Re: [gmx-users] Holes in the solvent!
Dear Chris, Thank you for your directions. NaCl concentration in my system is 0.14 M and I often visualize the whole system and can see the ions around the system but not in crystal form! Well, it sounds really strange to me! And I don't know if I proceed with such a system, I get scientific results or not?! I appreciate your further helps. Best Regards Arman On Tue, Oct 30, 2012 at 4:39 AM, Christopher Neale < chris.ne...@mail.utoronto.ca> wrote: > In addition to the comments of Dallas Warren, which seems quite possible > and should be checked, > are you sure that you are seeing real holes and not just salt crystals > that look like holes when you render only > the waters with VMD? I have found that, at NaCL concentrations above 1 M, > lipid bilayers catalyze the formation > of salt crystals when using TIP3P/4P water and the OPLS/AA-L force field > for ions. These crystals looked a lot > like vacuum holes to me until I visualized the salt. > > Chris. > > -- original message -- > > I am simulating a protein on a polymer surface for further adsorption free > energy calculation. > However, after performing the NVT run either for short or long durations I > found out that couple of holes appear in the physiological saline solution > (solvent)!!! > Additionally, even proceeding with a long NPT run the holes are still > present in the system. > I would be thankful if you could direct me what could be source of such a > strange outcome. > > Best Wishes > > Arman > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] hessian conversion
Hi Gmxers, has anyone ever converted the GROMACS hessian (in ps^(-2)) to CHARMM hessian (in KCal/mol), even considering the individual unit, GROMACS hessian numbers are far bigger than those in CHARMM? thanks, Yao -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Holes in the solvent!
In addition to the comments of Dallas Warren, which seems quite possible and should be checked, are you sure that you are seeing real holes and not just salt crystals that look like holes when you render only the waters with VMD? I have found that, at NaCL concentrations above 1 M, lipid bilayers catalyze the formation of salt crystals when using TIP3P/4P water and the OPLS/AA-L force field for ions. These crystals looked a lot like vacuum holes to me until I visualized the salt. Chris. -- original message -- I am simulating a protein on a polymer surface for further adsorption free energy calculation. However, after performing the NVT run either for short or long durations I found out that couple of holes appear in the physiological saline solution (solvent)!!! Additionally, even proceeding with a long NPT run the holes are still present in the system. I would be thankful if you could direct me what could be source of such a strange outcome. Best Wishes Arman -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] time-block analysis
Dear Leila:
I presume that "time-block analysis" is the same as block averaging, but it is
impossible to be sure without more
context. I suggest that you find the person who suggested that you do
"time-block analysis" and ask them.
Very generally, you will need to do your own scripting to do block averaging.
Look at Allen and Tildesley for
a good description of block averaging or look at the original (as far as I
know) reference:
Flyvbjerg, H.; Petersen, H. G., Error estimates on averages of correlated data.
J. Chem. Phys. 1989, 91 (1), 461-466
Basically, you will need to take your raw data and make block averages. Here is
a very simple script to
do that for a 2-column data file that has time in the first column and some
other data in the second column
MIN=0
MAX=1000
BLOCK=100
for ((min=MIN; min+=BLOCK; min='${min}'&&$1<'${max}'){s+=$2;n++}}END{print
('${max}'-'${min}')/2,s/n}'
done > my.block.averaged.data
I am sure that there are more elegant awk scripts that can do this, but the
intention here was to show how it is
done most clearly.
Chris.
-- original message --
Can I do time-block analysis by gromacs? If so, which command?
Is time-block analysis the same as block averaging?
Any help will highly appreciated.
--
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[gmx-users] g_density
Dear Ali:
I assure you that all relevant information has been provided. As I said, it's
not simple. If it is beyond your
abilities then perhaps you should find a local collaborator. These days, many
computational consortia have
computational specialists who can help you with your scripting and coding. I'm
not going to do it for you and
I think that we have reached the end of our useful discussion on this topic.
