[gmx-users] Continuation=yes From?

Dear Dr.Justin Regarding Umbrella Sampling tutorial: The CONTINUATION option in md_umbrella.mdp is YES, and you have noticed : From NPT I can't understand it's reason correctly! we run a NPT and then Pulling, then extracted some configurations from pull.trr file. I think we must continue from

[gmx-users] Fw: ionic liquids

-- Original Message -- From: prem...@iiserpune.ac.in To: vvcha...@gmail.com

[gmx-users] RE: How to use Inflategro with different lipid types

Hello, I would like to thank Justin and Tom for their kind replies to my question! I believe that by having the gromacs manual as a guide I would manage to bring the bilayer into physiological size by using Justin's advice. However, Tom's advice sounds simpler to implement. Unfortunately

[gmx-users] Re: polarizable water models

Dear Saly I am sorry but I am not able to help you on this because I do not have any experience with PRODRG and SDS surfactants. You can try to find something in literature but I have the impression that nobody has tested SDS with these water models. As I told you in the previous mail

[gmx-users] Adding OPLS-UA forcefield

Dear users, How would I go about adding a united-atom forcefield e.g. OPLS-UA, to gromacs 4.5.3? Thanks in advance, Zoe Zoe Hall Department of Chemistry Oxford University zoe.h...@chem.ox.ac.uk -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Adding OPLS-UA forcefield

On 02/05/11, Zoe Hall zoe.h...@chem.ox.ac.uk wrote: Dear users, How would I go about adding a united-atom forcefield e.g. OPLS-UA, to gromacs 4.5.3? Set aside a few weeks, look in share/top/oplsaa.ff, copy it to oplsua.ff in your working directory, rework the contents according to

Re: [gmx-users] reg lincs error and exploding problem during mdrun

vidhya sankar wrote: Thanks Justin, now i have different problem when i run mdrun_d programme with the following command ./mdrun_d -s 1HHO_md.tpr -o 1HHO_md.trr -c 1HHO_md.gro -e md.edr -nt 1 i got error as follows Step 0, time 0 (ps) LINCS WARNING LINCS warnings

Re: [gmx-users] Continuation=yes From?

mohsen ramezanpour wrote: Dear Dr.Justin Regarding Umbrella Sampling tutorial: The CONTINUATION option in md_umbrella.mdp is YES, and you have noticed : From NPT I can't understand it's reason correctly! This is a meaningless comment. It was left there from copying and pasting files

Re: [gmx-users] Continuation=yes From?

Dear Dr.Justin Thank you for your reply My is Protein-ligand,It is have the same conditions as tutorial.I did pull ligand in the z direction. Actualy I found your note about gen_vel ,but I didn't any about Continuation! You are right,But there is another problem: You have not used any-t

Re: [gmx-users] Adding OPLS-UA forcefield

I think that it used to be part of earlier (3.?) versions of gmx. Those files may be useful for your work. Erik Zoe Hall skrev 2011-05-02 11.29: Dear users, How would I go about adding a united-atom forcefield e.g. OPLS-UA, to gromacs 4.5.3? Thanks in advance, Zoe Zoe Hall Department of

Re: [gmx-users] Adding OPLS-UA forcefield

Erik Marklund wrote: I think that it used to be part of earlier (3.?) versions of gmx. Those files may be useful for your work. Presumably, most of OPLS-UA still is. Per atomtypes.atp, the first 134 opls_* types are for OPLS-UA. I don't know how other features may be impacted, but it

Re: [gmx-users] Continuation=yes From?

mohsen ramezanpour wrote: Dear Dr.Justin Thank you for your reply My is Protein-ligand,It is have the same conditions as tutorial.I did pull ligand in the z direction. Actualy I found your note about gen_vel ,but I didn't any about Continuation! Not that specific keyword, no, but I do

Re: [gmx-users] Continuation=yes From?

