[gmx-users] change in rename of 1POPC to 1LIG though coordinate and atom same in 1LIG of 1POPC, during solvation of system

2012-06-06 Thread Sangita Kachhap
Hello all I have to do MD simulation of membrane protein having docked ligand in POPC lipid bilayer. I am geeting error during solvation of system: Resname of 1POPC in system_shrink1.gro converted into 1LIG I have done following: GROMACS COMMAND 1) Generate topol.top using GROMOS96 53A6 parame

Re: [gmx-users] Trajectories

2012-06-06 Thread Erik Marklund
5 jun 2012 kl. 16.52 skrev Thomas Piggot: > Hi, > > I think Erik meant to say that the program is trjorder (not g_order) for the > ordering of molecules by distance. > > Cheers > > Tom Indeed I did. Sorry, and thanks for the correction. Erik > > On 05/06/12 14:41, Erik Marklund wrote: >>

Re: [gmx-users] Trajectories

2012-06-06 Thread Erik Marklund
Pymol has similar functionality, in case you prefer that over VMD. 5 jun 2012 kl. 22.23 skrev Peter C. Lai: > You can also use something like VMD where you load the trajectory then > select your atoms, then increment the frames and extract the xyz coordinates > of each of your atoms in the selec

Re: [gmx-users] Regarding error.

2012-06-06 Thread Erik Marklund
I use MacroMolecular Builder for all sorts of things, including filling in missing atoms. Erik 6 jun 2012 kl. 08.59 skrev Javier Cerezo: > There is no GROMACS tool that repairs incomplete structures, but you can find > other programs that can do it. Some of them have been previously posted in

[gmx-users] Regarding error.

2012-06-06 Thread Seera Suryanarayana
Dear all gromacs users, After added the counter ions to the top file and further i used 'grompp' commond,i got the following error. Fatal error: moleculetype CU1 is redefin

Re: [gmx-users] Regarding error.

2012-06-06 Thread Javier Cerezo
It seems that redefinition comes from including tow different ions.itp files, here: ; Include topology for ions #include "gromos43a1.ff/ions.itp" #include "ions.itp" Javier El 06/06/12 10:51, Seera Suryanarayana escribió: Dear all gromacs users, After added

[gmx-users] Question regarding genion

2012-06-06 Thread Matthias Ernst
Hi, I have to questions regarding genion. 1) Is there a possibility to tell genion in advance which group of molecules to replace by ions (for me, solvent is always the choice so I want to skript it but I did not find any parameters for this)? 2) I want to neutralize a charged system. Theref

Re: [gmx-users] Question regarding genion

2012-06-06 Thread Justin A. Lemkul
On 6/6/12 5:38 AM, Matthias Ernst wrote: Hi, I have to questions regarding genion. 1) Is there a possibility to tell genion in advance which group of molecules to replace by ions (for me, solvent is always the choice so I want to skript it but I did not find any parameters for this)? http:

Re: [gmx-users] change in rename of 1POPC to 1LIG though coordinate and atom same in 1LIG of 1POPC, during solvation of system

2012-06-06 Thread Justin A. Lemkul
On 6/6/12 3:09 AM, Sangita Kachhap wrote: Hello all I have to do MD simulation of membrane protein having docked ligand in POPC lipid bilayer. I am geeting error during solvation of system: Resname of 1POPC in system_shrink1.gro converted into 1LIG I have done following: GROMACS COMMAND 1)

Re: [gmx-users] Scaling/performance on Gromacs 4

2012-06-06 Thread Manu Vajpai
Apologies for reviving such an old thread. For clarifications, interlagos and bulldozer both have a modular architecture, as mentioned earlier. Each bulldozer module has 2 integer cores and one floating point unit shared between the two cores. So, although you have 64 cores (counting integer cores)

[gmx-users] Atomtype OW_tip4p not found

2012-06-06 Thread Amir Abbasi
Hi! I use tleap to generate topology file of a RNA molecule with parmbsc0 ff. Then I generate .gro and .top files of that with amb2gmx.pl. I'm manually add this lines to .top file ; Include water topology #include "amber99sb.ff/tip4p.itp" ; Include topology for ions #include "amber99sb.ff/ions.