Chris.
-- original message --
Dear Chris
I saw two your email :
static void center_x(int ecenter,rvec x[],matrix box,int n,int nc,atom_id ci[])
{
int i,m,ai;
rvec cmin,cmax,box_center,dx;
if (nc > 0) {
copy_rvec(x[ci[0]],cmin);
copy_rvec(x[ci[0]],cmax);
for(i=0; i cmax[m])
cmax[m]=x[ai][m];
}
}
calc_box_center(ecenter,box,box_center);
for(m=0; mhttp://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] Error during CNP simulation
Sorry Bharath, I simply can not believe that a macromolecule drifted 3 nm during energy minimization. What happened to the intervening solvent? I think that you have some problem with your technique here. Why did you use 120 constraints? Is this for bonds within the CNP? You need to do 2 things: a) figure out what is going wrong with your EM... what you describe seems impossible to me. b) simplify your system to debug the problem. So you get the same warnings about too many constraints if you omit the position restraints? Chris. -- original message -- You're right, my resizing from 7.5 nm to 15 nm refers to the dimension normal to the lipid bilayer (in this case, the x dimension) My bilayer center of mass is at around +3 nm, and I placed the CNP at around 10 nm to start with. I had periodic boundary conditions employed in all three dimensions. I didn't add the CNP using genbox or any other command- I manually manipulated the .gro coordinate file of the bilayer. When I ran an energy minimization of just the bilayer and the CNP, the nanoparticle moved, but very slightly- so far, so good. But, once I added water and did another energy minimization and checked the structure after convergence, the nanoparticle had drifted all the way up to around 0 nm, which meant it was only around 1 nm away from my bilayer before the MD run. So, yes, it drifted during the energy minimization. I should probably try what you said. I repeated the entire above process using a posre.itp file. I had created this posre.itp file using the the lipids in the bilayer, and the CNP atoms, and I used this file during the energy minimization after adding water, which is when i got the following error- "A charge group moved too far between two domain decomposition steps.". I also got a warning before the fatal EM, which said that the number of constraints I had imposed on the CNP (120) is greater than the number of possible degrees of freedom (48), which could cause the system to be unstable. I wasn't sure how to fix that, though. I'm sorry if I'm a bit vague, but I'd appreciate if you could advice me more on this issue. Thanks! Bharath -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] NVT input file
On 10/29/12 2:52 PM, Davoud Zare wrote: Dear Gromacs users, Does anyone know how to change the NVT input file for Justin tutorial (lysozymein a box of water), so that the temperature is slowly increased from 50K to 300K?, any general advise or modification of input file is highly appreciated. Read about simulated annealing in the manual and consult the following: http://manual.gromacs.org/online/mdp_opt.html#sa -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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] NVT input file
Dear Gromacs users, Does anyone know how to change the NVT input file for Justin tutorial (lysozymein a box of water), so that the temperature is slowly increased from 50K to 300K?, any general advise or modification of input file is highly appreciated. Cheers Davoud -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] NVT input file
Dear Gromacs users, Does anyone know how to change the NVT input file for Justin tutorial (lysozymein a box of water), so that the temperature is slowly increased from 50K to 300K? the nvt of the tutorial is attached, any general advise or modification of input file is highly appreciated. Cheers Davoud title = OPLS Lysozyme NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 300 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Angle between two six membered rings
