[gmx-users] regarding table for water water interactions

Hai all, My system is just a water Spc model. I am trying to create a table.xvg which would deal with nonbonded intearction for water-water for say SPC model. If i have to calculate the potential i have to consider the interaction between 1.O of water1--O of water

Re: [gmx-users] How to make a membrane system with 512 DPPCs

Du Jiangfeng (BIOCH) wrote: Dear Gromacs Users, There are easy to get membrane with 64 DPPC or 128 DPPC for all atoms simulation or coarse grained simulation, but is it possible to get a membrane with 512 lipids? If so, where? If you have a 128-lipid membrane: genconf -f 128.gro -o

Re: [gmx-users] How to make a membrane system with 512 DPPCs

On 2011-05-25 07:58:18AM -0500, Du Jiangfeng (BIOCH) wrote: Dear Gromacs Users, There are easy to get membrane with 64 DPPC or 128 DPPC for all atoms simulation or coarse grained simulation, but is it possible to get a membrane with 512 lipids? If so, where? We also tried to build a 512

Re: [gmx-users] How to make a membrane system with 512 DPPCs

On 2011-05-25 08:00:32AM -0500, Justin A. Lemkul wrote: Du Jiangfeng (BIOCH) wrote: Dear Gromacs Users, There are easy to get membrane with 64 DPPC or 128 DPPC for all atoms simulation or coarse grained simulation, but is it possible to get a membrane with 512 lipids? If so, where?

Re: [gmx-users] How to make a membrane system with 512 DPPCs

Peter C. Lai wrote: On 2011-05-25 08:00:32AM -0500, Justin A. Lemkul wrote: Du Jiangfeng (BIOCH) wrote: Dear Gromacs Users, There are easy to get membrane with 64 DPPC or 128 DPPC for all atoms simulation or coarse grained simulation, but is it possible to get a membrane with 512 lipids?

Re: [gmx-users] Charmm36 in Gromacs: missing dihedrals

Dear Mark and Justin, Thanks for the quick reply. I must have misunderstood the procedure. I was assuming that the generated top file should include the actual values used for the Urea-Bradley terms. Previously I have only included molecules using an itp file and was expecting similar behaviour.

Re: [gmx-users] dipole moment

I want to see the change in dipole moment alond the simulation. NIlesh On Wed, May 25, 2011 11:32 am, David van der Spoel wrote: On 2011-05-25 17.14, Nilesh Dhumal wrote: Hello, Can I calculate a dipole moment of a particular bond? It is easier to do it manually. Otherwise g_dipoles

Re: [gmx-users] dipole moment

Thanks for reply. Here are more details about my simulation. I have glucose molecule in my system. I am interested in change in dipole moment of OH bond of glucose along the simulation. I have made the index file. How can I select two groups (oxygen and hydrogen) or should I put particular

Re: [gmx-users] dipole moment

On 2011-05-25 18.03, Nilesh Dhumal wrote: Thanks for reply. Here are more details about my simulation. I have glucose molecule in my system. I am interested in change in dipole moment of OH bond of glucose along the simulation. The OH group is not neutral so your dipole is meaningless

Re: [gmx-users] sphere around a protein

Hi Justin, Revisiting some of the calculations I had tried to do few days back. Just as a recap I am trying to build a sphere around the protein. As you had suggested in the last messgae of this thread to make a new directory. I did that. I used the following commands: editconf -f 1li.gro

Re: [gmx-users] sphere around a protein

shivangi nangia wrote: Hi Justin, Revisiting some of the calculations I had tried to do few days back. Just as a recap I am trying to build a sphere around the protein. As you had suggested in the last messgae of this thread to make a new directory. I did that. I used the following

Re: [gmx-users] dipole moment

Basically I want to calculate the stretching vibration of the bond by fourier transfrom of dipole momenet autocorrelation fucntion or velocity autocorrelation function. Before going for vibration I wanted to check the fluctuation of dipole moment along the simulation. Can I calculate the

[gmx-users] query regarding replica exchange

Hi, I am planning to run replica exchange simulation using gromacs 4.0.7 . I have read the manual about REMD. Only thing I wanted to know is that how I can specify the name of host-machines where I am planning to run the simulations. I have 10 different quad-core computers each

Re: [gmx-users] dipole moment

On 2011-05-25 20.42, Nilesh Dhumal wrote: Basically I want to calculate the stretching vibration of the bond by fourier transfrom of dipole momenet autocorrelation fucntion or velocity autocorrelation function. Before going for vibration I wanted to check the fluctuation of dipole moment along

Re: [gmx-users] sphere around a protein

Hi Justin, Thanks a lot! Things worked. Now I, however, have a different problem in extension to what I am doing. I was able to created a sphere of water and methanol around a polypeptide and 1 Li+ ion. editconf -f 1li.gro -c -box 12 12 12 -o onlyli.gro genbox -cp onlyli.gro -cs mix.gro

