Re: [gmx-users] input/output error in production grompp

). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx

Re: [gmx-users] unknown residue (BGC)

. You will find numerous potential solutions. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

Re: [gmx-users] Errors in Minimization using grompp

cutoffs with finite values are almost never adequate for any purpose, however. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu

Re: [gmx-users] unknown residue (BGC)

, then the contents of the initial coordinate file matched the expectations of the force field and thus the topology and resulting structure are fine. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg

Re: [gmx-users] input/output error in production grompp

command. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

Re: [gmx-users] Errors in Minimization using grompp

-- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users

Re: [gmx-users] input/output error in production grompp

is still a complete mystery to me. -Justin On Wed, Jun 13, 2012 at 8:35 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: On 6/13/12 8:27 AM, Malai wrote: HI, Sorry for wrongly typing. The command I issued is: grompp -v -f hex1.mdp -c hex1.pdb

Re: [gmx-users] input/output error in production grompp

no sense at all to me. -Justin On Wed, Jun 13, 2012 at 9:14 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: On 6/13/12 9:11 AM, Malai wrote: Hello Justin, Thanks for reply. After getting this, I started to run production run but here i

Re: [gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation

systems on CPU are far more stable (energetically and structurally) than on GPU. I have never had any real luck on GPU. I get great performance, and then crashes ;) Maybe others can share their experiences. -Justin -- Justin A. Lemkul, Ph.D. Research

Re: [gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation

On 6/13/12 10:48 AM, ms wrote: On 13/06/12 16:36, Justin A. Lemkul wrote: Here, you're not preserving any of the previous state information. You're picking up from 2 ns, but not passing a .cpt file to grompp - the previous state is lost. Is that what you want? In conjunction with gen_vel

Re: [gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation

On 6/13/12 11:49 AM, ms wrote: On 13/06/12 16:59, Justin A. Lemkul wrote: On 6/13/12 10:48 AM, ms wrote: On 13/06/12 16:36, Justin A. Lemkul wrote: Here, you're not preserving any of the previous state information. You're picking up from 2 ns, but not passing a .cpt file to grompp

Re: [gmx-users] Error in production run

check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu

Re: [gmx-users] unable to access redmine

earlier, and apparently still is. I'm CC'ing this to Rossen in case he's not reading gmx-users. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http

Re: [gmx-users] Re: Dihedral Constraints

-tos/Dihedral_Restraints -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

Re: [gmx-users] simulated annealing mdp

-- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Re: Positive Potential Energy after equilibration

-- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] mdrun_mpi segmentation fault for run in vacuum

that the second command works while the first fails should lead to the opposite conclusion - your input is fine, but your invocation of mdrun was incorrect. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg

Re: [gmx-users] mdrun_mpi segmentation fault for run in vacuum

= steep emtol = 1000.0 emstep = 0.01 nsteps = 5 energygrps = system nstlist = 1 ns_type = simple rlist = 0 coulombtype = cutoff rcoulomb= 0 rvdw= 0 pbc = no -Justin -- Justin A. Lemkul, Ph.D

Re: [gmx-users] Press Equilibration

posts. Your pressure value is basically 4 ± 519. Is that significantly different from 1? No, likely not, but you can achieve a value of 1 or very close if you equilibrate for a sufficiently long time. -Justin -- Justin A. Lemkul, Ph.D. Research

Re: [gmx-users] g_rdf (lyzozyme tutorial)

, if there's a bug it should be fixed, but it may not be critical. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages

Re: [gmx-users] g_rdf (lyzozyme tutorial)

wrong with this gromacs version. That's why I asked which version you were using. This is a known bug that was introduced somewhere in the 4.0.x series, but was fixed in 4.0.7. Upgrade and the problem will be solved. -Justin -- Justin A. Lemkul, Ph.D

Re: [gmx-users] mdrun_mpi segmentation fault for run in vacuum

. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users

Re: [gmx-users] mdrun_mpi segmentation fault for run in vacuum

when using implicit solvent. There are a number of useful discussions in the list archive about such considerations; I would encourage you to spend some time reading before diving headfirst into something that may not turn out well. -Justin -- Justin