Hello all, I was trying to calculate the normal-normal angle between the two six membered rings using g_sgangle. I was considering the 3 atoms to define the plane for each six membered ring but I am not getting the correct values of normal-normal angle from g_sgangle in this way. Please suggest me the correct way to calculate it in gromacs . -- --- Thanks and Regards, Bipin Singh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] About Keepbyz script for Deleting sol Molecules
On 10/29/12 12:54 PM, vidhya sankar wrote: Dear justin Thank you For your Previous reply, I am deleting The Water Molecules using keepbyz script as mailed me I want to keep waters around the head groups of my lipid, so How to Choose wisely upperz and lowerz values to my system ? These are the upper and lower bounds of the membrane; generally one would choose some representative atom of the headgroup, like phosphorus. It's not an exact science. -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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] version 4.5.5 GPU with gtx670 and cuda 4.2
I heard rumors of a new GMX version months ago, and was told it was nearly ready, but since have not heard anything. So I don't know what the status is. It is becoming a problem as most of the GPUs supported are discontinued by NVIDIA and so you can't buy them anymore. At least in terms of the Geforce series of cards, not sure about the Tesla's, but those come with a much different price tag. Best, Jesper On Oct 29, 2012, at 10:03 AM, sebastian wrote: > Hi Jesper, > > thanks for the answer. > It does not matter which card I choose. > I was hopping that forcing the device does work but it does not seem to > be the case. > Probably I have to wait for an update or the 4.6 version. > > All the best, > > Sebastian > > On 10/29/2012 05:50 PM, Jesper Sørensen wrote: >> Hi Sebastian, >> >> This may just be my take, but the Keppler Cards are not supported yet as far >> as I understand it. >> They are at least not mentioned on the GROMACS GPU page in the Supported >> Cards section - granted that page has not been updated in quite a while. >> >> Specifically, does this work when you specify using the first card? >> >> Best, >> Jesper >> >> On Oct 29, 2012, at 7:03 AM, sebastian >> wrote: >> >> >>> Hey all together, >>> >>> I try to run the 4.5.5 gpu version with the NVIDIA gtx670 cards. >>> >>> Using: >>> >>> mdrun-gpu -v -s bla.tpr -device >>> "OpenMM:platform=Cuda,memtest=15,deviceid=1,force-device=yes" >>> >>> (diveceid=1 since I have two cards and want to use the second card). >>> I get the following error: >>> >>> OpenMM exception caught while initializating: cudaMemcpyToSymbol: SetSim >>> copy to cSim failed invalid device symbol >>> >>> The installed cuda version is 4.2 and the OpenMM version is 4.1.1 >>> >>> Since I have no idea whats going wrong any help is very welcomed >>> >>> Thanks a lot >>> >>> Sebastian >>> -- >>> gmx-users mailing listgmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> * Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Fwd: Re: [gmx-users] version 4.5.5 GPU with gtx670 and cuda 4.2
Original Message Subject:Re: [gmx-users] version 4.5.5 GPU with gtx670 and cuda 4.2 Date: Mon, 29 Oct 2012 18:03:12 +0100 From: sebastian To: Jesper Sørensen Hi Jesper, thanks for the answer. It does not matter which card I choose. I was hopping that forcing the device does work but it does not seem to be the case. Probably I have to wait for an update or the 4.6 version. All the best, Sebastian On 10/29/2012 05:50 PM, Jesper Sørensen wrote: > Hi Sebastian, > > This may just be my take, but the Keppler Cards are not supported yet as far > as I understand it. > They are at least not mentioned on the GROMACS GPU page in the Supported > Cards section - granted that page has not been updated in quite a while. > > Specifically, does this work when you specify using the first card? > > Best, > Jesper > > On Oct 29, 2012, at 7:03 AM, sebastian > wrote: > > >> Hey all together, >> >> I try to run the 4.5.5 gpu version