[gmx-users] Mmxcheck Messages and Timesteps

2007-09-19 Thread Shay Amram
Hello Gromacs users, I ran gmxcheck on a trr file I got from running energy minimization, Gmxcheck's output is: - Checking file 4PLMYWOrg01_em_tim.trr trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 # Atoms 55986 Reading f

Re: [gmx-users] Mmxcheck Messages and Timesteps

2007-09-19 Thread David van der Spoel
Shay Amram wrote: Hello Gromacs users, I ran gmxcheck on a trr file I got from running energy minimization, Gmxcheck’s output is: - */ Checking file 4PLMYWOrg01_em_tim.trr /* */ trn version: GMX_trn_file (single precision) /* */ Reading /* */ frame

RE: [gmx-users] RE: Neutralising charge distribution

2007-09-19 Thread Georgios Patargias
Hi Jeroen Thank you for your reply. I just wanted to know whether the correction term for the 'uniform background charge' is included in the code; I didn't meant to to take it out. Another thing is about the dipole correction that is applied for conducting boundary conditions. Is it switched

RE: [gmx-users] Mmxcheck Messages and Timesteps

2007-09-19 Thread Shay Amram
I thought as much but wanted to make sure. Thank you for your quick reply. -Shay -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Wednesday, September 19, 2007 11:38 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Mm

Re: [gmx-users] RE: Neutralising charge distribution

2007-09-19 Thread David van der Spoel
Georgios Patargias wrote: Hi Jeroen Thank you for your reply. I just wanted to know whether the correction term for the 'uniform background charge' is included in the code; I didn't meant to to take it out. Another thing is about the dipole correction that is applied for conducting boundar

[gmx-users] RE: Neutralising charge distribution

2007-09-19 Thread van Bemmelen
Hi George, Sorry, I got a bit carried away. Actually, I once thought of somehow taking it out myself, so probably that's why. ;-) About the dipole correction: I haven't experimented with it myself, but I'm pretty sure it's switched off when epsilon_surface is 0. That's also what the manual says (

RE: [gmx-users] RE: Neutralising charge distribution

2007-09-19 Thread Georgios Patargias
Hi Jeroen Thanks once again for your reply. Best wishes George -Original Message- From: [EMAIL PROTECTED] on behalf of van Bemmelen Sent: Wed 9/19/2007 11:16 AM To: gmx-users@gromacs.org Subject: [gmx-users] RE: Neutralising charge distribution Hi George, Sorry, I got a bit carried

Re: [gmx-users] topology of Alpha d-mannopyranosyl (1-6) alpha d-mannopyranose

2007-09-19 Thread Mark Abraham
parichita parichita wrote: Thaks for your suggesion... I want to use Gromacs for MD on my disaccharides in explicit water box.Now, the problem I encounter is that the pdb2gmx produces the topologies where hydrogens sitting on carbons are condensed on carbon atoms they sit on. I need them expl

Re: [gmx-users] topology of Alpha d-mannopyranosyl (1-6) alpha d-mannopyranose

2007-09-19 Thread parichita parichita
Thaks for your suggesion... I want to use Gromacs for MD on my disaccharides in explicit water box.Now, the problem I encounter is that the pdb2gmx produces the topologies where hydrogens sitting on carbons are condensed on carbon atoms they sit on. I need them explicitly since I would like

[gmx-users] MD simulation of Alpha d-mannopyranosyl (1-6) alpha d-mannopyranose

2007-09-19 Thread parichita parichita
Hi Somer, I want to simulate my Alpha d-mannopyranosyl (1-6) alpha d-mannopyranose explicitly using my NOE restrain. I am new to MD using GROMACS . Please,give some thought . Thanks in advance parichita Parichita Mazumder Junior Research Fello

[gmx-users] RE: Neutralising charge distribution

2007-09-19 Thread van Bemmelen
Actually, I'd say they're not incorrect, but incomplete (well, for many systems). There's no mention of the correction terms George was asking about, only the self correction term is taken into account in those equations. But they're in the code allright, and a lot can be induced from the mdp param

[gmx-users] POPC simulation

2007-09-19 Thread Moutusi Manna
thanks for reply.I want to perform simulation of popc membrane. Steps which i have done are as follows: 1. download popc128a.pdb, popc.it,lipids.itp (http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies) 2. download ffgmx_lipids files 3.convert POPC of .top & popc.itp i

Re: [gmx-users] POPC simulation

2007-09-19 Thread Justin A. Lemkul
Quoting Moutusi Manna <[EMAIL PROTECTED]>: > thanks for reply.I want to perform simulation of popc membrane. > Steps which i have done are as follows: > 1. download popc128a.pdb, popc.it,lipids.itp > (http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies) > 2. download ff

Re: Re: [gmx-users] Atomic distances problems using gmxcheck

2007-09-19 Thread yudaqi
Hello David: Yes, you are right. the value equals to the square of the distance, approximately. In fact, the force field I used was GROMOS96 43a1 force field. I have also tried the other kind of force fields, such as OPLS-AA/L all-atom force field, the same warning was reported, but the "sh

[gmx-users] Re: Atomic distances problems using gmxcheck (David van der Spoel)

2007-09-19 Thread yudaqi
Hello, David I have download the CVS version 3.3.2. it works well. Thank you very much for your hard work in gromacs. YuDaqi 在 2007-09-19三的 11:45 [EMAIL PROTECTED] > Re: Atomic distances problems using gmxcheck (David van der Spoel) ___

[gmx-users] "Impulsive" motion resulting from AFM pulling

2007-09-19 Thread Robert Johnson
Hello everyone, Eventually I want to pull a carbon nanotube through water at a constant rate. Before I get to this, I'm pulling a nanotube in vacuum just to make sure I'm using the pull code correctly. My system consists of a carbon nanotube aligned along the z axis and a single dummy atom fixed o

[gmx-users] VDW Default and PME question

2007-09-19 Thread Jason O'Young
Hi All, Does anyone know what the default vdw type if none is specified? Is the value in brackets in the manual the default? If so, there is none listed for VWD type. Additionally, if PME is selected as the coulombtype, do the cutoffs matter? I am a bit confused in this regard. Thanks i

[gmx-users] AFM Pulling and com motion

2007-09-19 Thread Zhou Bo
Hi GXM Users, I'm trying to execute some AFM Pulling. I followed the pull code tutorial from GMX WORKSHOP 2007, and I found there is no specific to com motion in mdp, so the default is "comm-mode=Linear" and "comm-grps=System". I was confused about it as I believed we should not stopcm when