[gmx-users] (no subject)

Your reported errors: >1..while running pdb2gmx > warning :'FE2' not found in residue topology database... What force field are you using in pdb2gmx? look at that .itp file and the files that it includes (.itp file is prefaced by 'ff' and is in share/gromacs/top/ or similar directory) If you

Re: [gmx-users] (no subject)

lalitha selvam wrote: Dear sir, i'm a new user of gromacs.i've done the installation correctly.while simulating my protein i encounter some of the problems.please give me ur suggetions or any reference to overcome this problem.this is my first experience of running the gromacs.kindly

[gmx-users] (no subject)

Dear sir, i'm a new user of gromacs.i've done the installation correctly.while simulating my protein i encounter some of the problems.please give me ur suggetions or any reference to overcome this problem.this is my first experience of running the gromacs.kindly look for my problems a

[gmx-users] Re: Re: angle restraints

David, Thanks for your reply. I am currently using 3.3.1 code. I am increase the force, to be able to calculate the free energy required of introducing the angle restraints in the system. I use small force increments each run, using a delta_lambda of 0. Decreasing or increasing in my view on

Re: [gmx-users] Re: question on pulling 2 groups in afm run

Hello Emily, Thanks a lot for your help. After Spercifying ngroups, mdrun works without error. I should download a new version of manual right now. :-) Linchen Gong >Hi Linchen, > >You may want to try add

[gmx-users] mdrun_mpi stops at random

Hi all, I have an issue doing parallel runs where the simulation would just hang at seemingly random intervals anywhere from an hour to a day. There are no error messages reported in the logs and nothing funny from dmesg. My set up is two dual-core Pentium D. I run with -np 4 to take ad

[gmx-users] Pressure error in MD relating to [FILE nsgrid.c, LINE 218]

Hello, I have been getting the following funky error. "Step 2 Warning: pressure scaling more than 1%, mu: 1.02018 1.02018 1.02018 Step 3 Warning: pressure scaling more than 1%, mu: 8.80037e+07 8.80037e+07 8.80037e+07 Step 4 Warning: pressure scaling more than 1%, mu: 4.6015e+10 4.6015e+10

[gmx-users] New website

Hi all, as some of you have noticed we have upgraded the website to work with Joomla! and have simultaneously chnaged design and layout. Please bear with us while we make the final adjustments. I'll shortly announce some new stuff that we will add, like feedback forms etc. Cheers, -- David.

Re: [gmx-users] position restraints

David Mobley wrote: David, OK, I am running MD using position restraints, and I don't get a separate energy output for "restraint energy" or some such; as far as I can tell the energy of the restraints is grouped in with the total potential energy and never reported separately. I would like it t

Re: [gmx-users] position restraints

David, OK, I am running MD using position restraints, and I don't get a separate energy output for "restraint energy" or some such; as far as I can tell the energy of the restraints is grouped in with the total potential energy and never reported separately. I would like it to be reported separat

Re: [gmx-users] position restraints

David Mobley wrote: Dear all, I'm trying to figure out if there is currently a way to calculate the position restraint energy (for example, if I'm using a posre.itp file to harmonically restrain some atoms) on the fly. Can anyone give me some pointers? I haven't turned up anything useful on thi

[gmx-users] position restraints

Dear all, I'm trying to figure out if there is currently a way to calculate the position restraint energy (for example, if I'm using a posre.itp file to harmonically restrain some atoms) on the fly. Can anyone give me some pointers? I haven't turned up anything useful on this since 2001 on the m

Re: [gmx-users] angle restraints

Maarten, What version of the code are you using? There was a bug in the angle restraints code until 3.3.1 (or 3.3 cvs) which caused angle restraints to turn off gradually as a function of lambda in free energy calculations, if I remember correctly. (See bugzilla for details: http://bugzilla.groma

[gmx-users] do_dssp : ssdump data

Where can I find the exhaustive list of one letter codes used from secondary structures? (H for helix, T for turn...) I looked at do_dssp.c to figure it out . the array map[]... semes to hold the relevant information, but I got very confused. Any help would be appreciated... Senthil ___

[gmx-users] Pressure Coupling for Lipid Bilayers

Hello, Would the following be a reasonable way to implement semiisotropic pressure coupling, for a 128 DMPC membrane: ; Pressure coupling is on Pcoupl = berendsen pcoupltype = semiisotropic tau_p = 1.0 1.0 compressibility = 4.5e-5 1.0e-30 ref_p = 1.0 1.0 [I'm not asking whether this will prod

Re: [gmx-users] afm pulling and comm_mode

Hi again, I pretty much went about the setting up of afm pulling calculations. Still I am a little bit concern about the results. When using gmx3.2.1 and applying a Linear removal of the center of mass (i.e. translation) I see the cell unit still moving during the simulation in a direction tha

Re: [gmx-users] Ngmx

i think since i do not have cell as of now.. i.e with 0.5 0.5 0.5 cell size and also with 1.0 1.0 1.0 cell size , gromacs is not able to generate pbc.On 5/11/06, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: Karam,If you think you know why, please share your thoughts.. that can help us provide an ans