Re: [gmx-users] Atomtype OW_tip4p not found

2012-06-06 Thread Justin A. Lemkul
On 6/6/12 7:19 AM, Amir Abbasi wrote: Hi! I use tleap to generate topology file of a RNA molecule with parmbsc0 ff. Then I generate .gro and .top files of that with amb2gmx.pl. I'm manually add this lines to .top file ; Include water topology #include "amber99sb.ff/tip4p.itp" ; Include topolog

Re: [gmx-users] Atomtype OW_tip4p not found

2012-06-06 Thread Justin A. Lemkul
On 6/6/12 7:36 AM, Amir Abbasi wrote: *From:* Justin A. Lemkul *To:* Amir Abbasi ; Discussion list for GROMACS users *Sent:* Wednesday, June 6, 2012 3:58 PM *Subject:* Re: [gmx-users] Atomtype OW_tip4p not foun

[gmx-users] Regarding Free energy (Energy barrier) calculation

2012-06-06 Thread neeru sharma
Dear Gromacs Users, Greetings of the day!! I am simulating a system of Protein-Mg-GTP complex. There are 2 states for the same, state 1 and state2. The difference lies in the presence of 2 specific H-bonds in the state 2 ,which are absent in state 1. Now, I need to find the energy barrier that wa

[gmx-users] Re: change in rename of 1POPC to 1LIG though coordinate and atom same in 1LIG of 1POPC, during solvation of system

2012-06-06 Thread Sangita Kachhap
ial type of multithreading called "clustered >> multithreading". This is slightly similar to the Intel cores with >> Hyper-Threading. >> >> >> Cheers, >> -- >> Szil?rd >> >> >> >> On Mon, Feb 20, 2012 at 5:12 PM, Sara Campos wrote: >

Re: [gmx-users] Re: change in rename of 1POPC to 1LIG though coordinate and atom same in 1LIG of 1POPC, during solvation of system

2012-06-06 Thread Justin A. Lemkul
On 6/6/12 8:52 AM, Sangita Kachhap wrote: On 6/6/12 3:09 AM, Sangita Kachhap wrote: Hello all I have to do MD simulation of membrane protein having docked ligand in POPC lipid bilayer. I am geeting error during solvation of system: Resname of 1POPC in system_shrink1.gro converted into 1LIG

[gmx-users] Segmentation fault - pdb2gmx specbond.dat

2012-06-06 Thread Steven Neumann
Dear Gmx Users, I created a plane surface made of 4 different atoms (400 atoms togehter). Each atom correspond to different residue - I added them to the aminoacids.rtp file. They are placed in different positions with LJ radius of 1.7A and they their center is 3.6 A away from each other (0.2A bet

[gmx-users] energy conservation: shift vs shifted user potential

2012-06-06 Thread Anja Kuhnhold
Dear gmx-users, I have a problem concerning energy conservation when using user potentials (tables). I'm using gromacs 4.5.4 I simulate a simple Lennard-Jones(6-12) +Fene polymer melt (1600 chains a 10 beads in a 26x26x26 periodic box). I tried different vdwtypes (cutoff always 3.24): The cut-o

[gmx-users] Cannot get correct pressure value with MTTK pressure coupling

2012-06-06 Thread Bao Kai
HI, all, I want to use MTTK for the pressure coupling for NPT simulation, while I can not get the correct pressure value. The following result is a simulation with 1000 SPC-E water molecules with temperature 303.15K and pressure 1 bar. Statistics over 101 steps [ 0. through 1000. ps

