[gmx-users] Fwd: Question on Gromacs: rlist, rvdw, rcoulomb

I am a user of gromacs. I am quite confused when I came across the relation of rlist and rvdw / rcoulomb in vdw and coulomb calculation. In cut-off, it says rvdw / rcoulomb should be greater than rlist, while in switch/shift, it says rvdw should be smaller than rlist... I guess in cut-off, it's

[gmx-users] re: extending the simulation

Hi, I extended by 3ns simulation by 2 more ns ... i.e total 5 ns but the .xtc file shows only the 3ns trajectories and after checking the md.log file , its showing that it completed those 2 ns steps also... then how can I get the trajectory for those 2ns ... I used the following commands for exten

Re: [gmx-users] crashed simulation: simulation of docked proteins in spc water crashes with LINCS warning

On 11/02/2011 3:47 PM, Sanjay Kumar Upadhyay wrote: Dear gmx-users I am experiencing some problems running a protein-protein docked structures in water(GROMOS43a1/SPC)with gmx-4.0.4 using 8 CPUs. I have 20 docked (protein-protein) structures of one common protein with two different homologous p

Re: [gmx-users] More than one settle type.

On 11/02/2011 2:50 PM, Sikandar Mashayak wrote: Hi I am performing SPC/E water simulation where I want to fix location of one water molecule and let others move. To do that I have defined two groups with name SOL0 and SOL, where SOL0 has just one water molecule and SOL grp contains all others

[gmx-users] crashed simulation: simulation of docked proteins in spc water crashes with LINCS warning

Dear gmx-users I am experiencing some problems running a protein-protein docked structures in water(GROMOS43a1/SPC)with gmx-4.0.4 using 8 CPUs. I have 20 docked (protein-protein) structures of one common protein with two different homologous protein, 10 from each group and started simulations fo

[gmx-users] More than one settle type.

Hi I am performing SPC/E water simulation where I want to fix location of one water molecule and let others move. To do that I have defined two groups with name SOL0 and SOL, where SOL0 has just one water molecule and SOL grp contains all others. In .mdp file I define freezegrps as SOL0 . When I d

[gmx-users] Problem with Gromacs Installation

Dear All, I installed gromacs-4.5.3 using cygwin on windows 7, following the instructions on http://www.gromacs.org/Downloads/Installation_Instructions/Cygwin_HOWTO. However, after installation, when I tried to run gromacs, I couldn't find the "share" folder in D:/cygwin/usr/local/gromacs. This

RE: [gmx-users] Dangling phospholipids

Or it could be a PBC issue, that sections of chain that appear to be dangling out into space actually enter the other side of the box. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 30

Re: [gmx-users] localpressure.dat file not created

ma...@physics.ucsb.edu wrote: On 10/02/2011 11:48 AM, ma...@physics.ucsb.edu wrote: I successfully ran version 4.5.3 to simulate a small DPPC bilayer patch using the files from Marrink's website by typing: /usr/bin/grompp -v -f mem.mdp -c mem.gro -p mem.top -o topol.tpr -maxwarn 100 mdrun I

Re: [gmx-users] localpressure.dat file not created

> On 10/02/2011 11:48 AM, ma...@physics.ucsb.edu wrote: >> I successfully ran version 4.5.3 to simulate a small DPPC bilayer patch >> using the files from Marrink's website by typing: >> >> /usr/bin/grompp -v -f mem.mdp -c mem.gro -p mem.top -o topol.tpr >> -maxwarn 100 >> >> mdrun >> >> In the .md

Re: [gmx-users] rotamers during minimization

abdullah ahmed wrote: Hello, I would like to know if gromacs is designed to try and keep as close to the original structure as much as possible? All motions are governed by the potential energy functions for bonded and nonbonded interactions. Gromacs is not biased towards keeping certain

[gmx-users] rotamers during minimization

Hello, I would like to know if gromacs is designed to try and keep as close to the original structure as much as possible? After minimizing a structure with phenyl-alanines I realized that a better minimization could be achieved if the rotamer had been changed during the minimization. However

Re: [gmx-users] ref_temp and gen_temp during simulated annealing

bipin singh wrote: Hello users, I have some doubt regarding the reference temperature(ref_temp)option during simulated annealing, i mean in the .mdp for simulated annealing what should be the correct ref_temp i.e. 0 K(starting temerature) or the target temperature(328K) and accordingly what

[gmx-users] ref_temp and gen_temp during simulated annealing

Hello users, I have some doubt regarding the reference temperature(ref_temp)option during simulated annealing, i mean in the .mdp for simulated annealing what should be the correct ref_temp i.e. 0 K(starting temerature) or the target temperature(328K) and accordingly what should be the value for ge