Thank you for your detailed axplain I understood completely On Mon, May 2, 2011 at 4:34 PM, Justin A. Lemkul jalem...@vt.edu wrote: mohsen ramezanpour wrote: Dear Dr.Justin Thank you for your reply My is Protein-ligand,It is have the same conditions as tutorial.I did pull ligand in the

[gmx-users] adding an identified number of water molecules

Hi all If I want to add a simulation box an identified number of water molecules what should I do? In manual I see -nmol and -ci in genbox for insert extra molecules but I don't know for solvent what should I do? Thanks alot Best Regards Maria -- gmx-users mailing list

Re: [gmx-users] adding an identified number of water molecules

Maria Hamilton wrote: Hi all If I want to add a simulation box an identified number of water molecules what should I do? In manual I see -nmol and -ci in genbox for insert extra molecules but I don't know for solvent what should I do? Please read about the -maxsol option. I think you

[gmx-users] adding to liquids in the simulation box: one is in the right side of the box and the other in the left side

Hi all To do this at first I fill my box using genbox with one of the liquids as solvent: I used -cs and I did not used -cp. and then I used genbox again to add the other liquid in it: first liquid as a solute and the second one is as solvent. But these two liquids gives me a solution. I want to

Re: [gmx-users] adding to liquids in the simulation box: one is in the right side of the box and the other in the left side

Maria Hamilton wrote: Hi all To do this at first I fill my box using genbox with one of the liquids as solvent: I used -cs and I did not used -cp. and then I used genbox again to add the other liquid in it: first liquid as a solute and the second one is as solvent. But these two liquids

[gmx-users] Re: adding to liquids in the simulation box: one is in the right side of the box and the other in the left side

To do this at first I fill my box using genbox with one of the liquids as solvent: I used -cs and I did not used -cp. and then I used genbox again to add the other liquid in it: first liquid as a solute and the second one is as solvent. But these two liquids gives me a solution. I want to

[gmx-users] Re: [gmx-developers] installing the parallel version of Gromacs 3.3.1

I am CC'ing this message to the general gmx-users list. The gmx-developers list is for discussion about development. Please send anything further via gmx-users. See comments below. West, Ana wrote: Dear Gromacs Community, I attempted to install the parallel version of Gromacs 3.3.1 on a

[gmx-users] Re: adding to liquids in the simulation box: one is in the right side of the box and the other in the left side

1.Does any liquid have an individual vdwradii.dat? I found only one vdwradii.dat file in GROMACS folder. 2.How can I freeze the first liquid? Thanks Regards Maria On Mon, May 2, 2011 at 6:10 PM, Vitaly Chaban vvcha...@gmail.com wrote: To do this at first I fill my box using genbox with one of

[gmx-users] Fw: Fw: ionic liquids

-- Original Message -- From: prem...@iiserpune.ac.in To: gmx-users@gromacs.org

[gmx-users] Re: gmx-users Digest, Vol 85, Issue 9

-- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110502/25076a8a/attachment-0001.html -- Message: 2 Date: Mon, 2 May 2011 17:19:00 +0430 From: Maria Hamilton hamilton.mari...@gmail.com Subject: [gmx-users

[gmx-users] g_traj -ox -com slight inconsistency

Dear Users: I have noticed an inconsistency with g_traj -ox -com output when using -f a.gro and either -s a.gro or -s a.tpr where a.tpr was constructed from a.gro. There does not appear to be any difference when not using the -com flag. The difference is on the order of =0.008 nm so I

[gmx-users] Re: adding to liquids in the simulation box: one is in the right side of the box and the other in the left side

On Mon, May 2, 2011 at 11:55 AM, Maria Hamilton hamilton.mari...@gmail.comwrote: 1.Does any liquid have an individual vdwradii.dat? vdwradii.dat is one for all atoms. It is in the same directory with built-in topologies. The atom names in your conf.gro and this vdwradii.dat should coincide,

Re: [gmx-users] adding to liquids in the simulation box: one is in the right side of the box and the other in the left side

Please do not reply to the entire digest. Parse any relevant text, choose an appropriate subject line, and reply. Otherwise, the archive gets hopelessly confused. Maria Hamilton wrote: Hi I want to build my simulation box as tutorial. However I change vdwradii.dat file according to the