Re: [gmx-users] sphere around a protein

shivangi nangia wrote: Hi Justin, Thanks a lot! Things worked. Now I, however, have a different problem in extension to what I am doing. I was able to created a sphere of water and methanol around a polypeptide and 1 Li+ ion. editconf -f 1li.gro -c -box 12 12 12 -o onlyli.gro genbox

Re: [gmx-users] sphere around a protein

Justin A. Lemkul wrote: shivangi nangia wrote: Hi Justin, Thanks a lot! Things worked. Now I, however, have a different problem in extension to what I am doing. I was able to created a sphere of water and methanol around a polypeptide and 1 Li+ ion. editconf -f 1li.gro -c -box 12 12

Re: [gmx-users] sphere around a protein

Hi, Please correct me if I am wrong. In that case then, I will have polyhisitine in the box size 12 12 12 and then If I add dhb anions and Li cations, they will be placed randomly in the box. When I add then the 1 Li cation, water methanol sphere, how is it necessary it will cover/solvate all

Re: [gmx-users] sphere around a protein

shivangi nangia wrote: Hi, Please correct me if I am wrong. In that case then, I will have polyhisitine in the box size 12 12 12 and then If I add dhb anions and Li cations, they will be placed randomly in the box. When I add then the 1 Li cation, water methanol sphere, how is it

Re: [gmx-users] query regarding replica exchange

You will need a file formatted like the following: node0 slots=4 max_slots=4 node1 slots=4 max_slots=4 ... node9 slots=4 max_slots=4 You will then need to use the -hostfile option to supply the filename to either mpiexec or mpirun (not mdrun). -- Josh On Wed, 2011-05-25 at 11:50 -0700, Sanku M

Re: [gmx-users] query regarding replica exchange

I was wondering if I try to run PBS script in a cluster, how can I get to generate the hostfile as I do not know in advance which machines will be allocated . From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users

Re: [gmx-users] query regarding replica exchange

Sanku M wrote: I was wondering if I try to run PBS script in a cluster, how can I get to generate the hostfile as I do not know in advance which machines will be allocated . This is a question for your sysadmin. Most such implementations ignore hostfiles for this very reason. -Justin

[gmx-users] g_velacc

Hello, I am trying to calculate the velocity autocorrelation function of OH bond in glucose molecule. The calculate velocity autocorrelation function is not smooth. Its fluctuating a lot so I am geting wide/think line. Why I am not geting a smooth line? I am using gromacs version 4.0.7.

[gmx-users] problem with replica exchange

Hi,  I am having a problem in running replica exchange simulation over multiple nodes. To run the simulation for 16 replicas over two 8-core processors, I generated a hostfile as follows: yethiraj30 slots=8 max_slots=8  yethiraj31 slots=8 max_slots=8 These two machines are intra-connected and I

[gmx-users] g_energy unable to -skip

Hello When I try to specify -skip with g_energy it still outputs the data from all frames into the .xvg file. I have to use eneconv -dt to strip out the data from said .edr (which yields a lot of data not found error messages) in order to get a compacted .xvg dataset... --

Re: [gmx-users] problem with replica exchange

On 26/05/2011 12:25 PM, jagannath mondal wrote: Hi, I am having a problem in running replica exchange simulation over multiple nodes. To run the simulation for 16 replicas over two 8-core processors, I generated a hostfile as follows: yethiraj30 slots=8 max_slots=8 yethiraj31 slots=8

Re: [gmx-users] query regarding replica exchange

Often, a PBS submission system will provide the host information to MPI automatically. However, you will have to refer to the documentation for your particular cluster (or talk to the sysadmin, as Justin mentioned) to determine if your particular cluster behaves this way, which MPI process

[gmx-users] How to calculate lateral pressure for monolayer compression or expansion

Dear Users, As I want to simulate surfactant monolayer with different molecular area in order to reproduce the LB experiment (isotherm plot). So I have to fix a number of surfactant molecules but only surface area is changed by applying the lateral pressure. However, I don't know how to calculate

[gmx-users] (no subject)

Dear Sir/Madam, In gromacs tutor we have water .gro file for spc potential. How to get .gro files from spc216.pdb of different potentials like tip3p tip4p ... etc. -- With Regards, Ravi Kumar Venkatraman, c/o Prof. Siva Umapathy, IPC Dept., IISc., Bangalore, INDIA. Phone No:

Re: [gmx-users] (no subject)

On 26/05/2011 2:55 PM, Ravi Kumar Venkatraman wrote: Dear Sir/Madam, In gromacs tutor we have water .gro file for spc potential. How to get .gro files from spc216.pdb of different potentials like tip3p tip4p ... etc. You don't need a file in .gro format, and coordinate files