with the NVIDIA gtx670 cards. >> >> Using: >> >> mdrun-gpu -v -s bla.tpr -device >> "OpenMM:platform=Cuda,memtest=15,deviceid=1,force-device=yes" >> >> (diveceid=1 since I have two cards and want to use the second card). >> I get the following error: >> >> OpenMM exception caught while initializating: cudaMemcpyToSymbol: SetSim >> copy to cSim failed invalid device symbol >> >> The installed cuda version is 4.2 and the OpenMM version is 4.1.1 >> >> Since I have no idea whats going wrong any help is very welcomed >> >> Thanks a lot >> >> Sebastian >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] version 4.5.5 GPU with gtx670 and cuda 4.2
Hi Sebastian, This may just be my take, but the Keppler Cards are not supported yet as far as I understand it. They are at least not mentioned on the GROMACS GPU page in the Supported Cards section - granted that page has not been updated in quite a while. Specifically, does this work when you specify using the first card? Best, Jesper On Oct 29, 2012, at 7:03 AM, sebastian wrote: > Hey all together, > > I try to run the 4.5.5 gpu version with the NVIDIA gtx670 cards. > > Using: > > mdrun-gpu -v -s bla.tpr -device > "OpenMM:platform=Cuda,memtest=15,deviceid=1,force-device=yes" > > (diveceid=1 since I have two cards and want to use the second card). > I get the following error: > > OpenMM exception caught while initializating: cudaMemcpyToSymbol: SetSim > copy to cSim failed invalid device symbol > > The installed cuda version is 4.2 and the OpenMM version is 4.1.1 > > Since I have no idea whats going wrong any help is very welcomed > > Thanks a lot > > Sebastian > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] About Keepbyz script for Deleting sol Molecules
Dear justin Thank you For your Previous reply, I am deleting The Water Molecules using keepbyz script as mailed me I want to keep waters around the head groups of my lipid, so How to Choose wisely upperz and lowerz values to my system ? Thanks in Advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] too much warnings and notes
Hi, On Oct 29, 2012, at 3:57 PM, Albert wrote: > On 10/29/2012 03:56 PM, Carsten Kutzner wrote: >> Hi, >> >> find the reason for the warnings in your mdp file settings >> and adjust them accordingly. >> >> You can also override the warnings with the -maxwarn >> option in grompp. >> >> Carsten > Hello Carsten: > > thanks for kind reply. > > the only thing I confused is the last one: > > NOTE 4 [file md.mdp]: > The sum of the two largest charge group radii (0.597592) is larger than > rlist (1.00) - rvdw (1.20) this is explained here: http://www.gromacs.org/Documentation/Errors http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb Carsten > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] too much warnings and notes
On 10/29/12 10:57 AM, Albert wrote: On 10/29/2012 03:56 PM, Carsten Kutzner wrote: Hi, find the reason for the warnings in your mdp file settings and adjust them accordingly. You can also override the warnings with the -maxwarn option in grompp. Carsten Hello Carsten: thanks for kind reply. the only thing I confused is the last one: NOTE 4 [file md.mdp]: The sum of the two largest charge group radii (0.597592) is larger than rlist (1.00) - rvdw (1.20) It is related to Note 3, which indicates you have a very large charge group. You will have artifacts related to neighbor searching (and potentially poor energy conservation) if you use such large groups. There is discussion on this note on the Gromacs website and in the list archive. I post the link to the Errors page daily, so surely you can find it :) -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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] too much warnings and notes
On 10/29/2012 03:56 PM, Carsten Kutzner wrote: Hi, find the reason for the warnings in your mdp file settings and adjust them accordingly. You can also override the warnings with the -maxwarn option in grompp. Carsten Hello Carsten: thanks for kind reply. the only thing I confused is the last one: NOTE 4 [file md.mdp]: The sum of the two largest charge group radii (0.597592) is larger than rlist (1.00) - rvdw (1.20) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] too much warnings and notes
