Hi,
I'm not sure if this is the problem but did you try to include the
energy and trajectory files when running grompp (flags -e and -t)?
Ran.
Inon Sharony wrote:
>
> Hello GROMACS users!
>
> I've posted a few questions in the last few days about
> double-precision energy minimization for normal mode analysis, and
> everything seems OK except I've been having a re-occurring problem:
>
> The energy minimization procedure ends in
> =========================================
> // grompp_d -f em.mdp -c b4nm_s_7.gro -n index.ndx
> // mdrun_d -c b4nm_s_8.gro -v yes
>
>
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 1e-06
>
> writing lowest energy coordinates.
>
> Polak-Ribiere Conjugate Gradients converged to machine precision in
> 994 steps,
> but did not reach the requested Fmax < 1e-06.
> Potential Energy = 3.83658151247483e+00
> Maximum force = 5.38105464411977e-05 on atom 1
> Norm of force = 2.07631890036341e-05
>
>
>
> The Hessian matrix write ends in:
> =================================
> // grompp_d -f nm.mdp -c b4nm_s_8.gro -n index.ndx
> // mdrun_d -c nm.gro -mtx nm.mtx -v yes
>
>
>
>
> Reading file topol.tpr, VERSION 3.3.3 (double precision)
> Loaded with Money
>
> Small system size (N=7), using full Hessian format.
> Allocating Hessian memory...
>
> starting normal mode calculation 'Single Molecule of Pentane'
> 7 steps.
>
> Maximum force: 3.51028e+02
> Maximum force probably not small enough to ensure that you are in a
> energy well. Be aware that negative eigenvalues may occur when the
> resulting matrix is diagonalized.
> Finished step 7 out of 7
>
> Writing Hessian...
>
>
>
>
> Clearly, the maximal force is minimized to about 1E-05 kJ / mole nm,
> but when the same *.gro file is read for the Hessian calculation, it
> reads about 1E+02!
> I think the reason is found in the *.tpr file of the energy
> minimization run:
>
> x (7x3):
> x[ 0]={ 3.17800e+00, 3.49300e+00, 3.38500e+00}
> x[ 1]={ 3.31300e+00, 3.51800e+00, 3.31600e+00}
> x[ 2]={ 3.42500e+00, 3.43000e+00, 3.37400e+00}
> x[ 3]={ 3.41400e+00, 3.28500e+00, 3.32700e+00}
> x[ 4]={ 3.52700e+00, 3.20300e+00, 3.38900e+00}
> x[ 5]={ 3.02600e+00, 3.50200e+00, 3.36900e+00}
> x[ 6]={ 3.60400e+00, 3.07000e+00, 3.38200e+00}
>
> This means that although the minimization was run in double precision,
> the atomic configuration is saved in single precision (the last two
> decimal places are not used). Does this mean that each time the
> optimized *.gro file is re-read, it needs to optimize these last two
> decimal places anew, and this makes the difference in SEVEN orders of
> magnitude in the maximal force?
>
> Can anyone offer a solution?
>
> Thanks in advance...
>
>
>
> Inon.
>
>
> Some background information:
> ----------------------------
>
> I'm running GROMACS 3.3.3 on the following system (with bash):
>
> /* composed by Inon Sharony August 6th, 2008 */
> /* ----------------------------------------- */
> /* */
> /* this file contains the hardware information for Sodium */
> /* the first part details the video card */
> /* the second part details the CPUs */
> /* the third part details the BIOS and motherboard */
> /* */
>
> lspci -v /* list PCI -verbose */
> =================================
>
> .
> .
> .
>
>
> 01:00.0 VGA compatible controller: nVidia Corporation GeForce 8500 GT
> (rev a1) (
> prog-if 00 [VGA controller])
> Subsystem: LeadTek Research Inc. Unknown device 2a94
> Flags: bus master, fast devsel, latency 0, IRQ 16
> Memory at e2000000 (32-bit, non-prefetchable) [size=16M]
> Memory at d0000000 (64-bit, prefetchable) [size=256M]
> Memory at e0000000 (64-bit, non-prefetchable) [size=32M]
> I/O ports at 2000 [size=128]
> Capabilities: [60] Power Management version 2
> Capabilities: [68] Message Signalled Interrupts: Mask- 64bit+
> Queue=0/0
> Enable-
> Capabilities: [78] Express Endpoint, MSI 00
> Capabilities: [100] Virtual Channel <?>
> Capabilities: [128] Power Budgeting <?>
> Capabilities: [600] Vendor Specific Information <?>
> Kernel driver in use: nvidia
> Kernel modules: nvidia, nvidiafb
>
>
> .
