hi, all, I was wondering to modify Shift electrostatic summation to a new one. The origin Shift form in Gromacs is like 1/r-1/Rc (Rc is cut-off), I need to modify to erfc(alpha*r)/r-erfc(alpha*Rc)/Rc, and the original long-range correction of Shift in code shift_util.

Re: [gmx-users] Shift Electrostatic Summation

Shuangxing Dai wrote: Hi, all, I was wondering to modify Shift electrostatic summation to a new one. The origin Shift form in Gromacs is like 1/r-1/Rc (Rc is cut-off), I need to modify to erfc(alpha*r)/r-erfc(alpha*Rc)/Rc, and the original long-range correction of Shift in code shift_util.

Re: [gmx-users] problem in energy minimisation during inflategro process.

Hi, In addition to Mark's comments: > ; Include chain topologies > #include "rr1_A.itp" > #include "rr1_B.itp" > > ; Include position restrain protein > #ifdef POSRES_PROTEIN > #include "rr1_A_pr.itp" > #include "rr1_B_pr.itp" > #endif > This is rubbish. Position restraints are defined as part o

[gmx-users] Shift Electrostatic Summation

Hi, all, I was wondering to modify Shift electrostatic summation to a new one. The origin Shift form in Gromacs is like 1/r-1/Rc (Rc is cut-off), I need to modify to erfc(alpha*r)/r-erfc(alpha*Rc)/Rc, and the original long-range correction of Shift in code shift_util.c is q^2/(2*Rc) ( someth

Re: [gmx-users] problem in energy minimisation during inflategro process.

nitu sharma wrote: Dear Justin but even after doing this when i I have tried to do second step of inflategro i.e energy minimisation step I got the error like this-- Fatal error: number of coordinates in coordinate file (inflated_dmpc.pdb, 13253) does not match topology (infl

Re: [gmx-users] intermolecular distance restraint

warren deng wrote: Hi Gromacs users, In my simulation, I need to restrain distances between atoms on two protein molecules. But the Gromacs manual on NOE seems to imply that the atom indices belong to the same molecule type. So I am wondering whether it is possible to create distance restrai

[gmx-users] problem in energy minimisation during inflategro process.

Dear Justin I am doing inflategro process for scaling and packing of lipid around my protein . the first step is successfully completed ,there is 9 lipid removed a/c to that I have updated my topology file --- ; Include forcefield parameters #include "ffG53a6_lipid.itp"

[gmx-users] intermolecular distance restraint

Hi Gromacs users, In my simulation, I need to restrain distances between atoms on two protein molecules. But the Gromacs manual on NOE seems to imply that the atom indices belong to the same molecule type. So I am wondering whether it is possible to create distance restraint between two molecule

RE: [gmx-users] localp

I think the local pressure can only be calculated with a modified unsupported version of gromacs that you can download. However, this was only done with gromacs version 3.0 not even 3.3 -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Be

Re: [gmx-users] Generate topology for infinite alpha helix with pbc?

Zhiping Xu wrote: > Hi all: > I have a basic question here. I want to simulate a infinite alpha-helix > protein, say alanine represented using a unit cell containning 11 residues. > Now I want to simulate it in GROMACS but don't know how to generate TOP > for the structure, i.e. the connectivity

[gmx-users] Generate topology for infinite alpha helix with pbc?

Hi all: I have a basic question here. I want to simulate a infinite alpha-helix protein, say alanine represented using a unit cell containning 11 residues. Now I want to simulate it in GROMACS but don't know how to generate TOP for the structure, i.e. the connectivity between the 1st residue and

Re: [gmx-users] Pressure Coupling Problem

I don't know the conditions you use with your system, but sometimes there are problems when you use pressure coupling in a system with positionally restrained or fixed atoms. Cheers. Lucio. From: Joe Joe Sent: Friday, April 10, 2009 12:12 PM To: Discussion list for GROMACS users Subject:

Re: [gmx-users] shell molecular dynamics

Shuangxing Dai wrote: Thank you for help. The harmonic potential between core and shell is attractive. The charges they have are opposite, this means that there will only be attractive force between them. My result also show that they nearly overlap. Is this reasonable and shell model correctly

Re: [gmx-users] shell molecular dynamics

Thank you for help. The harmonic potential between core and shell is attractive. The charges they have are opposite, this means that there will only be attractive force between them. My result also show that they nearly overlap. Is this reasonable and shell model correctly used? If not, where is

Re: [gmx-users] NAN at high temperatures and high pressures

Popov Konstantin wrote: Hello, I run simulations with polyethylene molecules with harmonic potential for C-H bonds and Morse potential for C-C bonds. The system consists of 1000 carbon atoms and 2002 hydrogen atoms. The simulation runs with PBC at constant density (~0.8 g cm-3) and no press

