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

To: Discussion list for GROMACS users > Message-ID: <4fcf5364....@vt.edu> > Content-Type: text/plain; charset=UTF-8; format=flowed > > > > On 6/6/12 8:52 AM, Sangita Kachhap wrote: > >>> On 6/6/12 3:09 AM, Sangita Kachhap wrote: >>>> >>>>

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

emkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > > ---------- > > Message: 2 > Date: Wed, 06 Jun 2012 06:08:55 -0400 > From: "Justin A. Lemkul" >

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

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

[gmx-users] How to get md_0_2. prefix for all output files during entexding production run, like got during first run md_0_1.

How to get md_0_2. prefix for all output > files duringentexding production run, like got during first run > md_0_1. > To: Discussion list for GROMACS users > Message-ID: <4fafeb85.20...@vt.edu> > Content-Type: text/plain; charset=UTF-8; format=flowed > > &

[gmx-users] How to get md_0_2. prefix for all output files during entexding production run, like got during first run md_0_1.

state.cpt state_prev.cpt traj.trr traj.xtc confout.gro During first 1 ns production I have got all files with prefix md_0_1. How I can get it (prefix md_0_2. for all the above files)in next 1 ns production run. Anyone please suggest. With regards Sangita Kachhap SRF BIC,IMTECH CHANDIGARH

[gmx-users] solvent group size (12548) is not a multiple of 3

gt; >1. Re: keep the nanotube cylindrical. (Elton Carvalho) >2. poor performance in Hemiltonian Replica Exchange (francesco oteri) >3. Re: poor performance in Hemiltonian Replica Exchange > (Michael Shirts) >4. solvent group size (12548) is not a multiple of

[gmx-users] solvent group size (12548) is not a multiple of 3

lipid hydrohphobic core) genbox -cp system_shrink1.gro -cs spc216.gro -o system_shrink1_solv.gro -p topol.top grompp -f ions.mdp -c system_shrink1_solv.gro -p topol.top -o ions.tpr genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA -nname CL -nn 4 (at

[gmx-users] Nubmer of coordinate not matching in topol.top and sol.gro

8 > > It seems some force has been imposed on the pull molecules. > But in the pullf.xvg the force is ZERO. > I used the latest gromacs version, But for the gromacs4.0 it works very well > (works as what I think). > Can someone help me about the issue? > > Thanks a lot &g

[gmx-users] Number of cooredinate in topol.top and solv.gro not matching

on/How-tos/Making_Disulfide_Bonds > > Mark > -- next part ---------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120502/9c7e1646/attachment-0001.html > > -- > > Messag

[gmx-users] Number of coordinate in topol.top and solv.gro not matching

=/usr/bin/cpp ; Parameters describing what to do, when to stop and what to save " Then also it showing same error. Please help me to solve this problem. I am using gromacs-4.5.5 and installed with fftw-3.3.1 . With regards Sangita Kachhap SRF B

[gmx-users] Fatal error: Bond atom type names can't be single digits

em is occuring? With regards Sangita Kachhap SRF BIC,IMTECH CHANDIGARH __ सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए, चण्