[gmx-users] need help with topology file

Hi, I am trying to use two types of force fields for my system which has protein and fullerene. i want to use OPLS for protein and ffG53a6 for fullerene(as i don't have opls readily available for this). When i use two itp files in #include section grompp does not allow me to do that with the follo

Re: [gmx-users] problem with fullerene simulations

Oh sorry, i used spc.itp now and it works. Thanks. Srinivas. On Fri, Jul 22, 2011 at 5:48 PM, Justin A. Lemkul wrote: > > > jampani srinivas wrote: > >> Hi Justin, >> >> Thanks for your reply, i have no particular choice i was using it for my >> other work a

Re: [gmx-users] problem with fullerene simulations

, but i suspect some thing is going wrong with atom types in .atp file. any suggestions? Thanks Srinivs. On Fri, Jul 22, 2011 at 5:11 PM, Justin A. Lemkul wrote: > > > jampani srinivas wrote: > >> Hi Gromacs users, >> >> I am trying to run a fullerene simulaton in

[gmx-users] problem with fullerene simulations

Hi Gromacs users, I am trying to run a fullerene simulaton in TIP4P water model, i am using the "c70_G53a6.itp " file downloaded from http://tfy.tkk.fi/soft/downloads/. i have added TIP4P water model using genbox command, later when i am tryin

Re: [gmx-users] domain decomposition

Hi Try with -dd 2 x 2 x 2 option with 8 nodes and check the performance. I too got the same problems, i could overcome with symmetrical -dd option. Srinivas. On Fri, May 7, 2010 at 8:57 AM, irene farabella < i.farabe...@mail.cryst.bbk.ac.uk> wrote: > Hello! > > I am new to Gromacs and especiall

Re: [gmx-users] RE: [Bug 404] energy increase in nvt and nve simiulations

Dear Berk, Yes the system is stable and the small velocity appears only at step 0 as you said. This looks fine now, Thanks a lot for you continuous support Thanks very much. Srinivas. On Mon, Apr 26, 2010 at 7:43 AM, Berk Hess wrote: > Hi, > > So the system seems to be stable now? > > The wa

Re: [gmx-users] RE: [Bug 404] energy increase in nvt and nve simiulations

Dear Berk, First of all thanks very much for your kind patience and help. As a new user i am facing some problems and not clear about many options and how to use them. I was reading several messages of yours from mailing list which are very close to my problem. After reading several of them from m

Re: [gmx-users] RE: [Bug 404] energy increase in nvt and nve simiulations

Dear Berk, I have run it for 5ns, as you said for first 1ns i have not seen much drift in the energy there after energy is slowly increasing in each step. Should i run it again and send you the edr file? can you please let me know on which version of gromacs you have run this file? Thanks very m

Re: [gmx-users] RE: [Bug 404] energy increase in nvt and nve simiulations

Dear Berk, I am sorry for poor communication, Herewith i am giving my md.mdp file. I this file as you could see i am using two temp coupling groups Tmp1 is protein and a 2nm spherical layer of water around it, and the second one Tmp2 which has only water. Now i want to fix the Tmp2 and apply 0 K t

Re: [gmx-users] problem with total energy

Srinivas. On Fri, Apr 9, 2010 at 1:26 AM, Mark Abraham wrote: > On 9/04/2010 1:25 PM, jampani srinivas wrote: > >> Dear Justin, >> >> I am sorry for the poor description of the problem, OK let me explain >> you clearly here. >> >> I have taken a decapepti

Re: [gmx-users] problem with total energy

tion. Thanks very much for your kind help. Srinivas. On Thu, Apr 8, 2010 at 8:21 PM, Justin A. Lemkul wrote: > > > jampani srinivas wrote: > >> Dear Justin, >> Thanks for your responce. Here is my mdp file. >> +++ >> ti

Re: [gmx-users] problem with total energy

Thanks Srinivas. On Thu, Apr 8, 2010 at 7:52 PM, Justin A. Lemkul wrote: > > > jampani srinivas wrote: > >> Hi >> Thanks for your response, I am allowing the two groups (frozen and >> non-frozen) groups interact each other, i guess i am getting the energy of

Re: [gmx-users] problem with total energy

in advance. Srinivas. On Wed, Apr 7, 2010 at 4:47 PM, ms wrote: > jampani srinivas ha scritto: > > Dear Berk, > > > > I am sorry if i am confusing you with my poor description of problem, > > actually I have submitted simulation with two temperature coupling groups > (i

[gmx-users] problem with total energy

Dear Berk, I am sorry if i am confusing you with my poor description of problem, actually I have submitted simulation with two temperature coupling groups (i think you already know that from our earlier conversations) and found that there is a continuous increase in the total energy of the system.