> .
> .
>
> -------------------------------------------------------------------------------------------------------------------------------------------------------------
>
>
> cat /proc/cpuinfo /* CPUs information */
> ========================================
>
> processor : 0
> vendor_id : GenuineIntel
> cpu family : 6
> model : 15
> model name : Intel(R) Core(TM)2 Quad CPU Q6600 @ 2.40GHz
> stepping : 11
> cpu MHz : 1596.000
> cache size : 4096 KB
> physical id : 0
> siblings : 4
> core id : 0
> cpu cores : 4
> fpu : yes
> fpu_exception : yes
> cpuid level : 10
> wp : yes
> flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge
> mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe
> syscall nx lm constant_tsc arch_perfmon pebs bts rep_good pni monitor
> ds_cpl vmx est tm2 ssse3 cx16 xtpr lahf_lm
> bogomips : 4802.25
> clflush size : 64
> cache_alignment : 64
> address sizes : 36 bits physical, 48 bits virtual
> power management:
>
>
> .
> .
> .
>
> -------------------------------------------------------------------------------------------------------------------------------------------------------------
>
>
> /usr/sbin/dmidecode
> ===================
>
> # dmidecode 2.7
> SMBIOS 2.4 present.
> 39 structures occupying 1779 bytes.
> Table at 0x000E3300.
>
> Handle 0x0000, DMI type 4, 35 bytes.
> Processor Information
> Socket Designation: J1PR
> Type: Central Processor
> Family: <OUT OF SPEC>
> Manufacturer: Intel(R) Corporation
> ID: FB 06 00 00 FF FB EB BF
> Version: Intel(R) Core(TM)2 Quad CPU Q6600 @ 2.40GHz
> Voltage: 1.6 V
> External Clock: 266 MHz
> Max Speed: 4000 MHz
> Current Speed: 2400 MHz
> Status: Populated, Enabled
> Upgrade: <OUT OF SPEC>
> L1 Cache Handle: 0x0003
> L2 Cache Handle: 0x0001
> L3 Cache Handle: Not Provided
> Serial Number: Not Specified
> Asset Tag: Not Specified
> Part Number: Not Specified
>
>
> .
> .
> .
>
> /* BIOS information */
>
> Handle 0x0004, DMI type 0, 24 bytes.
> BIOS Information
> Vendor: Intel Corp.
> Version: DPP3510J.86A.0326.2007.1206.2256
> Release Date: 12/06/2007
> Address: 0xF0000
> Runtime Size: 64 kB
> ROM Size: 1024 kB
> Characteristics:
> PCI is supported
> BIOS is upgradeable
> BIOS shadowing is allowed
> Boot from CD is supported
> Selectable boot is supported
> EDD is supported
> 8042 keyboard services are supported (int 9h)
> Serial services are supported (int 14h)
> Printer services are supported (int 17h)
> CGA/mono video services are supported (int 10h)
> ACPI is supported
> USB legacy is supported
> ATAPI Zip drive boot is supported
> BIOS boot specification is supported
> Function key-initiated network boot is supported
> Targeted content distribution is supported
> BIOS Revision: 0.0
> Firmware Revision: 0.0
>
>
> .
> .
> .
>
> /* Motherboard information */
>
> Handle 0x0006, DMI type 2, 20 bytes.
> Base Board Information
> Manufacturer: Intel Corporation
> Product Name: DP35DP
> Version: AAD81073-207
> Serial Number: USDP747001WP
> Asset Tag: Base Board Asset Tag
> Features:
> Board is a hosting board
> Board is replaceable
> Location In Chassis: Base Board Chassis Location
> Chassis Handle: 0x0007
> Type: Unknown
> Contained Object Handles: 0
>
>
>
> --Inon Sharony
> ×× ×× ×©×¨×× ×
> +972(3)6407634
> atto.TAU.ac.IL/~inonshar
> Please consider your environmental responsibility before printing
> this e-mail.
>
> _______________________________________________
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--
------------------------------------------------------
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: [EMAIL PROTECTED]
Skype: ran.friedman
------------------------------------------------------
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