[gmx-users] domain decomposition error

2009-10-11 Thread nikhil damle
Hi, I am trying to run a vacuum simulation of a system associated with ATP and peptide. Being vacuum MD i removed pressure coupling and included plain electrostatic cut-offs while calculating potential. Energy minimisation converged to machine precesion even though not upto the specified cut-of

Re: [gmx-users] domain decomposition error

2009-10-11 Thread Justin A. Lemkul
nikhil damle wrote: Hi, I am trying to run a vacuum simulation of a system associated with ATP and peptide. Being vacuum MD i removed pressure coupling and included plain electrostatic cut-offs while calculating potential. Energy minimisation converged to machine precesion even though not u

Re: [gmx-users] domain decomposition error

2009-10-11 Thread nikhil damle
Hi, It is a vacuum simulation. That's why a molecule can be considered in isolation and i do not need to use periodic box. Secondly, even when i try to run the process on 2 nodes it gives same error. So number of processors might not be the actual reason. Regards, Nikhil __

Re: [gmx-users] domain decomposition error

2009-10-11 Thread Justin A. Lemkul
nikhil damle wrote: Hi, It is a vacuum simulation. That's why a molecule can be considered in isolation and i do not need to use periodic box. Secondly, even when i try to run the process on 2 nodes it gives same error. So number of processors might not be the actual reason. I still dis

[gmx-users] pH studies

2009-10-11 Thread parthiban
Hi can any one could help me in, How to include the pH for doing MD studies. My interest is to include the pH at the initial time duration and to change the pH from 4 to 7 during the course of simulation. is there any possibility in performing such work in gromacs. Thanks in advance Parthiban _

Re: [gmx-users] pH studies

2009-10-11 Thread Justin A. Lemkul
parthi...@ncbs.res.in wrote: Hi can any one could help me in, How to include the pH for doing MD studies. My interest is to include the pH at the initial time duration and to change the pH from 4 to 7 during the course of simulation. is there any possibility in performing such work in gromacs

Re: [gmx-users] velacc & box of water

2009-10-11 Thread Jamie Seyed
Thanks to Justin & Mark for answering my second question... Could any one give me a hint on my first question that I copy it again? --about g_velacc and calculating the diffusion constant from that. In mailing list people say that we need to divide it by mass squared and 1/3. Then I found another r

Re: [gmx-users] velacc & box of water

2009-10-11 Thread Jamie Seyed
Dear Gmx users, Does any one know why genbox stops when I use this command: "genbox -cp resize.gro -cs spc216.gro -o b4em.pdb -p topol.top" or when I use this command: "genbox -cs spc216.gro -box 1 1 1 -maxsol 500 -o out.gro -p topol.top" It goes until Reading solvent configuration Solvent configur

Re: [gmx-users] velacc & box of water

2009-10-11 Thread Justin A. Lemkul
Jamie Seyed wrote: Dear Gmx users, Does any one know why genbox stops when I use this command: "genbox -cp resize.gro -cs spc216.gro -o b4em.pdb -p topol.top" or when I use this command: "genbox -cs spc216.gro -box 1 1 1 -maxsol 500 -o out.gro -p topol.top" It goes until Reading solvent configu

Re: [gmx-users] velacc & box of water

2009-10-11 Thread Jamie Seyed
Hi Justin, yes resize.gro is a created file from editconf which has box size of 5.05918 on the last line my command was "editconf -bt cubic -f spc216.pdb -o resize.gro -d 1" and for second command I changed 1 to 5 but it still stops in the same point. I am trying to examine 2 methods that you & Ma

Re: [gmx-users] velacc & box of water

2009-10-11 Thread Justin A. Lemkul
Jamie Seyed wrote: Hi Justin, yes resize.gro is a created file from editconf which has box size of 5.05918 on the last line my command was "editconf -bt cubic -f spc216.pdb -o resize.gro -d 1" Do you actually have separate spc216.pdb and spc216.gro files? Just trying to make sure this ac

Re: [gmx-users] velacc & box of water

2009-10-11 Thread Jamie Seyed
I converted spc216.pdb to gro using editconf. SO they must be the same(?). The version is 4.0.5 ...it was fine before... yes ran it just now for fws tuto... how long it takes time in your machine? On Sun, Oct 11, 2009 at 1:33 PM, Justin A. Lemkul wrote: > > > Jamie Seyed wrote: > >> Hi Justin,