Re: [gmx-users] NAN at high temperatures and high pressures

Popov Konstantin wrote: Hello, I run simulations with polyethylene molecules with harmonic potential for C-H bonds and Morse potential for C-C bonds. The system consists of 1000 carbon atoms and 2002 hydrogen atoms. The simulation runs with PBC at constant density (~0.8 g cm-3) and no pressur

[gmx-users] NAN at high temperatures and high pressures

Hello, I run simulations with polyethylene molecules with harmonic potential for C-H bonds and Morse potential for C-C bonds. The system consists of 1000 carbon atoms and 2002 hydrogen atoms. The simulation runs with PBC at constant density (~0.8 g cm-3) and no pressure coupling. At the tempera

[gmx-users] restart problem

Hi, I've installed version 4.0.4 and tried again but still have the same problem in restarting my simulation with a checkpoint file. I'm uisng 4 cpus in 1 node and double precision options: mpirun -np 4 mdrun_d -cpi state.cpt -append yes -cpt 30 The error message is: "Program mdrun_d,

Re: [gmx-users] trajectory file not moving in vmd

Halie Shah wrote: Hi! I'm am trying to visualize the energy minimization trajectory path of my protein+ligand in VMD. I imported the .trr file into the ending energy minimized pdb file, and I was able to see the frames of the trr (53 all together with nstxout=1). But when I ran the traject

Re: [gmx-users] mdrun_mpi error Signal: Segmentation fault

nam kim wrote: process crashes around 100 steps out of 1000 requested. Fine, but you still haven't answered my question. Do you receive any other messages? Do other systems run on the specific hardware you're using? You may just have some instability in this particular system that is c

[gmx-users] trajectory file not moving in vmd

Hi! I'm am trying to visualize the energy minimization trajectory path of my protein+ligand in VMD. I imported the .trr file into the ending energy minimized pdb file, and I was able to see the frames of the trr (53 all together with nstxout=1). But when I ran the trajectory I saw barely any chang

Re: [gmx-users] shell molecular dynamics

Shuangxing Dai wrote: Hi, all, I am doing shell molecular dynamics and I have read the sw.itp. Now my question is: 1. For the shell "atom", what element should be used in .pdb file, since the 77-78th digits of pdb file is element symbol ? Anything you like. Gromacs does not use this informa

[gmx-users] shell molecular dynamics

Hi, all, I am doing shell molecular dynamics and I have read the sw.itp. Now my question is: 1. For the shell "atom", what element should be used in .pdb file, since the 77-78th digits of pdb file is element symbol ? 2. What does the 1 in [ polarization ] part mean in sw.itp? 3. Is it reasonab

Re: [gmx-users] mdrun_mpi error Signal: Segmentation fault

process crashes around 100 steps out of 1000 requested. On Fri, Apr 10, 2009 at 4:32 PM, Justin A. Lemkul wrote: > > > nam kim wrote: >> >> I have segmentation fault error while running mdrun_mpi( gromacs 4.0.4). >> I have installed gromacs 4.0.4 two month ago and been working fine. >> Today, I j

Re: [gmx-users] About a restart problem

kyungchan chae wrote: Hello, I have a problem in using checkpoint file (Gromacs 4) to restart my simulation When I restart my parallel simulation by using 'append' option : mdrun -cpi state.cpt -append yes -cpt 30 the following error messages showed up: "Program mdrun, VERSION 4.0.99_d

[gmx-users] About a restart problem

Hello, I have a problem in using checkpoint file (Gromacs 4) to restart my simulation When I restart my parallel simulation by using 'append' option : mdrun -cpi state.cpt -append yes -cpt 30 the following error messages showed up: "Program mdrun, VERSION 4.0.99_development_20090120

Re: [gmx-users] Regarding RMSF !

Venkat Reddy wrote: Hai Everyone ! I hav a small doubt regarding RMSF . How can we calculate rmsf for helices and sheets only in a protein (excluding loops )??? By using the tool designed for the task with an index file designed for the task :-) g_rmsf -n helices_and_sheets.ndx Mark _

[gmx-users] Regarding RMSF !

Hai Everyone ! I hav a small doubt regarding RMSF . How can we calculate rmsf for helices and sheets only in a protein (excluding loops )??? Thanks for ur valuable time. -- With Best Wishes Venkat Reddy Chirasani M.Tech Bioinformatics UNIVERSITY OF HYDERABAD __

Re: [gmx-users] Mg ion not recognize.

Hi. Mg is probably in the force field already. You don't need to run it through pdb2gmx. Add it manually after generation of the topology for the protein. #include "ions.itp" in the topology file and add the correct name (check ions.itp) under [ molecules ]. Be sure to have all atoms matching in o

Re: [gmx-users] calculating com-com distances.

Hi Fernando, > I've obtained the vectors for the rectangular box in g_energy, > using Box_XX, Box_YY and Box_ZZ options; I didn't use the vectors of the > skewed box.) You have to use the three vectors from the tricilinic representation to obtain the correct distance in the periodic system. Check