[gmx-users] (no subject)

Dear GMX Users, I am wish to perform  a conformational transition simulation using coarse-grained models (SBM http://smog-server.org/). I wanted to apply flooding to explore the conformational transition and have open-close transition my trajectory. But what I find is that when I start from a o

[gmx-users] Conformational transition using essential dynamics

Dear GMX Users, I am wish to perform  a conformational transition simulation using coarse-grained models (SBM http://smog-server.org/). I wanted to apply flooding to explore the conformational transition and have open-close transition my trajectory. But what I find is that when I start from a o

Re: [gmx-users] g_lie and ligand only simulation

Dear users, Sorry for repeating the same question. I just wanted to know whether is it ok if I have rlist > rcoulomb in ligand-water and prot-lig-water rerun md (with RF-0) while having rlist = rcoulomb in the original simulation using PME? Thank you Regards Kavya On Wed, Nov 6, 2013 at 11

Re: [gmx-users] Re: Gromacs-4.6 on two Titans GPUs

Hi Dwey, On 05/11/13 22:00, Dwey Kauffman wrote: Hi Szilard, Thanks for your suggestions. I am indeed aware of this page. In a 8-core AMD with 1GPU, I am very happy about its performance. See below. My intention is to obtain a even better one because we have multiple nodes. ### 8 core AMD

Re: [gmx-users] Re: Analysis tools and triclinic boxes

On 11/5/13 7:14 PM, Stephanie Teich-McGoldrick wrote: Message: 5 Date: Mon, 04 Nov 2013 13:32:52 -0500 From: Justin Lemkul Subject: Re: [gmx-users] Analysis tools and triclinic boxes To: Discussion list for GROMACS users Message-ID: <5277e854.9000...@vt.edu> Content-Type: text/plain; charset=

Re: [gmx-users] g_lie and ligand only simulation

On 11/6/13 5:47 AM, Kavyashree M wrote: Dear users, Sorry for repeating the same question. I just wanted to know whether is it ok if I have rlist > rcoulomb in ligand-water and prot-lig-water rerun md (with RF-0) while having rlist = rcoulomb in the original simulation using PME? The energi

Re: [gmx-users] g_lie and ligand only simulation

Thank you.. On Wed, Nov 6, 2013 at 7:39 PM, Justin Lemkul wrote: > > > On 11/6/13 5:47 AM, Kavyashree M wrote: > >> Dear users, >> >> Sorry for repeating the same question. I just wanted to know >> whether is it ok if I have rlist > rcoulomb in ligand-water and >> prot-lig-water rerun md (wi

[gmx-users] Number of water molecules around any methyl carbon

Hi all, I would like to calculate the number of water molecules around any of the methyl carbon atoms of tert-butyl alcohol. Currently, I have defined an index group containing all three of the methyl carbon atoms and used trjorder -nshell to calculate the number of oxygen atoms within a specifi

[gmx-users] Enterobactin binding to Iron(III)

I was told before I would need to use quantum calculations to do this. What software and method would you suggest to do this? Thanks. -Jonathan Saboury -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://w

[gmx-users] stopped simulation

Hi gmx users, I have simulated ionomer in water solution using gromos force field. But in middle of simulation(after 2 ns) the simulation stopped and I received these messages: WARNING: Listed nonbonded interaction between particles 174 and 188 at distance 3f which is larger than the table lim

[gmx-users] Group protein not found in indexfile

Hello I am having trouble running a dimmer invacuo simulation. I can do energy minimization on it, but when I attempt to generate md.tpr file I get this weird message about “Group Protein not found in index”. I don’t see why I would need an index file. I have no trouble generating a md.tpr fil

Re: [gmx-users] Number of water molecules around any methyl carbon

On 11/6/13 10:55 AM, rankinb wrote: Hi all, I would like to calculate the number of water molecules around any of the methyl carbon atoms of tert-butyl alcohol. Currently, I have defined an index group containing all three of the methyl carbon atoms and used trjorder -nshell to calculate the

Re: [gmx-users] stopped simulation

On 11/6/13 12:53 PM, Ehsan Sadeghi wrote: Hi gmx users, I have simulated ionomer in water solution using gromos force field. But in middle of simulation(after 2 ns) the simulation stopped and I received these messages: WARNING: Listed nonbonded interaction between particles 174 and 188 at

Re: [gmx-users] Group protein not found in indexfile

On 11/6/13 1:52 PM, Steve Seibold wrote: Hello I am having trouble running a dimmer invacuo simulation. I can do energy minimization on it, but when I attempt to generate md.tpr file I get this weird message about “Group Protein not found in index”. I don’t see why I would need an index file.