Re: [gmx-users] PRODRG

mohsen ramezanpour wrote: Dear Dr.Justin I have read this section before. There are 2 problem: 1:ADDHYD atomname and DELHYD atomname commands dosen't work! they result in ERROR in PRODRG You have to run PRODRG twice. The first time, you get the wrong output. Note the atom name that PROD

Re: [gmx-users] PRODRG

Dear Dr.Justin I have read this section before. There are 2 problem: 1:ADDHYD atomname and DELHYD atomname commands dosen't work! they result in ERROR in PRODRG 2:Actually I don't know the additional hydrogen is necessary or not! Because it may be necessary for proper protonation. My drug(Sertra

Re: [gmx-users] Re: server_for_Gaussian

You can benefit from the WebMO server. It will not run very "expensive" jobs but is a handy ! http://www.webmo.net/ Support for Gamess 1999+, Gaussian 94/98/03/09, MolPro 2002/2006/2009, Mopac 7/93/200X, NWChem 4/5, PQS 3.3, PSI 3+, QChem 2/3, and Tinker 4/5 On Thu, Feb 10, 2011 at 12:43 PM, Tho

Re: [gmx-users] WHAM with multiple force constants

On Feb 10, 2011, at 3:08 PM, jk...@ifr88.cnrs-mrs.fr wrote: Hi, I'm running an Umbrella Sampling analysis, with 1A steps in the reaction coordinate (distance) to estimate a PMF. However, owing to (high?) energetic barriers between my two proteins, some coordinates are not sampled. I inte

[gmx-users] WHAM with multiple force constants

Hi, I'm running an Umbrella Sampling analysis, with 1A steps in the reaction coordinate (distance) to estimate a PMF. However, owing to (high?) energetic barriers between my two proteins, some coordinates are not sampled. I intend to run simulations with stronger force constants to preven

Re: [gmx-users] Error: No such moleculetype Protein

Hi, I have worked around the problem. I was not including a .itp file. But now I am getting Segmentation Fault: Excluding 1 bonded neighbours for DSPC 104 Excluding 1 bonded neighbours for W 1397 Excluding 1 bonded neighbours for NA+ 0 Excluding 1 bonded neighbours for CL- 4 Number of fg atoms 4

Re: [gmx-users] Error: No such moleculetype Protein

Hi Tsjerk, Thanks for the reply. Yes, I had a reference to 'Protein' group in my .mdp file while running the CGMD. Now, after CG run I am trying to convert the CG to FG model using: g_fg2cg -pfg topol_fg.top -pcg system_cg.top -n 0 -c cg.gro -o fg.gro So do I need to supply any other parameter t

Re: [gmx-users] Error: No such moleculetype Protein

Hi Anirban, Probably you have a reference to a group 'Protein' in your .mdp file. Cheers, Tsjerk On Thu, Feb 10, 2011 at 12:01 PM, Anirban Ghosh wrote: > Hi, > I am trying to convert a CG system containing multiple copies of a protein + > lipid + water + ions to an all-atom system using the sp

[gmx-users] Re: server_for_Gaussian

Message: 2 Date: Thu, 10 Feb 2011 16:10:45 +0530 From: shahid nayeem Subject: [gmx-users] server_for_Gaussian To: Discussion list for GROMACS users Message-ID: Content-Type: text/plain; charset=ISO-8859-1 Dear All If any one is aware of a server on which one can upload job for runnin

Re: [gmx-users] server_for_Gaussian

shahid nayeem wrote: Dear All If any one is aware of a server on which one can upload job for running Gaussian, Please let me know. This I need to modify charges in the topology file created by ProDrg server. Gaussian is commercial software. Making is available freely to the public is pro

Re: [gmx-users] pull code

Poojari, Chetan wrote: Hi Justin, Thank you very much for your suggestions. I will use constraint force to force a peptide into a membrane with pulling for longer time. yes with "POSRES_LIPID" i am keeping the lipids rigid while pulling the peptide inside. Should the lipids be flexible wh

[gmx-users] Error: No such moleculetype Protein

Hi, I am trying to convert a CG system containing multiple copies of a protein + lipid + water + ions to an all-atom system using the special gromacs_reverse version command g_fg2cg. However I am getting the error: --

[gmx-users] server_for_Gaussian

Dear All If any one is aware of a server on which one can upload job for running Gaussian, Please let me know. This I need to modify charges in the topology file created by ProDrg server. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/g

RE: [gmx-users] pull code

Hi Justin, Thank you very much for your suggestions. I will use constraint force to force a peptide into a membrane with pulling for longer time. yes with "POSRES_LIPID" i am keeping the lipids rigid while pulling the peptide inside. Should the lipids be flexible while pulling?? I am usin