[gmx-users] Re: mixtures. I want to build my simulation box as tutorial

Hi I want to build my simulation box as tutorial. However I change vdwradii.dat file according to the tutorial liquid 2 mix with liquid 1. What should I do? Your question is not clear. -- Dr. Vitaly V. Chaban, Department of Chemistry University of Rochester, Rochester, New York

Re: [gmx-users] Re: [gmx-developers] installing the parallel version of Gromacs 3.3.1

Hi all! There also another problem. You are using intel compilers on amd based machine. Intel compilers uses cpuid to identify processor and optimization and they doesnt include amd cpuids at all. So you will have bad performance on amd cpus. I'd recomend to use recent versions of gcc

[gmx-users] Unsteady Density

Hello, I have been trying to use CHARMM forcefield to simulate 1000 molecules of Methanol in a box but I seem to fall short on the density every time I run. At first, I had my rlist at 1 but CHARMM recommends greater than 1.2-1.4 nm so I changed accordingly, then I changed it so that the short

Re: [gmx-users] Unsteady Density

Fabian Casteblanco wrote: Hello, I have been trying to use CHARMM forcefield to simulate 1000 molecules of Methanol in a box but I seem to fall short on the density every time I run. At first, I had my rlist at 1 but CHARMM recommends greater than 1.2-1.4 nm so I changed accordingly, then I

[gmx-users] Re: Unsteady Density

I have been trying to use CHARMM forcefield to simulate 1000 molecules of Methanol in a box but I seem to fall short on the density every time I run. At first, I had my rlist at 1 but CHARMM recommends greater than 1.2-1.4 nm so I changed accordingly, then I changed it so that the short

[gmx-users] Re: Unsteady Density

Hello, Thanks for your response. Here are my responses to your points: nstlist=1 is overkill. I will change this back to 5 except for EM like you said. I originially thought that maybe the density not settling was because the neighbor searching frequency had not been updated frequently enough

Re: [gmx-users] Re: Unsteady Density

Fabian Casteblanco wrote: Hello, Thanks for your response. Here are my responses to your points: nstlist=1 is overkill. I will change this back to 5 except for EM like you said. I originially thought that maybe the density not settling was because the neighbor searching frequency had not

Re: [gmx-users] RE: How to use Inflategro with different lipid types

Hi, I recently came across the CELLmicrocosmos 2.2 MembraneEditor, in which one can easily generate coordinates for mixed membranes and AFAIK also insert a protein. http://cm2.cellmicrocosmos.org/ http://pubs.acs.org/doi/abs/10.1021/ci1003619 I haven't had the chance/need to actually try it,

[gmx-users] Re: Unsteady Density

The last time I had performed this with nstlist=5 and for the actual MD run, I had a density of approximately 0.781 g/cm3 compared to literature value of 0.791 g/cm3 at 298K. So, what is the problem? It is satisfactory coincidence. -- Dr. Vitaly V. Chaban, Department of Chemistry

[gmx-users] Re: Unsteady Density

Thanks Justin. I'm currently running the MD run separately so that the average value won't be affected by the unequilibrated values at the beginning of the NPT run where the density started in the 400s and ran up to the ~high 700s. I had done this before when I had nstlist at 5 but I did run NPT

Re: [gmx-users] Re: Unsteady Density

Fabian Casteblanco wrote: Thanks Justin. I'm currently running the MD run separately so that the average value won't be affected by the unequilibrated values at the beginning of the NPT run where the density started in the 400s and ran up to the ~high 700s. I had done this before when I had

[gmx-users] tabulated potentials for non-bonded interactions

Hi Is it possible to use use specified potentials only for vdw type non-bonded interactions while keeping usual PME,bonded, pairs interactions? When I specifiy User for vdwtype force in .mdp file, I am observing that mdrun expects table for bonded interactions also through -tableb option and by

[gmx-users] g_select is pretty fantastic

Dear g_select developers: This is a shout out of thanks for this new tool, which I find very useful. For users who have not played around with this, I'd suggest trying it (especially if you are already familiar with VMD-style selection syntax). I want to make special thanks for the