Re: [gmx-users] stopped simulation

Many thanks Justin. What is an appropriate cut-off value? My box size is d= 0.5 nm; based on the definition of cut-off radius, its value shouble be smaller than d/2; therefore 0.24 is an appropriate cut-off value. Am I right? Cheers, Ehsan - Original Message - From: "Justin Lemkul" To:

Re: [gmx-users] stopped simulation

On 11/6/13 2:14 PM, Ehsan Sadeghi wrote: Many thanks Justin. What is an appropriate cut-off value? My box size is d= 0.5 nm; based on the definition of cut-off radius, its value shouble be smaller than d/2; therefore 0.24 is an appropriate cut-off value. Am I right? No. The cutoff value is

Re: [gmx-users] stopped simulation

What is this cut-off radius mentioned in the manual? The cut-off radius used to truncate non-bonded inter-actions may not exceed half the shortest box vector. Cheers, Ehsan - Original Message - From: "Justin Lemkul" To: "Discussion list for GROMACS users" Sent: Wednesday, November 6, 2

Re: [gmx-users] stopped simulation

On 11/6/13 2:27 PM, Ehsan Sadeghi wrote: What is this cut-off radius mentioned in the manual? The cut-off radius used to truncate non-bonded inter-actions may not exceed half the shortest box vector. It refers to the longest cutoff used to evaluate nonbonded interactions, whatever that may

Re: [gmx-users] Number of water molecules around any methyl carbon

Count the number of O observed near each C singly and compare the four numbers. Mark On Nov 6, 2013 4:57 PM, "rankinb" wrote: > Hi all, > > I would like to calculate the number of water molecules around any of the > methyl carbon atoms of tert-butyl alcohol. Currently, I have defined an > inde

[gmx-users] About g_potential

Dear Justin and all the colleagues, I am just trying to use g_potential to do the analysis of model. However, one thing puzzled me is about the slice number -sl. When different slice numbers are defined, the calculated potential is also different. I do not know the reason of that. Could you ple

Re: [gmx-users] Analysis tools and triclinic boxes

Hi, They ought to, and we hope they do, but historically quality control of analysis tools was threadbare, there is no testing of that kind of thing now, and certainly no implied warranty. Especially at the existing price point! ;-) That comment could easily refer to (or be) an archaic code versi

Re: [gmx-users] stopped simulation

On Wed, Nov 6, 2013 at 8:22 PM, Justin Lemkul wrote: > > > On 11/6/13 2:14 PM, Ehsan Sadeghi wrote: > >> Many thanks Justin. What is an appropriate cut-off value? My box size is >> d= >> 0.5 nm; based on the definition of cut-off radius, its value shouble be >> smaller than d/2; therefore 0.24 is

Re: [gmx-users] stopped simulation

On 11/6/13 4:52 PM, Mark Abraham wrote: On Wed, Nov 6, 2013 at 8:22 PM, Justin Lemkul wrote: On 11/6/13 2:14 PM, Ehsan Sadeghi wrote: Many thanks Justin. What is an appropriate cut-off value? My box size is d= 0.5 nm; based on the definition of cut-off radius, its value shouble be smalle

[gmx-users] Re: single point calculation with gromacs

Dear Justin, I am sorry for the late reply. I still can't figure it out. Could you please send me the mdp file which was used for your single point calculations. I want to do some comparison and then solve the problem. Thanks very much! All the best, Qinghua -- View this message in context:

Re: [gmx-users] Re: Gromacs-4.6 on two Titans GPUs

I've gone to conclusion that simulation with 1 or 2 GPU simultaneously gave me the same performance mdrun -ntmpi 2 -ntomp 6 -gpu_id 01 -v -deffnm md_CaM_test, mdrun -ntmpi 2 -ntomp 6 -gpu_id 0 -v -deffnm md_CaM_test, Doest it be due to the small CPU cores or addition RAM ( this system has 32 gb

[gmx-users] nose-hoover vs v-rescale in implicit solvent

Does it make more sense to use nose-hoover or v-rescale when running in implicit solvent GBSA? I understand that this might be a matter of opinion. Thanks, Gianluca - Gianluca Interlandi, PhD gianl...@u.washington.edu