Re: [gmx-users] velacc & box of water

2009-10-11 Thread Justin A. Lemkul
Jamie Seyed wrote: I converted spc216.pdb to gro using editconf. SO they must be the I suppose that's fine, I just don't see all the need for interconverting file formats. It just opens up the possibility of more errors if you don't keep track of what you're doing :) same(?). The versio

Re: [gmx-users] velacc & box of water

2009-10-11 Thread Jamie Seyed
Oh, I just changed the [-cs spc216.gro] to [-cp spc216.gro] and this is working normally...??!! Do you have any idea? On Sun, Oct 11, 2009 at 1:52 PM, Justin A. Lemkul wrote: > > > Jamie Seyed wrote: > >> I converted spc216.pdb to gro using editconf. SO they must be the >> > > I suppose that's

Re: [gmx-users] velacc & box of water

2009-10-11 Thread Justin A. Lemkul
Jamie Seyed wrote: Oh, I just changed the [-cs spc216.gro] to [-cp spc216.gro] and this is working normally...??!! Do you have any idea? Oops, I hadn't seen that before. That is what you should do. The -cp flag is the coordinate file that should have solvent added to it, and that's what

Re: [gmx-users] pH studies

2009-10-11 Thread Miguel Machuqueiro
On 11-10-2009 16:48, Justin A. Lemkul wrote: parthi...@ncbs.res.in wrote: Hi can any one could help me in, How to include the pH for doing MD studies. My interest is to include the pH at the initial time duration and to change the pH from 4 to 7 during the course of simulation. is there a

Re: [gmx-users] velacc & box of water

2009-10-11 Thread Justin A. Lemkul
Jamie Seyed wrote: Hi Justin, But this seems that did not change the number of molecule in the output (only the volume and density are changing) and it seems that -maxsol has not been used... my full command "genbox -cp spc216.gro -maxsol 500 -o out.gro -p topol.top -box 4 4 4" if I change 5

[gmx-users] Updated topology generation tool available

2009-10-11 Thread Justin A. Lemkul
Hi All, I have added uploaded a new version of TopolGen, version 1.1, to the Users' Contributions section of the website. This program is written in Perl and is designed to generate a topology for use with the OPLS-AA force field from an all-atom PDB file. Based on input from many users of

[gmx-users] Inserting protein in Bilayer

2009-10-11 Thread sunny mishra
Hi All, I am working on the CG simulations of the proteins and lipid bilayers. I am confused of how to set up the whole system for simulations. I got the DSPC lipid bilayer from martini website and I have 1SU4.pdb file with me. I cleaned the .pdb file and now I want to include the 14 DSPC molecule

Re: [gmx-users] Inserting protein in Bilayer

2009-10-11 Thread Justin A. Lemkul
sunny mishra wrote: Hi All, I am working on the CG simulations of the proteins and lipid bilayers. I am confused of how to set up the whole system for simulations. I got the DSPC lipid bilayer from martini website and I have 1SU4.pdb file with me. I cleaned the .pdb file and now I want to incl

Re: [gmx-users] Inserting protein in Bilayer

2009-10-11 Thread sunny mishra
Hi Justin, Thanks for the quick reply. I am also following the martini tutorial in order to do the CG simulations. Here are the following steps which I am doing. Please have a look at them. 1) Cleaned the 1SU4.pdb file and renamed it to 1SU4_clean.pdb 2) converted 1SU4_clean.pdb to its CG structu

Re: [gmx-users] Inserting protein in Bilayer

2009-10-11 Thread sunny mishra
Hi Justin, I have set up the whole system correctly but now at the final step when I do mdrun it gives me the fatal error by saying that Number of grid cells is zero. Probably the system and box collapsed. Do you have any idea about this? Sunny On Sun, Oct 11, 2009 at 4:45 PM, sunny mishra w

Re: [gmx-users] Inserting protein in Bilayer

2009-10-11 Thread Justin A. Lemkul
sunny mishra wrote: Hi Justin, Thanks for the quick reply. I am also following the martini tutorial in order to do the CG simulations. Here are the following steps which I am doing. Please have a look at them. 1) Cleaned the 1SU4.pdb file and renamed it to 1SU4_clean.pdb 2) converted 1SU4_cle