Hi, find the reason for the warnings in your mdp file settings and adjust them accordingly. You can also override the warnings with the -maxwarn option in grompp. Carsten On Oct 29, 2012, at 3:52 PM, Albert wrote: > hello: > > I am generating a .tpr file for proten/ligand system, but it has so much > warnings: > > > NOTE 1 [file md.mdp]: > nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting > nstcomm to nstcalcenergy > > > NOTE 2 [file md.mdp]: > leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 > > Generated 23436 of the 23436 non-bonded parameter combinations > Generating 1-4 interactions: fudge = 1 > Generated 20254 of the 23436 1-4 parameter combinations > Excluding 3 bonded neighbours molecule type 'Protein' > turning all bonds into constraints... > Excluding 3 bonded neighbours molecule type 'LIG' > turning all bonds into constraints... > Excluding 3 bonded neighbours molecule type 'POPC' > turning all bonds into constraints... > Excluding 2 bonded neighbours molecule type 'SOL' > turning all bonds into constraints... > Excluding 1 bonded neighbours molecule type 'NA' > turning all bonds into constraints... > Excluding 1 bonded neighbours molecule type 'CL' > turning all bonds into constraints... > Setting gen_seed to 6947582 > Velocities were taken from a Maxwell distribution at 300 K > > NOTE 3 [file complex.top]: > The largest charge group contains 12 atoms. > Since atoms only see each other when the centers of geometry of the charge > groups they belong to are within the cut-off distance, too large charge > groups can lead to serious cut-off artifacts. > For efficiency and accuracy, charge group should consist of a few atoms. > For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. > > Number of degrees of freedom in T-Coupling group Protein_LIG is 9475.34 > Number of degrees of freedom in T-Coupling group POPC is 33353.66 > Number of degrees of freedom in T-Coupling group Water_and_ions is 53973.00 > Largest charge group radii for Van der Waals: 0.299, 0.299 nm > Largest charge group radii for Coulomb: 0.299, 0.299 nm > > NOTE 4 [file md.mdp]: > The sum of the two largest charge group radii (0.597592) is larger than > rlist (1.00) - rvdw (1.20) > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] too much warnings and notes
hello: I am generating a .tpr file for proten/ligand system, but it has so much warnings: NOTE 1 [file md.mdp]: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file md.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 23436 of the 23436 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 20254 of the 23436 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'LIG' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'POPC' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'NA' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'CL' turning all bonds into constraints... Setting gen_seed to 6947582 Velocities were taken from a Maxwell distribution at 300 K NOTE 3 [file complex.top]: The largest charge group contains 12 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. Number of degrees of freedom in T-Coupling group Protein_LIG is 9475.34 Number of degrees of freedom in T-Coupling group POPC is 33353.66 Number of degrees of freedom in T-Coupling group Water_and_ions is 53973.00 Largest charge group radii for Van der Waals: 0.299, 0.299 nm Largest charge group radii for Coulomb: 0.299, 0.299 nm NOTE 4 [file md.mdp]: The sum of the two largest charge group radii (0.597592) is larger than rlist (1.00) - rvdw (1.20) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Holes in the solvent!
