Re: [gmx-users] mdrun -rerun problems

at the same time if this may help somebody in the future. We are still trying to figure out how to solve this problem anyway. Thanks for your time. George Mark Abraham wrote: George Abadir wrote: Hi all, I am running simulations of carbon nanotubes and amino acids in water. I need

Re: [gmx-users] Question about DNA simulation

mgoette2[at]gwdg.de WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/ George Abadir wrote: Hi, Actually I think that although the .atp file seems to be used, the masses in the ffamberxxnb.itp file must be changed from the zero values to the correct ones: when I ran a simulation without

Re: [gmx-users] Question about DNA simulation

Hi, Actually I think that although the .atp file seems to be used, the masses in the ffamberxxnb.itp file must be changed from the zero values to the correct ones: when I ran a simulation without changing them I got infinite velocities and which did nor happen when I changed the masses to

[gmx-users] Angle parameters in Amber port and in Gromacs

Hi, While performing simulations of urea in water using the AMBER port for GROMACS, I noticed that the harmonic angle potential parameters in AMBER99 port (in ffamber99bon.itp) for the angle HNH (hydrogen-nitrogen-hydrogen) are (120,292.88), which are exactly the same parameters used by

[gmx-users] Urea molecule deformed in urea-water simulations using ffamber99

Hi, I am doing a simple simulation of one urea molecule dissolved in water. I am using the ffamber_urea.itp introduced in the AMBER port for GROMACS. I build a box using editconf and solvate the urea molecule using genbox with the fftip3p.itp water model also included with the AMBER port.

[gmx-users] CNT Potassium doping with GROMACS

Hi, I want to make a simulation of CNT in an environment of potassium atoms to see how they will be adsorbed on the CNT surface (this is a way of doping carbon nanotubes). I built a .pdb file with a CNT and some potassium atoms with random coordinates around the nanotube. When I run x2top

Re: [gmx-users] CNT Potassium doping with GROMACS

] C C 00' but still get the same error. Your help is much appreciated, Thank you in advance, George George Abadir wrote: Hi, I want to make a simulation of CNT

[gmx-users] CNT-protein interaction

Hi, I have built a topology file for a protein and a topolgy file for a carbon naontube. I am trying to combine them by solvating the protein in water and inserting the CNT molecule using the -ci option with genbox. However, when I view the resulting file, I can only see the protein in

[gmx-users] Human Serum Albumin problem

Hi, I have downloaded the 1HA2.pdb (describing human serum albumin) file from www.pdb.org and ran pdb2gmx to make a topology file for it. I got an error message Source code file: hizzie.c, line: 267 Fatal error: Incomplete ring in HIS1. I also tried the '-missing' option and '-ignh' option

[gmx-users] Visualization Problem

Hi, I finished a simulation of a carbon nanotube in water. I made a movie of the simulation using 'trjconv' to view with Pymol. The problem is that starting from the third frame it messes the carbon nanotube bonds. I changed the start time and again in the third frames it messed things

Re: [gmx-users] Visualization Problem

the 'pbc whole' option anyway but it didn't work. Thank you very much, Regards, George Itamar Kass wrote: Shalom George Maybe your nanotube 'jump' over the PBC? Try 'trjconv -pbc whole ...' Best, Itamar George Abadir wrote: Hi, I finished a simulation of a carbon nanotube in water. I

[gmx-users] Positive Potential Energy

Hi, I am running a carbon nanotube in water simulation. I set the reaction field dielectric constant (epsilon_rf) to 80 (that of water) and the dielectric constant (epsilon_r) to 1. The energy minimization (which ignores the temperature coupling) runs well and I get a negative potential

[gmx-users] Carbon Nanotube-Protein interaction

Hi, I want to perform a simulation of CNT-protein interaction. I have a topology file for the carbon nanotube alone and a topology file for the protein alone. I don't know how to combine them, and if after them the result can be solvated as usual using genbox. Your help is much