Re: [gmx-users] Inserting protein in Bilayer

2009-10-11 Thread Justin A. Lemkul
sunny mishra wrote: Hi Justin, I have set up the whole system correctly but now at the final step when I do mdrun it gives me the fatal error by saying that Number of grid cells is zero. Probably the system and box collapsed. Then "correctly" is debatable :) Do you have any idea about thi

[gmx-users] trr file in VMD

2009-10-11 Thread Paymon Pirzadeh
Hello, How can we use the trr file in VMD? I thought since we ask in the mdp file to output the velocities, then in VMD we should be able to see molecules colored based on their velocities through the trajectory options. Am I correct? Payman ___ gmx-use

Re: [gmx-users] trr file in VMD

2009-10-11 Thread Amit Choubey
yes you can do that by opening the gro file and then loading the .trr file . amit On Sun, Oct 11, 2009 at 6:22 PM, Paymon Pirzadeh wrote: > Hello, > How can we use the trr file in VMD? I thought since we ask in the mdp > file to output the velocities, then in VMD we should be able to see > molec

Re: [gmx-users] trr file in VMD

2009-10-11 Thread Paymon Pirzadeh
I did that but, it did not work! I just get a constant color. On Sun, 2009-10-11 at 18:27 -0700, Amit Choubey wrote: > yes you can do that by opening the gro file and then loading the .trr > file . > > amit > > On Sun, Oct 11, 2009 at 6:22 PM, Paymon Pirzadeh > wrote: > Hello, >

Re: [gmx-users] trr file in VMD

2009-10-11 Thread Justin A. Lemkul
Paymon Pirzadeh wrote: I did that but, it did not work! I just get a constant color. Unless the velocity is written to a field that VMD recognizes, I don't think you'll be able to see the velocities colored. For example, VMD can color by B-factor or occupancy, neither of which would be us

Re: [gmx-users] trr file in VMD

2009-10-11 Thread Mark Abraham
Paymon Pirzadeh wrote: I did that but, it did not work! I just get a constant color. At the very least you would need to choose a representation that would colour by velocities. I don't know whether VMD can do that, or read .trr velocities in the first place, however. You might be better serv

[gmx-users] Re:Re: how to calculate the non-bond interaction between solvent and solvent in pure solvent system (Justin A. Lemkul)

2009-10-11 Thread Jinyao Wang
> >Jinyao Wang wrote: >> Hi gmx-users锛? >> >> I want to calculate the non-bond interaction (LJ+Coulomb) between solvent and >> solvent in pure solvent system. After the simulation of my pure solvent >> system, I calculated the interaction between solvent and solvent using the >> rerun option of th

Re: [gmx-users] trr file in VMD

2009-10-11 Thread Mark Abraham
Justin A. Lemkul wrote: Paymon Pirzadeh wrote: I did that but, it did not work! I just get a constant color. Unless the velocity is written to a field that VMD recognizes, I don't think you'll be able to see the velocities colored. For example, VMD can color by B-factor or occupancy, nei

Re: [gmx-users] trr file in VMD

2009-10-11 Thread Paymon Pirzadeh
Well, I would like to have each molecule's velocity magnitude in each frame (like an xtc file), and then watch it in VMD to see how different parts of a system will evolve in terms of their kinetics. Then, I think using the scale in the trajectory option of VMD, we might be able to see sth. no?

Re: [gmx-users] Re:Re: how to calculate the non-bond interaction between solvent and solvent in pure solvent system (Justin A. Lemkul)

2009-10-11 Thread Justin A. Lemkul
Jinyao Wang wrote: Jinyao Wang wrote: Hi gmx-users锛? I want to calculate the non-bond interaction (LJ+Coulomb) between solvent and solvent in pure solvent system. After the simulation of my pure solvent system, I calculated the interaction between solvent and solvent using the rerun option of

Re: [gmx-users] Re:Re: how to calculate the non-bond interaction between solvent and solvent in pure solvent system (Justin A. Lemkul)