On Mon, Oct 29, 2012 at 2:38 PM, Arman Mahboubi Soufiani wrote: > Dear Friends, > > Thank you for your kind and informative responses. As Dr. Chaban noted, I > checked the density and it was roughly 880 gr.cm-3 which seems low! Dear Arman - You did not mention the experimental density of your system. Whereas we expect saline solution to exhibit the density of > 1000 kg/m3, we have no idea about your polymer composition and spatial structure. Dr. Vitaly V. Chaban MEMPHYS - Center for Biomembrane Physics Department of Physics, Chemistry and Pharmacy University of Southern Denmark Campusvej 55, 5230 Odense M, Denmark > > I greatly appreciate your further helps. > > Best Wishes > > Arman > > On Mon, Oct 29, 2012 at 1:20 PM, Dr. Vitaly Chaban > wrote: >> >> >> On 10/26/12 3:25 PM, Arman M. Soufiani wrote: >> >> > Dear Gromacs users, >> >> > >> >> > I am simulating a protein on a polymer surface for further adsorption >> >> free >> >> > energy calculation. >> >> > However, after performing the NVT run either for short or long >> >> durations I >> >> > found out that couple of holes appear in the physiological saline >> >> solution >> >> > (solvent)!!! >> >> > Additionally, even proceeding with a long NPT run the holes are still >> >> > present in the system. >> >> > I would be thankful if you could direct me what could be source of >> >> such a >> >> > strange outcome. >> >> > >> >> >> >> That sounds very odd, but perhaps your unit cell is not sufficiently >> >> solvated to >> >> start with. If you have voids, you may have available volume. >> >> >> >> -Justin >> >> >> You must compare the simulated density with the experimental density. >> >> There is no other way to conclude if your holes are genuine or not in >> this kind of matter. >> >> >> Dr. Vitaly V. Chaban >> MEMPHYS - Center for Biomembrane Physics >> Department of Physics, Chemistry and Pharmacy >> University of Southern Denmark >> Campusvej 55, 5230 Odense M, Denmark >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] About Box vector and solvation
On 10/29/12 9:59 AM, vidhya sankar wrote: Dear Justin Thank you For you Previous reply. When I use inflate script There is Automatic Change in the box Vector At the End line of .gro file (output of inflate script) Then I have Done EM without Changing the Box Vector in the output of inflate script. in the screen i Have Observed the Following Discrepancy As follows . Step=2, Dmax= 1.2e-02 nm, Epot= -7.91260e+04 Fmax= 2.30915e+03, atom= 6104 Step=4, Dmax= 7.2e-03 nm, Epot= -7.93164e+04 Fmax= 7.83650e+03, atom= 85 Step=7, Dmax= 1.2e-02 nm, Epot= -8.08972e+04 Fmax= 7.87323e+03, atom= 85 Step=9, Dmax= 7.5e-03 nm, Epot= -8.11951e+04 Fmax= 3.15522e+03, atom= 85 It quits Step 3 ,4 and step 8 ( When i open em.log files Energy Corresponding to 3 and 4 As follows) Step Time Lambda Step Time Lambda Step Time Lambda 88.00.0 3 3.00.0 44.00.0 What it shows ? How to rectify this Problem ( I have used .mdp file in your Website) There is nothing to do. These steps corresponded to no change in energy. It happens sometimes with EM. Can i change the box Vector in .gro file of EM output ( I cannot change Box vector in System_inflated .gro As you Told me) Never manually change a box vector. Why would you do this? Do you understand what InflateGRO is doing and why you shouldn't be making ad hoc changes? Let the script do the work for you. -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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] .gro file problem
On 10/29/12 9:59 AM, Albert wrote: On 10/28/2012 09:06 PM, Justin Lemkul wrote: Visual inspection with a text editor should tell you what's wrong. Either the file is incomplete (i.e. header or box vectors missing) or the coordinates are large (indicating the system became unstable at some point). The fact that VMD loads the file suggests that the latter may be true. An incomplete file would not load, but one with screwy coordinates still would. -Justin -- Hello Justin: thanks a lot for kind advices. I check the file with gedit and I didn't find anything unusual within the text comparing with the original .gro file. They have the exact the same row and columns. Generated by trjconv : MOR t= 116.00 Generated