Re: [gmx-users] Ngmx

the problem continues even if i rescale my box to 1.0 1.0 1.0 :(On 5/11/06, karamyog singh <[EMAIL PROTECTED] > wrote:hmm.. i know about the no. of atoms in bcc. please tell me what to do if i want more than 1 unit cell? gromacs is not supporting periodic boundary conditions for my cell and i think

Re: [gmx-users] Ngmx

Karam,If you think you know why, please share your thoughts.. that can help us provide an answer.Still, gromacs supports all periodic boundary conditions, except for real exotic stuff like spherical (and I can think of a few others). But any crystal packing can be handled. Maybe the easiest for you

Re: [gmx-users] Ngmx

hmm.. i know about the no. of atoms in bcc. please tell me what to do if i want more than 1 unit cell?gromacs is not supporting periodic boundary conditions for my cell and i think i know y. On 5/11/06, Mark Abraham <[EMAIL PROTECTED]> wrote: karamyog singh wrote:> Thnx Mark. I stil have a doubt. I

Re: [gmx-users] Ngmx

Hi Karamyog,First build the crystal consisting of the number of atoms you want to include, using the crystal lattice vectors. Than build your unit cell as to contain these. Again use the crystal lattice vectors, but scale them for the size of your crystal unit cell. So, if your crystal is 10x10x10

Re: [gmx-users] Ngmx

karamyog singh wrote: Thnx Mark. I stil have a doubt. If want to simulate a crystal structure,then how should i go about it? wht changes should be made in the above file? even if i replace the 27th atom with 0.5 0.25 0.5, then too it will overlay some other atom. 0.5 == 0 if the size is 0.5.

Re: [gmx-users] Ngmx

Thnx Mark. I stil have a doubt. If want to simulate a crystal structure,then how should i go about it? wht changes should be made in the above file? even if i replace the 27th atom with 0.5 0.25 0.5, then too it will overlay some other atom. I understand wht the fault with my conf.gro file is, but

Re: [gmx-users] Ngmx

karamyog singh wrote: Respected gentlemen, I have written another code for simulating atomic oxygen. the code is running fine. however when i view my run using ngmx, the entire box doesn't get filled up.It just shows one plane of atoms. I have a box of 27 atoms but ngmx shows only 9. Can any1 t

[gmx-users] Ngmx

Respected gentlemen, I have written another code for simulating atomic oxygen. the code is running fine. however when i view my run using ngmx, the entire box doesn't get filled up.It just shows one plane of atoms. I have a box of 27 atoms but ngmx shows only 9. Can any1 tell me why and the solutio

Re: [gmx-users] Topology question

Anthony Cruz wrote: Hi users: I made a small molecule topology using the PRODRG topology generation server but I want to use it with the G43a1 GROMOS96 43a1 Forcefield. How I could change the parameters from GROMACS to GROMOS??? thanks Anthony __

[gmx-users] Topology question

Hi users: I made a small molecule topology using the PRODRG topology generation server but I want to use it with the G43a1 GROMOS96 43a1 Forcefield. How I could change the parameters from GROMACS to GROMOS??? thanks Anthony ___ gmx-users mailing

[gmx-users] Re: question on pulling 2 groups in afm run

Hi Linchen, You may want to try adding the line "ngroups=2" to the pull.ppa, right under "runtype = afm". It's in the new manual (version 3.3, section 6.2.3). Otherwise, I believe the number of groups defaults to 1, and that's why mdrun gets confused about finding a group_2, afm_rate2, et

[gmx-users] angle restraints

Dear users, I have a small system with a number of small peptides. I want to constraint the angle between the N-term to C-term vectors of different peptides. This works well, but if I do a FEP calculation the dG/dl becomes smaller than zero at some point. I expected it to be at least allways grea

Re: [gmx-users] Value for bonded force constant (Kb)

Hi Gmxions, The value Kb = 1673.6 KJ/mol nm2 working good for restraining distance (type6, Harmonic potential) between Fe(II) and corresponding ligating atoms N and O (of amino acids) at the end of 5000 steps of energy minimization. That is newly introduced Kb value is able to restraint at around

Re: [gmx-users] How many ps needs a simulation?

Hi Jahan,You mention your computer restarted. Now that sounds serious. Can you give more details about that? What happens in the log-file before the crash. Was it gromacs or something else that caused it? Are you running windows or *nix? Furthermore, as mentioned before, how long the simulation sho

[gmx-users] question on pulling 2 groups in afm run

Dear gromacs users, I met a problem on pulling 2 groups in a afm pulling run. When mdrun processes input file, error messages such as "unknown left-hand : group_2" appear for group_2, afm_rate2, afm_k2, afm_dir2 and afm_init2. However, pulling one group is OK. My pull.ppa is verbose

RE: [gmx-users] How many ps needs a simulation?

Mark, > rofl... didn't see until now we both had the same response to > this question! Yeah, spun me out a bit too when your repsonse arrived after I had sent mine ;-) Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Mona