Re: [gmx-users] pdb2gmx error

-- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] simulated annealing mdp

are scaled linearly between the values listed in annealing_temp over the times set in annealing_time. The values set for ref_t are irrelevant, but one does need to set appropriate values for other temperature coupling parameters. -Justin -- Justin

Re: [gmx-users] Re: Positive Potential Energy after equilibration

not suitable or the simulation is not long enough. Make sure you're analyzing other observables to judge the quality of your model (RDF, H-bonding, density, etc). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech

Re: [gmx-users] mdrun_mpi segmentation fault for run in vacuum

tau-t = 0.1 ref-t = 300 Eva -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal

Re: [gmx-users] simulated annealing mdp

protocol.. Seems reasonable. Stating this up front in the original message would have saved some time. Otherwise, we make assumptions ;) -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA

Re: [gmx-users] mdrun_mpi segmentation fault for run in vacuum

nstxtcout = 0 nstlog = 0 nstcalcenergy = -1 nstenergy = 0 tcoupl = berendsen tc-grps = system tau-t = 0.1 ref-t = 300 Eva -Justin -- Justin A. Lemkul, Ph.D. Research

Re: [gmx-users] Hbonds and PBC

with periodicity. g_hbond only needs to measure simple distances and angles, which should be unaffected by PBC. Try it and see. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540

Re: [gmx-users] RE: Energy Minimization - not getting correct lipid area

a topology; outputting a coordinate file is more or less a side effect. Since we already have a topology for DPPC, and the coordinate file matches but simply needs to be in a different format, editconf is the easiest solution. -Justin -- Justin

Re: [gmx-users] Re: bond autocorrelation function

-- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx

Re: [gmx-users] problems occur during simulation

to address the problem at hand. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

Re: [gmx-users] Coordinate file for lipid bilayer

of lipids. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

Re: [gmx-users] radius of gyration

of a skeptical reviewer. Why not embed the protein in a membrane? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages

Re: [gmx-users] Rhamnose on 53a6

...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http

Re: [gmx-users] LINCS warnings

-- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] Positive Potential Energy after equilibration

-- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing

Re: [gmx-users] radius of gyration

don't use gnuplot so I can't offer you any advice as to how you can manipulate the way the data are displayed. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231

Re: [gmx-users] radius of gyration

graph for Rg versus simulation time which I am interested in? That's precisely what you will have. Look at the data labels in the .xvg file and you will see what each data set is. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department

Re: [gmx-users] radius of gyration

in the terminal. -Justin Regards D.M *From:* Justin A. Lemkul jalem...@vt.edu *To:* delara aghaie d_agh...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Monday, 11 June 2012, 17:46

Re: [gmx-users] Re: Fatal error: Atomtype O2 not found

will be nonsense. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

Re: [gmx-users] RE: Bonds and atom-pairs in g_hbond

-- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list

Re: [gmx-users] parameters for bond types for GROMOS force field.

. There are double bonds defined for lipids like POPC. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

Re: [gmx-users] Temperature in NVT file

-- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list

Re: [gmx-users] parameters for bond types for GROMOS force field.

, the atom order is irrelevant - if pdb2gmx finds the atoms it needs, it builds the topology. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http

Re: [gmx-users] Capping error in pdb2gmx

-- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users

Re: [gmx-users] Question about documentation of -a switch in g_hbond

angle is less than 35 degrees, you can vary between 0 and 35 easily to show the same thing as being within a certain range of being 180 degrees in terms of D-H-A. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia

Re: [gmx-users] Re : Capping error in pdb2gmx

database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul

Re: [gmx-users] Fatal error: Atomtype O2 not found

-EM-vacuum.tpr How did you produce the topology? Did you modify it in any way? As the error message states, O2 is not a valid atom type for CHARMM27. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech

Re: [gmx-users] Re: Fatal error: Atomtype O2 not found

atom types that don't exist. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

Re: [gmx-users] Re: Fatal error: Atomtype O2 not found

-- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] Re: Fatal error: Atomtype O2 not found

with a simple protein with canonical amino acids, changing an .rtp file (or anything else in the force field) is never required. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu

Re: [gmx-users] Re: Automated Topology Builder job partially completed

/Adding_a_Residue_to_a_Force_Field -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

Re: [gmx-users] Electrostatic interaction energy

and the best you can do is calculate short-range nonbonded energies between your chosen groups. Whether or not that is useful is something you must demonstrate. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia

Re: [gmx-users] parameters for bond types for GROMOS force field.