Re: [gmx-users] Cannot get correct pressure value with MTTK pressure coupling

2012-06-06 Thread Justin A. Lemkul
On 6/6/12 11:07 AM, Bao Kai wrote: HI, all, I want to use MTTK for the pressure coupling for NPT simulation, while I can not get the correct pressure value. The following result is a simulation with 1000 SPC-E water molecules with temperature 303.15K and pressure 1 bar. Statistics over 1

[gmx-users] hydrophobic contacts

2012-06-06 Thread Turgay Cakmak
Hi All, To be able to get information about the hydrophobic contacts, I prepared index.ndx which includes 2 groups of atoms that belong to hydrophobic residues of my system. Then, I used the command “g_dist -f traj.xtc -s topol.tpr -n index.ndx -dist 0.4 -lt -o lifetime.xvg” . which gave th

[gmx-users] g_sas

2012-06-06 Thread Meisam Rezaei
Hi Gromacs Users I want to plot SAS of residues with errobar. I want to know what is the meaning of third column in file of residue.xvg (output of g_sas)? which of the following expression is true about third column? 1) first answer=sqrt(summation(s_i - s_mean)/(N-1))) 2) second answer= first ans

Re: [gmx-users] Selecting atom indices of residues whose centers of mass match a position range

2012-06-06 Thread Teemu Murtola
Hi, On Wed, Jun 6, 2012 at 12:13 AM, Justin A. Lemkul wrote: > On 6/5/12 2:55 PM, Andrew DeYoung wrote: >> I would like to use g_select_d to generate an index file containing the >> atoms of BF4 residues whose centers of mass are in the range z<12.24 nm. >> I have tried the following: >> >> g_sel

Re: [gmx-users] Tabulated potentials for dihedrals - regd

2012-06-06 Thread ramesh cheerla
Dear Mark, Thank you for your reply, According to my understanding functional form of dihedral function type 9 is same as dihedral function type 1 i.e k(1 + cos(n (phi)- phis)) except the difference that function type 9 is used to handle the multiple potential functions

[gmx-users] GPU crashes

2012-06-06 Thread Justin A. Lemkul
Hi All, I'm wondering if anyone has experienced what I'm seeing with Gromacs 4.5.5 on GPU. It seems that certain systems fail inexplicably. The system I am working with is a heterodimeric protein complex bound to DNA. After about 1 ns of simulation time using mdrun-gpu, all the energies be

[gmx-users] Re: change in rename of 1POPC to 1LIG though coordinate and atom same in 1LIG of 1POPC, during solvation of system

2012-06-06 Thread Sangita Kachhap
gt; Protein_chain_A 1 >> LIG 1 >> POPC 128 >> SOL 1829 >> >> >> > > OK, that makes sense. Did InflateGRO remove any lipids? If it did, that is > not > reflected correctly in the topology. No it did,n

[gmx-users] cluster fomation in triolein simulation

2012-06-06 Thread mahnam karim
In God We Trust Hello Dear gmx-users I want to simulate oliver oil by Gromacs. I made topology of triolein with G45a3 force field at NPT ensemble (according to SCHULER paper ; Journal of Computational Chemistry, Vol. 22, No. 11, 1205–1218 (2001).I generated a box with 216 triole

Re: [gmx-users] Tabulated potentials for dihedrals - regd

2012-06-06 Thread Mark Abraham
On 7/06/2012 4:33 AM, ramesh cheerla wrote: Dear Mark, Thank you for your reply, According to my understanding functional form of dihedral function type 9 is same as dihedral function type 1 i.e k(1 + cos(n (phi)- phis)) except the difference that function type 9 i

[gmx-users] Regarding g_sham

2012-06-06 Thread bipin singh
Hello All, I have a doubt regarding -tsham option of g_sham (single histogram analysis). While using g_sham do we need to mention the temperature at which simulation were performed or it should be the constant (298.15K) for all analysis ( no matter at what temperature simulations were performed).