by trjconv : MOR t= 116.0 You shouldn't have two separate title lines. I don't know how trjconv would have produced garbled output like this, but I suspect it's the cause of your problems. -Justin 48328 65MET N1 4.934 1.182 7.535 0.0471 0.2110 0.3278 65METHT12 4.975 1.148 7.620 -2.1539 -2.5438 0.4303 65METHT23 4.879 1.108 7.497 0.2031 0.2641 -0.0060 65MET CA4 5.035 1.229 7.441 -0.1568 -0.5819 -0.2954 65MET HA5 5.090 1.312 7.481 2.2845 -1.6076 -1.3193 65MET CB6 5.149 1.126 7.437 0.4809 0.1027 0.0700 65METHB17 5.166 1.099 7.544 -2.2162 1.7701 1.0201 65METHB28 5.117 1.032 7.386 -3.2381 0.4514 1.4551 65MET CG9 5.283 1.173 7.379 0.1733 0.3849 -0.4145 65METHG1 10 5.340 1.078 7.384 0.4424 0.6052 2.0263 . . . 9511CL CL48320 2.101 1.980 2.259 0.0337 -0.1667 0.2316 9512CL CL48321 4.165 3.237 10.196 -0.4009 0.1697 0.4481 9513CL CL48322 5.414 4.564 9.686 -0.1624 -0.0698 -0.2503 9514CL CL48323 2.032 1.126 1.460 0.0876 -0.4133 -0.1336 9515CL CL48324 3.278 3.994 9.006 0.1073 -0.1139 0.6701 9516CL CL48325 1.793 3.569 9.888 0.0911 0.2208 -0.0272 9517CL CL48326 1.046 2.735 1.322 0.1044 0.2204 0.4059 9518CL CL48327 3.384 4.016 1.983 0.0078 0.1266 -0.1903 9519CL CL48328 0.044 3.730 0.932 -0.2059 0.0577 0.3350 6.69862 6.69862 10.42296 thank you very much -- 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://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] version 4.5.5 GPU with gtx670 and cuda 4.2
Hey all together, I try to run the 4.5.5 gpu version with the NVIDIA gtx670 cards. Using: mdrun-gpu -v -s bla.tpr -device "OpenMM:platform=Cuda,memtest=15,deviceid=1,force-device=yes" (diveceid=1 since I have two cards and want to use the second card). I get the following error: OpenMM exception caught while initializating: cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol The installed cuda version is 4.2 and the OpenMM version is 4.1.1 Since I have no idea whats going wrong any help is very welcomed Thanks a lot Sebastian -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] About Box vector and solvation
Dear Justin Thank you For you Previous reply. When I use inflate script There is Automatic Change in the box Vector At the End line of .gro file (output of inflate script) Then I have Done EM without Changing the Box Vector in the output of inflate script. in the screen i Have Observed the Following Discrepancy As follows . Step= 2, Dmax= 1.2e-02 nm, Epot= -7.91260e+04 Fmax= 2.30915e+03, atom= 6104 Step= 4, Dmax= 7.2e-03 nm, Epot= -7.93164e+04 Fmax= 7.83650e+03, atom= 85 Step= 7, Dmax= 1.2e-02 nm, Epot= -8.08972e+04 Fmax= 7.87323e+03, atom= 85 Step= 9, Dmax= 7.5e-03 nm, Epot= -8.11951e+04 Fmax= 3.15522e+03, atom= 85 It quits Step 3 ,4 and step 8 ( When i open em.log files Energy Corresponding to 3 and 4 As follows) Step Time Lambda Step Time Lambda Step Time Lambda 8 8.0 0.0 3 3.0 0.0 4 4.0 0.0 What it shows ? How to rectify this Problem ( I have used .mdp file in your Website) Can i change the box Vector in .gro file of EM output ( I cannot change Box vector in System_inflated .gro As you Told me) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] .gro file problem
On 10/28/2012 09:06 PM, Justin Lemkul wrote: Visual inspection with a text editor should tell you what's wrong. Either the file is incomplete (i.e. header or box vectors missing) or the coordinates are large (indicating the system became unstable at some point). The fact that VMD loads the file suggests that the latter may be true. An incomplete file would not load, but one with screwy coordinates still would. -Justin -- Hello Justin: thanks a lot for kind advices. I check the file with gedit and I didn't find anything unusual within the text comparing with the original .gro file. They have the exact the same row and columns. Generated by trjconv : MOR t= 116.00 Generated by trjconv : MOR t= 116.0 48328 65MET N1 4.934 1.182 7.535 0.0471 0.2110 0.3278 65METHT12 4.975 1.148 7.620 -2.1539 -2.5438 0.4303 65METHT23 4.879 1.108 7.497 0.2031 0.2641 -0.0060 65MET CA4 5.035 1.229 7.441 -0.1568 -0.5819 -0.2954 65MET HA5 5.090 1.312 7.481 2.2845 -1.6076 -1.3193 65MET CB6 5.149 1.126 7.437 0.4809 0.1027 0.0700 65METHB17 5.166 1.099 7.544 -2.2162 1.7701 1.0201 65METHB28 5.117 1.032 7.386 -3.2381 0.4514 1.4551 65MET CG9 5.283 1.173 7.379 0.1733 0.3849 -0.4145 65METHG1 10 5.340 1.078 7.384 0.4424 0.6052 2.0263 . . . 