2009-10-11 Thread Mark Abraham
Jinyao Wang wrote: >> Jinyao Wang wrote: >>> Hi gmx-users锛? >>> >>> I want to calculate the non-bond interaction (LJ+Coulomb) between solvent >>> and >>> solvent in pure solvent system. After the simulation of my pure solvent >>> system, I calculated the interaction between solvent and solvent usi

Re: [gmx-users] trr file in VMD

2009-10-11 Thread Justin A. Lemkul
Paymon Pirzadeh wrote: Well, I would like to have each molecule's velocity magnitude in each frame (like an xtc file), and then watch it in VMD to see how different parts of a system will evolve in terms of their kinetics. Then, I think using the scale in the trajectory option of VMD, we might

[gmx-users] Re:Re: how to calculate the non-bond interaction between solvent and solvent in pure solvent system (XAvier Periole)

2009-10-11 Thread Jinyao Wang
>From: XAvier Periole >Subject: Re: [gmx-users] how to calculate the non-bond interaction > between solvent and solvent in pure solvent system >To: Discussion list for GROMACS users >Message-ID: >Content-Type: text/plain; charset=GB2312; format=flowed; delsp=yes > >> I want to cal

Re: [gmx-users] Re:Re: how to calculate the non-bond interaction between solvent and solvent in pure solvent system (XAvier Periole)

2009-10-11 Thread Mark Abraham
Jinyao Wang wrote: > >> From: XAvier Periole >> Subject: Re: [gmx-users] how to calculate the non-bond interaction >> between solvent and solvent in pure solvent system >> To: Discussion list for GROMACS users >> Message-ID: >> Content-Type: text/plain; charset=GB2312; format=flowed;

Re: [gmx-users] Re:Re: how to calculate the non-bond interaction between solvent and solvent in pure solvent system (XAvier Periole)

2009-10-11 Thread Justin A. Lemkul
Jinyao Wang wrote: From: XAvier Periole Subject: Re: [gmx-users] how to calculate the non-bond interaction between solvent and solvent in pure solvent system To: Discussion list for GROMACS users Message-ID: Content-Type: text/plain; charset=GB2312; format=flowed; delsp=yes I want t

Re: Re: [gmx-users] Re:Re: how to calculate the non-bond interaction between solvent and solvent in pure solvent system (Justin A. Lemkul)

2009-10-11 Thread Jinyao Wang
>> Hi Justin, Thank you for your reply. But I still don't know how to set the >> "energygrps" option in the rerun.mdp for calculating the interaction between >> solvent molecule and solvent molecule in pure solvent system. As you said >> that these terms should be obtained running the g_energy,coul

Re: [gmx-users] Re:Re: how to calculate the non-bond interaction between solvent and solvent in pure solvent system (Justin A. Lemkul)

2009-10-11 Thread Justin A. Lemkul
Jinyao Wang wrote: Hi Justin, Thank you for your reply. But I still don't know how to set the "energygrps" option in the rerun.mdp for calculating the interaction between solvent molecule and solvent molecule in pure solvent system. As you said that these terms should be obtained running the g_

Re: [gmx-users] Re:Re: how to calculate the non-bond interaction between solvent and solvent in pure solvent system (Justin A. Lemkul)

2009-10-11 Thread Mark Abraham
Jinyao Wang wrote: >>> Hi Justin, Thank you for your reply. But I still don't know how to set the >>> "energygrps" option in the rerun.mdp for calculating the interaction between >>> solvent molecule and solvent molecule in pure solvent system. As you said >>> that these terms should be obtained ru

[gmx-users] Pressure problem: pressure is too large during MD simulation

2009-10-11 Thread Pan Wu
Hi gmx users,I am now simulating one protein with solvent, in all atom forcefield, gromacs official distributed version. The pressure of system seems to be unreasonable large, and during the whole process, the box keeps increasing. Here is how I set up the system, 1. I solvate the prote

RE: [gmx-users] Pressure problem: pressure is too large during MDsimulation

2009-10-11 Thread Dallas B. Warren
Plot the fluctuations of the pressure with time for the simulation. Far better way I think to get an idea of what is going on with a property than just looking at values in a log file. Especially when you are starting out. With pressure coupling, it is not unusual to have a fluctuation of a h