[gmx-users] Initial Temperature

Hi, When I do a Berendsen temperature coupling , I set the reference tepmerature to 300K. However, the log file says the initial temperature is 0K. Why does this happen and how can one control the initial temperature? Thank you very much, Regards, George

Re: [gmx-users] Initial Temperature

Thanks Dallas and Mark for your replies. Best regards, George Mark Abraham wrote: George Abadir wrote: Hi, When I do a Berendsen temperature coupling , I set the reference tepmerature to 300K. However, the log file says the initial temperature is 0K. Why does this happen and how can

[gmx-users] Pressure Coupling

Hi, I want to fix the pressure during the simulation so I use pressure coupling. I set the reference potential to 1 (the unit is bar as the manual says). Nevertheless, the log file shows much higher pressures (can reach the order of 1e+03 and again it seems the unit is bar). Moreover, it

Re: [gmx-users] Pressure Coupling

Thank you very much for the reply, and I'll try to better search the board first :) Cheers, George Dallas B. Warren wrote: Issue like this has been discussed previously, try searching the emailing list for a solution first before posting. Means you get your answer faster :-) Pressure is a

Re: [gmx-users] Segmentation Fault

minimization succeed? Cheers, Tsjerk On 4/24/07, George Abadir [EMAIL PROTECTED] wrote: It says: Starting mdrun 'ICE in water' 30 steps, 45.0 ps Back off! I just backed up final traj.trr to ./#finaltraj.trr.20# Segmentation Fault Thank you, George Mark Abraham wrote: George Abadir wrote: Hi

[gmx-users] Segmentation Fault

Hi, I am doing a simulation of a carbon nanotube in water. I have done the energy minimization successfully and when I passed to the molecular dynamics simulation it terminated with Segmentation Fault. It seems the only way to bypass this is to reduce the time step dt to 0.1 fs which is

Re: [gmx-users] Segmentation Fault

It says: Starting mdrun 'ICE in water' 30 steps, 45.0 ps Back off! I just backed up final traj.trr to ./#finaltraj.trr.20# Segmentation Fault Thank you, George Mark Abraham wrote: George Abadir wrote: Hi, I am doing a simulation of a carbon nanotube in water. I have done

Re: [gmx-users] Energy Minimization problem

minimize the system. Btw...did you define FLEXIBLE for water molecules during your em runs? Best Venky On Apr 18, 2007, at 5:24 PM, George Abadir wrote: Hi, I am doing an energy minimization for a carbon nanotube (end capped with hydrogen atoms) in a box of water. I get the following

[gmx-users] Energy Minimization problem

and energy of course). Is it likely that double precision simulation can make such a big difference? If not (which I think) is there any other way to solve the problem? Thank you very much in advance, George Abadir ___ gmx-users mailing listgmx-users

Re: [gmx-users] Carbon Nanotube Simulations

A finite one. Thanks alot, George Robert Johnson wrote: Do you want to simulate an infinite nanotube or a finite one? Bob On 3/28/07, George Abadir [EMAIL PROTECTED] wrote: There is no C1 and C2 atom in the input PDB file, and the topology file is not generated because x2top doesn't

Re: [gmx-users] Carbon Nanotube Simulations

simply from tubegen and I defined the residue type in the rtp file. Thanks Mark Abraham wrote: George Abadir wrote: Hi, thank you very much for your help. I capped the CNT with hydrogen atoms (i.e., I changed the carbon atoms at the ends of the tube into hydrogen atoms), but now I get

[gmx-users] Carbon Nanotube Simulations

Hi, I added CNT residue in the ffgmx.rtp as follows: [ CNT ] [ atoms ] C C0.00 0 Then I used x2top to

[gmx-users] Generating carbon nanotubes for GROMACS

Hi, I am using Tubegen to generate carbon nanotubes for my simulations. Is there any better method to do this? Thank you very much, George ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] Carbon Nanotube Simulations

Hi, I am using Tubegen to generate a PDB file for carbon nanotubes. When I use the x2top command I get an error :Library file ffG43a1.n2t not found in current dir nor in default directories. The same error is repeated with every other force field. Where can I find this file or how can I