9511CL CL48320 2.101 1.980 2.259 0.0337 -0.1667 0.2316 9512CL CL48321 4.165 3.237 10.196 -0.4009 0.1697 0.4481 9513CL CL48322 5.414 4.564 9.686 -0.1624 -0.0698 -0.2503 9514CL CL48323 2.032 1.126 1.460 0.0876 -0.4133 -0.1336 9515CL CL48324 3.278 3.994 9.006 0.1073 -0.1139 0.6701 9516CL CL48325 1.793 3.569 9.888 0.0911 0.2208 -0.0272 9517CL CL48326 1.046 2.735 1.322 0.1044 0.2204 0.4059 9518CL CL48327 3.384 4.016 1.983 0.0078 0.1266 -0.1903 9519CL CL48328 0.044 3.730 0.932 -0.2059 0.0577 0.3350 6.69862 6.69862 10.42296 thank you very much -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Holes in the solvent!
On 10/29/12 9:38 AM, Arman Mahboubi Soufiani wrote: Dear Friends, Thank you for your kind and informative responses. As Dr. Chaban noted, I checked the density and it was roughly 880 gr.cm-3 which seems low! I greatly appreciate your further helps. Most water models underestimate water density, so that is likely a contributing factor. You haven't told us much about your setup, so it's hard to guess what you should be expecting. You also haven't said how large your polymer is in relation to the size of the box, so that could affect the outcome, as well. A picture showing these "holes" would also be useful, as they very well could be a PBC effect and thus totally normal. From your description, I was assuming the holes were within the solvent, but if they are at the box "edges" then likely what you are seeing is normal. -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 mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Holes in the solvent!
Dear Friends, Thank you for your kind and informative responses. As Dr. Chaban noted, I checked the density and it was roughly 880 gr.cm-3 which seems low! I greatly appreciate your further helps. Best Wishes Arman On Mon, Oct 29, 2012 at 1:20 PM, Dr. Vitaly Chaban wrote: > >> On 10/26/12 3:25 PM, Arman M. Soufiani wrote: > >> > Dear Gromacs users, > >> > > >> > I am simulating a protein on a polymer surface for further adsorption > >> free > >> > energy calculation. > >> > However, after performing the NVT run either for short or long > >> durations I > >> > found out that couple of holes appear in the physiological saline > >> solution > >> > (solvent)!!! > >> > Additionally, even proceeding with a long NPT run the holes are still > >> > present in the system. > >> > I would be thankful if you could direct me what could be source of > >> such a > >> > strange outcome. > >> > > >> > >> That sounds very odd, but perhaps your unit cell is not sufficiently > >> solvated to > >> start with. If you have voids, you may have available volume. > >> > >> -Justin > > > You must compare the simulated density with the experimental density. > > There is no other way to conclude if your holes are genuine or not in > this kind of matter. > > > Dr. Vitaly V. Chaban > MEMPHYS - Center for Biomembrane Physics > Department of Physics, Chemistry and Pharmacy > University of Southern Denmark > Campusvej 55, 5230 Odense M, Denmark > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] criterion of the convergence of the simulation
What do you mean by "convergence"? The point at which the molecule finishes adapting to the system conditions and starts exploring the energy landscape? The point at which it has explored the whole conformational space? Or something else? On 29 October 2012 10:44, Atila Petrosian wrote: > Dear all > > I want to know what is criterion of the convergence of the simulation in > the gromacs. > > Any help will highly appreciated. > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli-Zografou 157 71 Athens GREECE email: tev...@pharm.uoa.gr teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