Re: [gmx-users] problem with the size of freeze groups

in my procedure? can you please help me to solve this problem? Thanks very much for your kind help. Srinivas. On Wed, Mar 17, 2010 at 8:25 PM, jampani srinivas wrote: > > Dear Berk, > > >> Sorry for the delayed reply, We have compiled the gromacs with readir.c >> t

[gmx-users] continuous energy increase in NVT and NVE simulations

Dear All, I am running MD simulation with TIP4P water and OPLS force field in NVT and NVE. I have noticed a continuous energy increase in both NVE and NVT simulations when i freeze a selected portion of my system. Recently i had problem with temperature coupling, Berk has sent me a file which has

Re: [gmx-users] T-coupling groups

Dear Zuzana, Recently i have done similar selection, I have got this error only when i miss some atoms or when i have some atoms in both groups. I would suggest you to check your groups carefully or you can make indexes for these selections in VMD and check whether you are missing some atoms from

Re: [gmx-users] problem with the size of freeze groups

Dear Berk, > Sorry for the delayed reply, We have compiled the gromacs with readir.c > that you have sent me, now it is working fine. > > Thank you very much for your kind help. > > Srinivas. > > > On Wed, Mar 3, 2010 at 1:56 PM, jampani srinivas wrote: > Dear B

Re: [gmx-users] problem with the size of freeze groups

er freezing groups. > > Thanks again for your kind help. > srinivas. > > > On Fri, Feb 26, 2010 at 5:37 PM, jampani srinivas wrote: > > Dear Berk, > > I have checked my inputs and tcl scripts that i have used for > the selection, i could see that my selection doesn&#x

Re: [gmx-users] problem with the size of freeze groups

Dear Berk, Thanks for your previous responses, Can you please let me know if you have any solution for the size of freezing groups? I am still not able to do if i have larger freezing groups. Thanks again for your kind help. srinivas. On Fri, Feb 26, 2010 at 5:37 PM, jampani srinivas wrote

Re: [gmx-users] problem with the size of freeze groups

files, and help me if you have solution for this problem. Thanks and Regards Srinivas. On Fri, Feb 26, 2010 at 12:39 PM, jampani srinivas wrote: > Dear Berk, > > I am using VERSION 4.0.5. As you said if there is no problem i should get > it correctly, i don't know where it

Re: [gmx-users] problem with the size of freeze groups

Dear Berk, I am using VERSION 4.0.5. As you said if there is no problem i should get it correctly, i don't know where it is going wrong. I have written a small script in tcl to use in vmd to get my selections. i will check the script and the selection again. I will let you know my results again.

Re: [gmx-users] problem with the size of freeze groups

Dear Berk, They are same, freeze and Tmp2 are exactly the same groups. I just put them like that for my convenience, just to avoid confusion in my second email i made it uniform. Thanks Srinivas. On Fri, Feb 26, 2010 at 11:59 AM, Berk Hess wrote: > That is what I suspected, by I don't know wh

Re: [gmx-users] problem with the size of freeze groups

Dear Berk, It looks to me some thing is wrong when i change the radius from 35 to 25, herewith i am giving grpopts for both systems + grpopts: (system with 35 A) nrdf: 33141.4 0 ref_t: 300 0 tau_t: 0.1 0.1 ++

Re: [gmx-users] problem with the size of freeze groups

Hi Berk, I am extremely sorry, here is the correct log file grpopts: nrdf: 0 0 ref_t: 300 0 tau_t: 0.1 0.1 Thanks Srinivas. On Fri, Feb 26, 2010 at 11:01 AM, Berk Hess wrote: > Ah, but that d

Re: [gmx-users] problem with the size of freeze groups

HI Thanks, My log file shows me "nrdf: 0" ### grpopts: nrdf: 0 ref_t:0 tau_t: 0 ### Thanks Srinivas. On Fri, Feb 26, 2010 at 10:25 AM, Berk Hess wrote: > Hi, > > Then I have no clue what might be wrong. > Have you ch

Re: [gmx-users] problem with the size of freeze groups

Dear Berk, Thanks for your response, As you mentioned i have separated t-coupling group for frozen and non-frozen groups, still the result is same. Herewith i am giving my md.mdp file, Can you suggest me if i am missing any options in my md.mdp file? Thanks again Srinivas. md.mdp file

[gmx-users] problem with freezing group size

Dear all, I am sorry for poorly describing my problem about the freezing group size. Here I am giving my question very briefly, can anybody help me please? I would like to know the relation between the size of freezing group and the temperature coupling. when I separate the temperature coupling f

[gmx-users] problem with the size of freeze groups

Dear Gromacs Users, I would like to compare the diffusion coefficient of water in different confined spheres with the bulk solvent, I have taken a solvent box of size 7nm, and I have created a sphere with radius 25 Å as lowest and 35 Å as highest spheres. I have not used the pressure coupling for