(peptide, 5-ring) 1000 -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

Re: [gmx-users] parameters for bond types for GROMOS force field.

bonds, the force constant is irrelevant since the bond is rigid. If not using constraints, then you'll have to find or derive suitable parameters yourself. Welcome to the inconvenient world of parameterization :) -Justin Thanks again, James 2012/6/8 Justin A. Lemkul jalem...@vt.edu

Re: [gmx-users] Energy Minimization - not getting correct lipid area

-- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users

Re: [gmx-users] Re: Energy Minimization - not getting correct lipid area

-- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx

Re: [gmx-users] RE: Energy Minimization - not getting correct lipid area

to keep the correct order). Further manual modifications are necessary based on how many lipids InflateGRO removes. -Justin Erica From: Justin A. Lemkul [via GROMACS] [ml-node+s5086n4998239...@n6.nabble.com] Sent: Friday, June 08, 2012 4:02 PM To: Hicks

Re: [gmx-users] RE: Energy Minimization - not getting correct lipid area

-- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] RE: Energy Minimization - not getting correct lipid area

in the topology file. H OK, I seem to remember 124 being what my system produced, but that's irrelevant. Check out the lines above. Erica From: Justin A. Lemkul [via GROMACS] [ml-node+s5086n4998244...@n6.nabble.com] Sent: Friday, June 08, 2012 5:21 PM To: Hicks

Re: [gmx-users] RE: Energy Minimization - not getting correct lipid area

thing I can think that has gone wrong. -Justin From: Justin A. Lemkul [via GROMACS] [ml-node+s5086n4998247...@n6.nabble.com] Sent: Friday, June 08, 2012 5:42 PM To: Hicks, Erica Subject: RE: Energy Minimization - not getting correct lipid area On 6/8/12 6:33 PM

Re: [gmx-users] GPU crashes

-behaved systems (even the benchmarks). For instance, the backbone RMSD of lysozyme is twice as large in the case of a 4.0-nm cutoff relative to the all-vs-all setup, and the energy drift is quite substantial. -Justin -- Justin A. Lemkul, Ph.D. Research

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

to 1LIG though coordinate and atom same in 1LIG of 1POPC, during solvation of system (Justin A. Lemkul) 2. Segmentation fault - pdb2gmx specbond.dat (Steven Neumann) 3. energy conservation: shift vs shifted user potential (Anja Kuhnhold) 4. Cannot get correct pressure

Re: [gmx-users] Regarding g_sham

-- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] How to set up constraint distcance pulling

-- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list

Re: [gmx-users] Regarding Free Energy calculation tutorial

. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users

Re: [gmx-users] How to set up constraint distcance pulling

On 6/7/12 9:14 AM, xiaowu759 wrote: Date: Thu, 07 Jun 2012 07:59:27 -0400 From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu Subject: Re: [gmx-users] How to set up constraint distcance pulling To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org

Re: [gmx-users] dssp doubt

/Errors Are there any suggestions or corrections? Thanks in advance.. Turgay -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages

Re: [gmx-users] About Umbrella sampling

-- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx

Re: [gmx-users] Atomtype OW_tip4p not found

On 6/7/12 6:18 PM, Amir Abbasi wrote: *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Wednesday, June 6, 2012 4:08 PM *Subject:* Re: [gmx-users

Re: [gmx-users] qmmm and real-life meaning of null lennard-jones parameters

be that you have to have some valid topology to start with. Perhaps someone else can comment on this methodological issue. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu

Re: [gmx-users] Trouble with packing lipids around a protein using InflateGRO

is not named confout.gro, it is name em.gro. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

Re: [gmx-users] Question regarding genion

of the -neutral option not working without specifying a concentration? I have also found that -neutral must always be used in conjunction with -conc. It would be nice if this were not the case. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist

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

list the moleculetype names in that order in [molecules]. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal

Re: [gmx-users] Atomtype OW_tip4p not found

atom type exists in Amber99SB, so I don't know the origin of the error. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu

Re: [gmx-users] Atomtype OW_tip4p not found

On 6/6/12 7:36 AM, Amir Abbasi wrote: *From:* Justin A. Lemkul jalem...@vt.edu *To:* Amir Abbasi amir.abbas...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Wednesday, June 6, 2012 3

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

lipids? If it did, that is not reflected correctly in the topology. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages

Re: [gmx-users] Cannot get correct pressure value with MTTK pressure coupling

-- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users

[gmx-users] GPU crashes

implicit_solvent= GBSA gb_algorithm= OBC rgbradii= 0 -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal

Re: [gmx-users] trajectory analysis

you read there. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

Re: [gmx-users] Trajectories

-frame .pdb or .gro file would work, but I believe that .xtc and .trr files have to have the same number of atoms in each frame to be interpreted correctly. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech

Re: [gmx-users] Selecting atom indices of residues whose centers of mass match a position range

-- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] How to add DMSO as solvent?

-- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group error during minimization with TPO residue

discussed issues with the format. I also added the ions.itp, spce.itp, and ff_dum.itp to the directory. However, after inputting the same commands and using the single TPO residue, I received the same error. Alex Cumberworth -- Justin A. Lemkul, Ph.D. Research

Re: [gmx-users] Re: dangling bond at at one of the terminal ends

into something useful for your system. How do the .rtp entries compare to the contents of your coordinate file? Is the absence of phosphate relevant? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech

Re: [gmx-users] Water molecules cannot be settled, why?

be found at http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http

Re: [gmx-users] Writing and compiling new analyses for gromacs

on how to approach it? Write good code? ;) I don't really know what you're asking here, but if you want pointers for writing code, you'll need to at least state what you're doing. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department

Re: [gmx-users] Writing and compiling new analyses for gromacs

On 6/4/12 5:16 PM, Shay Teaching wrote: 2012/6/4 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu On 6/4/12 2:59 PM, Shay Teaching wrote: Dear Gromacs users, I want to write new analyses for gromacs and compile it (so I'll have g_whatever) as part

Re: [gmx-users] Atomtype 1

newlines? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

Re: [gmx-users] Atomtype 1

=eWlkPXpoYW94aWl0YzIwMDI-sig=703fa929658518b2720b087c59cd85f2dabf8844 --- *12年6月3日，周日, Justin A. Lemkul /jalem...@vt.edu/* 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] Atomtype 1 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2012年6月3日,周日,下午8:46

Re: [gmx-users] Atomtype 1

=703fa929658518b2720b087c59cd85f2dabf8844 --- *12年6月3日，周日, Justin A. Lemkul /jalem...@vt.edu/* 写道： 发件人: Justin A. Lemkul jalem...@vt.edu 主题: Re: [gmx-users] Atomtype 1 收件人: Discussion list for GROMACS users gmx-users@gromacs.org 日期: 2012年6月3日,周日,下午9:19 On 6/3/12 9:16 AM, xi

Re: [gmx-users] Re: dangling bond at at one of the terminal ends

present and named as the force field expects them to be. You can't have anything missing or anything extra. Also, copying and pasting error messages directly from the terminal is vastly more helpful than a description. -Justin -- Justin A. Lemkul, Ph.D

Re: [gmx-users] About extend the run,,

, as will reading mdrun -h for an explanation of what the -cpt option is doing. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages

Re: [gmx-users] About extend the run,,

On 6/2/12 11:23 AM, rama david wrote: Thank you Justin for quick reply On Sat, Jun 2, 2012 at 8:12 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: To perform these task I am using following command 1. grompp -f New mdp file just change in saving

Re: [gmx-users] how to run production MD for only a fragment of protein

-- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] umbrella windows...

. You'll be covering extra space that winds up just wasting time. The PMF will level off long before the 5.0 nm of COM separation, which in itself is overkill. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech

Re: [gmx-users] Incomplete frame

to be written. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

Re: [gmx-users] Incomplete frame

filesystem is unstable. It's hard to say exactly why. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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