Re: [gmx-users] Restarting crashed simmulation.

Thanks sir Justin and sir Mark On Sat, 12 May 2018 3:27 pm Mark Abraham, wrote: > Hi, > > Or use the existing tool one has for a group of related files, called a > directory or folder ;-) It's not compulsory to do your whole thesis in the > same folder, too :-D > >

Re: [gmx-users] Gmx insert

On 5/12/18 1:49 PM, rose rahmani wrote: Hi, I want to place peptide at certain distance from surface as an initial distance. How can i do it? Is it possible with gmx insert molecule? No. Use editconf -center to assign its position. -Justin --

[gmx-users] Gmx insert

Hi, I want to place peptide at certain distance from surface as an initial distance. How can i do it? Is it possible with gmx insert molecule? Best regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

[gmx-users] Problem with gmx clustsize ..(Not enough memory. Failed to calloc)

Dear Gromacs users I am trying to analyse a MD simulation of 30 lipopeptides in water, in particular I would like to obtain the average number of these molecules in each assembly, along the time. I have tried g_clustsize with my simulation box with only the lipopeptides. For that I prepared a tpr

Re: [gmx-users] SMD regarding

THAnk you Dr. Justin That’s convincing a lot. On Sat, 12 May 2018 at 8:14 PM, Justin Lemkul wrote: > > > On 5/12/18 10:41 AM, RAHUL SURESH wrote: > > Thank you Dr. Mark > > > > Is it valid to do such simulation despite causing the distortion in > lipids? > > Lipids are highly

Re: [gmx-users] SMD regarding

On 5/12/18 10:41 AM, RAHUL SURESH wrote: Thank you Dr. Mark Is it valid to do such simulation despite causing the distortion in lipids? Lipids are highly dynamic. They can tilt, flip-flop, pack and expand. What you need to do is perform your simulation in such a way that the lipids are

Re: [gmx-users] SMD regarding

Thank you Dr. Mark Is it valid to do such simulation despite causing the distortion in lipids? On Sat, 12 May 2018 at 8:06 PM, Mark Abraham wrote: > Hi, > > It's clear that pulling on a membrane protein will affect the behavior of > the lipids in the membrane. > >

Re: [gmx-users] SMD regarding

Hi, It's clear that pulling on a membrane protein will affect the behavior of the lipids in the membrane. Mark On Sat, May 12, 2018, 14:21 RAHUL SURESH wrote: > Dear users, > > I have a complex [ dimer ] membrane protein. I want to perform sMD for this > complex

[gmx-users] SMD regarding

Dear users, I have a complex [ dimer ] membrane protein. I want to perform sMD for this complex structure. Is it valid and possible to perform pull code for the complex protein structure in the presence of lipid bilayer ? If yes, will it not disturb the lipid configurations of the system?

Re: [gmx-users] Implicit membrane in Gromacs, regarding

Thank you, Dr. Mark, On Sat, May 12, 2018 at 3:58 PM, Mark Abraham wrote: > Hi, > > If you'd tried it, either charmm GUI would have refused to make a file, or > made a file that doesn't do that, because GROMACS can't. > > Mark > > On Sat, May 12, 2018, 10:51 RAHUL

Re: [gmx-users] Implicit membrane in Gromacs, regarding

Hi, If you'd tried it, either charmm GUI would have refused to make a file, or made a file that doesn't do that, because GROMACS can't. Mark On Sat, May 12, 2018, 10:51 RAHUL SURESH wrote: > Dear Users, > > How far is it possible to simulate a protein in implicit

Re: [gmx-users] Restarting crashed simmulation.

Hi, Or use the existing tool one has for a group of related files, called a directory or folder ;-) It's not compulsory to do your whole thesis in the same folder, too :-D Mark On Fri, May 11, 2018, 21:01 Justin Lemkul wrote: > > > On 5/11/18 2:11 PM, neelam wafa wrote: > >

[gmx-users] Implicit membrane in Gromacs, regarding

Dear Users, How far is it possible to simulate a protein in implicit membrane using gromacs? Charmm-Gui provides an option to construct a PDB with GBSW as an implicit membrane. Will that be a supported input file for gromacs? -- *Regards,* *Rahul * -- Gromacs Users mailing list * Please

[gmx-users] gmx potential command

Dear Justin,I used gmx potential command to obtained electrostatic potential across the DPPE membrane. I think my finding isn't true because there is a peak at the center of bilayer and in the head group there are two maximum that are small and mild in the head group. In the same case for DPPC,